Starting phenix.real_space_refine on Sun May 19 16:30:35 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8aza_15757.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8aza_15757.pdb Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- run=minimization_global+local_grid_search+nqh_flips resolution=3.15 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8aza_15757.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8aza_15757.pdb" real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8aza_15757.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/8aza_15757.map" } resolution = 3.15 refinement { run = *minimization_global rigid_body *local_grid_search morphing \ simulated_annealing adp occupancy *nqh_flips } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.030 sd= 0.128 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 20 5.16 5 C 3204 2.51 5 N 872 2.21 5 O 882 1.98 5 H 5008 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 9986 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1205 Classifications: {'peptide': 76} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 71} Chain: "A" Number of atoms: 4697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 4697 Inner-chain residues flagged as termini: ['pdbres="LEU A 175 "', 'pdbres="THR A 189 "', 'pdbres="ASN A 197 "', 'pdbres="ARG A 205 "', 'pdbres="GLU A 230 "', 'pdbres="ASN A 234 "'] Classifications: {'peptide': 284} Modifications used: {'COO': 4, 'NH3': 4} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 263} Chain breaks: 3 Chain: "B" Number of atoms: 4084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 4084 Inner-chain residues flagged as termini: ['pdbres="LEU B 49 "', 'pdbres="GLU B 59 "', 'pdbres="ARG B 171 "', 'pdbres="ALA B 206 "', 'pdbres="PRO B 228 "', 'pdbres="ARG B 247 "'] Classifications: {'peptide': 246} Modifications used: {'COO': 4, 'NH3': 4} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 229} Chain breaks: 3 Time building chain proxies: 1.60, per 1000 atoms: 0.16 Number of scatterers: 9986 At special positions: 0 Unit cell: (71.949, 76.911, 96.759, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 20 16.00 O 882 8.00 N 872 7.00 C 3204 6.00 H 5008 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.32 Conformation dependent library (CDL) restraints added in 369.9 milliseconds 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1166 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 5 sheets defined 38.4% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'C' and resid 163 through 169 Processing helix chain 'C' and resid 181 through 187 Processing helix chain 'C' and resid 216 through 223 Processing helix chain 'C' and resid 228 through 233 Processing helix chain 'A' and resid 57 through 72 Processing helix chain 'A' and resid 103 through 106 No H-bonds generated for 'chain 'A' and resid 103 through 106' Processing helix chain 'A' and resid 118 through 136 removed outlier: 3.677A pdb=" N LEU A 125 " --> pdb=" O ARG A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 192 No H-bonds generated for 'chain 'A' and resid 190 through 192' Processing helix chain 'A' and resid 208 through 224 removed outlier: 3.933A pdb=" N LEU A 223 " --> pdb=" O TRP A 220 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N SER A 224 " --> pdb=" O GLU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 242 removed outlier: 4.216A pdb=" N TYR A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 272 Processing helix chain 'A' and resid 283 through 296 Proline residue: A 292 - end of helix removed outlier: 3.996A pdb=" N THR A 296 " --> pdb=" O PRO A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 312 removed outlier: 4.018A pdb=" N ILE A 307 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLN A 308 " --> pdb=" O GLU A 304 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 17 No H-bonds generated for 'chain 'B' and resid 15 through 17' Processing helix chain 'B' and resid 60 through 72 Processing helix chain 'B' and resid 103 through 107 Processing helix chain 'B' and resid 118 through 135 Processing helix chain 'B' and resid 165 through 167 No H-bonds generated for 'chain 'B' and resid 165 through 167' Processing helix chain 'B' and resid 210 through 224 Processing helix chain 'B' and resid 262 through 272 Processing helix chain 'B' and resid 277 through 279 No H-bonds generated for 'chain 'B' and resid 277 through 279' Processing helix chain 'B' and resid 283 through 296 Proline residue: B 292 - end of helix Processing helix chain 'B' and resid 299 through 313 removed