Starting phenix.real_space_refine on Sun May 19 16:31:31 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 c_beta_restraints=False ramachandran_plot_restraints.enabled=True secondary_structure.enabled=False resolution=3.15 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { 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" 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" } resolution = 3.15 refinement { run = *minimization_global rigid_body local_grid_search morphing \ simulated_annealing adp occupancy nqh_flips } pdb_interpretation { secondary_structure { enabled = False } c_beta_restraints = False } 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: 0.01s 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: 2.66, per 1000 atoms: 0.27 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: 3