outlier: 4.095A pdb=" N VAL B 306 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE B 307 " --> pdb=" O LEU B 303 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 189 through 191 Processing sheet with id= B, first strand: chain 'A' and resid 81 through 86 removed outlier: 7.006A pdb=" N VAL A 94 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ILE A 84 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N GLY A 92 " --> pdb=" O ILE A 84 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N SER A 34 " --> pdb=" O TYR A 23 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N TYR A 23 " --> pdb=" O SER A 34 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 43 through 48 removed outlier: 5.255A pdb=" N SER B 34 " --> pdb=" O TYR B 23 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N TYR B 23 " --> pdb=" O SER B 34 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 83 through 87 removed outlier: 3.657A pdb=" N GLY B 83 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU B 87 " --> pdb=" O PHE B 90 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 152 through 154 159 hydrogen bonds defined for protein. 432 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.71 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.14: 4999 1.14 - 1.31: 805 1.31 - 1.48: 2082 1.48 - 1.65: 2202 1.65 - 1.82: 31 Bond restraints: 10119 Sorted by residual: bond pdb=" N HIS A 37 " pdb=" H HIS A 37 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.77e+01 bond pdb=" NE2 GLN C 199 " pdb="HE22 GLN C 199 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.77e+01 bond pdb=" N GLU A 279 " pdb=" H GLU A 279 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.74e+01 bond pdb=" N SER A 271 " pdb=" H SER A 271 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.69e+01 bond pdb=" N VAL B 46 " pdb=" H VAL B 46 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.68e+01 ... (remaining 10114 not shown) Histogram of bond angle deviations from ideal: 100.74 - 107.39: 625 107.39 - 114.05: 11788 114.05 - 120.71: 3367 120.71 - 127.37: 2466 127.37 - 134.03: 93 Bond angle restraints: 18339 Sorted by residual: angle pdb=" CA TRP A 118 " pdb=" CB TRP A 118 " pdb=" CG TRP A 118 " ideal model delta sigma weight residual 113.60 117.81 -4.21 1.90e+00 2.77e-01 4.92e+00 angle pdb=" N ASP A 278 " pdb=" CA ASP A 278 " pdb=" C ASP A 278 " ideal model delta sigma weight residual 111.82 114.39 -2.57 1.16e+00 7.43e-01 4.90e+00 angle pdb=" N ILE A 212 " pdb=" CA ILE A 212 " pdb=" C ILE A 212 " ideal model delta sigma weight residual 110.23 108.06 2.17 1.04e+00 9.25e-01 4.37e+00 angle pdb=" CA PHE A 229 " pdb=" C PHE A 229 " pdb=" N GLU A 230 " ideal model delta sigma weight residual 116.84 113.45 3.39 1.71e+00 3.42e-01 3.92e+00 angle pdb=" CA PHE A 229 " pdb=" C PHE A 229 " pdb=" O PHE A 229 " ideal model delta sigma weight residual 120.51 123.27 -2.76 1.43e+00 4.89e-01 3.73e+00 ... (remaining 18334 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 4198 17.81 - 35.62: 378 35.62 - 53.44: 135 53.44 - 71.25: 31 71.25 - 89.06: 6 Dihedral angle restraints: 4748 sinusoidal: 2580 harmonic: 2168 Sorted by residual: dihedral pdb=" CA PRO B 281 " pdb=" C PRO B 281 " pdb=" N SER B 282 " pdb=" CA SER B 282 " ideal model delta harmonic sigma weight residual 180.00 161.43 18.57 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA MET A 98 " pdb=" C MET A 98 " pdb=" N PRO A 99 " pdb=" CA PRO A 99 " ideal model delta harmonic sigma weight residual -180.00 -162.69 -17.31 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA HIS A 159 " pdb=" C HIS A 159 " pdb=" N VAL A 160 " pdb=" CA VAL A 160 " ideal model delta harmonic sigma weight residual -180.00 -162.82 -17.18 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 4745 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 453 0.029 - 0.057: 207 0.057 - 0.086: 52 0.086 - 0.114: 38 0.114 - 0.143: 9 Chirality restraints: 759 Sorted by residual: chirality pdb=" CA ILE B 78 " pdb=" N ILE B 78 " pdb=" C ILE B 78 " pdb=" CB ILE B 78 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.09e-01 chirality pdb=" CA VAL B 116 " pdb=" N VAL B 116 " pdb=" C VAL B 116 " pdb=" CB VAL B 116 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.43e-01 chirality pdb=" CA ILE A 81 " pdb=" N ILE A 81 " pdb=" C ILE A 81 " pdb=" CB ILE A 81 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.33e-01 ... (remaining 756 not shown) Planarity restraints: 1443 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 280 " 0.031 5.00e-02 4.00e+02 4.74e-02 3.59e+00 pdb=" N PRO B 281 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 281 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 281 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 180 " 0.030 5.00e-02 4.00e+02 4.52e-02 3.27e+00 pdb=" N PRO C 181 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO C 181 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 181 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 53 " 0.025 5.00e-02 4.00e+02 3.76e-02 2.26e+00 pdb=" N PRO A 54 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 54 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 54 " 0.021 5.00e-02 4.00e+02 ... (remaining 1440 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.03: 461 2.03 - 2.67: 13923 2.67 - 3.31: 30817 3.31 - 3.96: 40124 3.96 - 4.60: 58849 Nonbonded interactions: 144174 Sorted by model distance: nonbonded pdb=" H ALA B 19 " pdb=" O ARG B 36 " model vdw 1.384 1.850 nonbonded pdb=" O LEU A 153 " pdb=" H LYS A 161 " model vdw 1.414 1.850 nonbonded pdb=" O ASN A 234 " pdb="HE21 GLN A 237 " model vdw 1.425 1.850 nonbonded pdb=" O GLU B 221 " pdb=" H ARG B 225 " model vdw 1.467 1.850 nonbonded pdb=" H LEU A 153 " pdb=" O LYS A 161 " model vdw 1.486 1.850 ... (remaining 144169 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 49 or (resid 59 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name OE1 or name OE2 or name HA o \ r name HB2 or name HB3 or name HG2 or name HG3)) or resid 60 through 107 or (res \ id 108 and (name N or name CA or name C or name O or name CB or name CG or name \ ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or name \ HB3 or name HD2 or name HE1 or name HE2)) or resid 109 through 171 or (resid 20 \ 6 and (name N or name CA or name C or name O or name CB or name HA or name HB1 o \ r name HB2 or name HB3)) or resid 207 through 209 or (resid 210 and (name N or n \ ame CA or name C or name O or name CB or name CG or name ND1 or name CD2 or name \ CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD1 or nam \ e HD2 or name HE1)) or resid 211 through 228 or (resid 247 and (name N or name C \ A or name C or name O or name CB or name CG or name CD or name NE or name CZ or \ name NH1 or name NH2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 \ or name HD2 or name HD3 or name HE or name HH11 or name HH12 or name HH21 or nam \ e HH22)) or resid 248 through 314)) selection = (chain 'B' and (resid 8 through 48 or (resid 49 and (name N or name CA or name C \ or name O or name CB or name CG or name CD1 or name CD2 or name H or name HA or \ name HB2 or name HB3 or name HG or name HD11 or name HD12 or name HD13 or name \ HD21 or name HD22 or name HD23)) or (resid 59 and (name N or name CA or name C o \ r name O or name CB or name CG or name CD or name OE1 or name OE2 or name HA or \ name HB2 or name HB3 or name HG2 or name HG3)) or resid 60 through 135 or (resid \ 136 and (name N or name CA or name C or name O or name CB or name CG or name ND \ 1 or name CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or name H \ B3 or name HD2 or name HE1 or name HE2)) or resid 137 through 170 or (resid 171 \ and (name N or name CA or name C or name O or name CB or name CG or name CD or n \ ame NE or name CZ or name NH1 or name NH2 or name H or name HA or name HB2 or na \ me HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE or name HH11 o \ r name HH12 or name HH21 or name HH22)) or (resid 206 and (name N or name CA or \ name C or name O or name CB or name HA or name HB1 or name HB2 or name HB3)) or \ resid 207 through 227 or (resid 228 and (name N or name CA or name C or name O o \ r name CB or name CG or name CD or name HA or name HB2 or name HB3 or name HG2 o \ r name HG3 or name HD2 or name HD3)) or (resid 247 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 \ or name NH2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name \ HD2 or name HD3 or name HE or name HH11 or name HH12 or name HH21 or name HH22)) \ or resid 248 through 314)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 5 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.50 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will not be refined Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 0.290 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 12.070 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:7.570 Internal consistency checks: 0.000 Total: 20.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5111 Z= 0.180 Angle : 0.569 5.908 6939 Z= 0.292 Chirality : 0.040 0.143 759 Planarity : 0.005 0.047 886 Dihedral : 16.129 78.514 1916 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.78 % Favored : 94.05 % Rotamer: Outliers : 1.65 % Allowed : 20.92 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.31), residues: 588 helix: -1.37 (0.29), residues: 244 sheet: -2.56 (0.61), residues: 55 loop : -0.77 (0.33), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 225 TYR 0.009 0.001 TYR C 191 PHE 0.012 0.001 PHE A 229 TRP 0.014 0.001 TRP A 118 HIS 0.002 0.001 HIS A 16 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 97 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 280 ARG cc_start: 0.7290 (tpp80) cc_final: 0.7026 (tpp80) outliers start: 9 outliers final: 4 residues processed: 103 average time/residue: 0.2171 time to fit residues: 28.7815 Evaluate side-chains 83 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 79 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 TRP Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 223 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 48 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 chunk 2 optimal weight: 20.0000 chunk 16 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 chunk 31 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 58 optimal weight: 6.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5111 Z= 0.233 Angle : 0.581 6.267 6939 Z= 0.292 Chirality : 0.040 0.139 759 Planarity : 0.005 0.042 886 Dihedral : 6.984 87.850 679 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.75 % Allowed : 23.85 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.33), residues: 588 helix: -0.71 (0.32), residues: 247 sheet: -2.69 (0.60), residues: 53 loop : -0.43 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 121 TYR 0.011 0.001 TYR A 213 PHE 0.009 0.001 PHE A 297 TRP 0.017 0.001 TRP A 118 HIS 0.004 0.001 HIS A 50 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 84 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 ASN cc_start: 0.8525 (p0) cc_final: 0.8216 (p0) REVERT: B 280 ARG cc_start: 0.7503 (tpp80) cc_final: 0.7147 (tpp80) outliers start: 15 outliers final: 13 residues processed: 91 average time/residue: 0.2560 time to fit residues: 31.0928 Evaluate side-chains 92 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 79 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 170 TRP Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 220 TRP Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 170 TRP Chi-restraints excluded: chain B residue 213 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 50 optimal weight: 40.0000 chunk 53 optimal weight: 20.0000 chunk 19 optimal weight: 20.0000 chunk 30 optimal weight: 20.0000 chunk 22 optimal weight: 20.0000 chunk 37 optimal weight: 30.0000 chunk 57 optimal weight: 2.9990 chunk 58 optimal weight: 8.9990 chunk 13 optimal weight: 20.0000 chunk 32 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 overall best weight: 10.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 HIS A 136 HIS A 156 ASN B 133 ASN B 156 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5111 Z= 0.298 Angle : 0.625 6.682 6939 Z= 0.320 Chirality : 0.041 0.146 759 Planarity : 0.005 0.035 886 Dihedral : 6.586 74.946 675 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 20.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 5.14 % Allowed : 23.85 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.33), residues: 588 helix: -0.88 (0.31), residues: 248 sheet: -2.81 (0.61), residues: 53 loop : -0.53 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 295 TYR 0.027 0.002 TYR C 191 PHE 0.017 0.002 PHE A 229 TRP 0.019 0.002 TRP A 220 HIS 0.003 0.001 HIS B 145 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 79 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 LEU cc_start: 0.9548 (OUTLIER) cc_final: 0.9322 (tt) REVERT: B 98 MET cc_start: 0.1651 (ptp) cc_final: 0.1109 (ptp) outliers start: 28 outliers final: 22 residues processed: 91 average time/residue: 0.1835 time to fit residues: 23.1867 Evaluate side-chains 97 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 74 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 170 TRP Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 220 TRP Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 246 HIS Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 170 TRP Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 261 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 18 optimal weight: 0.9980 chunk 8 optimal weight: 20.0000 chunk 48 optimal weight: 9.9990 chunk 6 optimal weight: 50.0000 chunk 39 optimal weight: 30.0000 chunk 51 optimal weight: 4.9990 chunk 16 optimal weight: 20.0000 chunk 58 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 chunk 45 optimal weight: 5.9990 chunk 38 optimal weight: 0.5980 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 133 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5111 Z= 0.183 Angle : 0.571 6.334 6939 Z= 0.283 Chirality : 0.040 0.139 759 Planarity : 0.005 0.034 886 Dihedral : 6.192 69.467 675 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.30 % Allowed : 26.24 % Favored : 70.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.34), residues: 588 helix: -0.59 (0.33), residues: 247 sheet: -2.66 (0.61), residues: 52 loop : -0.37 (0.36), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 121 TYR 0.010 0.001 TYR B 215 PHE 0.006 0.001 PHE A 229 TRP 0.015 0.001 TRP A 220 HIS 0.005 0.001 HIS C 220 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 81 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 ASN cc_start: 0.8941 (p0) cc_final: 0.8738 (p0) REVERT: B 21 LEU cc_start: 0.9537 (OUTLIER) cc_final: 0.9315 (tt) REVERT: B 98 MET cc_start: 0.1700 (ptp) cc_final: 0.1061 (ptp) outliers start: 18 outliers final: 14 residues processed: 87 average time/residue: 0.1533 time to fit residues: 18.3099 Evaluate side-chains 93 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 78 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 190 TYR Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 170 TRP Chi-restraints excluded: chain A residue 220 TRP Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 246 HIS Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 170 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 57 optimal weight: 8.9990 chunk 9 optimal weight: 40.0000 chunk 19 optimal weight: 20.0000 chunk 6 optimal weight: 50.0000 chunk 46 optimal weight: 20.0000 chunk 4 optimal weight: 10.0000 chunk 54 optimal weight: 8.9990 chunk 43 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 30 optimal weight: 0.9980 chunk 35 optimal weight: 9.9990 overall best weight: 7.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN B 86 ASN B 133 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5111 Z= 0.234 Angle : 0.592 6.505 6939 Z= 0.298 Chirality : 0.040 0.137 759 Planarity : 0.005 0.033 886 Dihedral : 6.064 68.250 675 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 18.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 4.04 % Allowed : 25.87 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.34), residues: 588 helix: -0.72 (0.32), residues: 247 sheet: -2.57 (0.62), residues: 52 loop : -0.41 (0.36), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 121 TYR 0.022 0.002 TYR B 134 PHE 0.013 0.001 PHE A 229 TRP 0.018 0.001 TRP B 220 HIS 0.004 0.001 HIS C 220 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 76 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 ASN cc_start: 0.9043 (p0) cc_final: 0.8815 (p0) REVERT: B 98 MET cc_start: 0.1801 (ptp) cc_final: 0.1182 (ptp) outliers start: 22 outliers final: 18 residues processed: 88 average time/residue: 0.1183 time to fit residues: 14.8560 Evaluate side-chains 92 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 74 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 190 TYR Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 170 TRP Chi-restraints excluded: chain A residue 220 TRP Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 246 HIS Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 159 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 6 optimal weight: 50.0000 chunk 22 optimal weight: 20.0000 chunk 27 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 39 optimal weight: 5.9990 chunk 40 optimal weight: 20.0000 chunk 58 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 35 optimal weight: 0.0170 chunk 30 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 overall best weight: 5.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5111 Z= 0.204 Angle : 0.596 6.836 6939 Z= 0.295 Chirality : 0.040 0.135 759 Planarity : 0.005 0.035 886 Dihedral : 5.821 65.364 675 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.30 % Allowed : 26.61 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.34), residues: 588 helix: -0.60 (0.33), residues: 247 sheet: -2.53 (0.63), residues: 52 loop : -0.35 (0.37), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 280 TYR 0.020 0.001 TYR B 134 PHE 0.013 0.001 PHE A 229 TRP 0.016 0.001 TRP B 220 HIS 0.004 0.001 HIS C 220 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 684.35 seconds wall clock time: 12 minutes 20.19 seconds (740.19 seconds total)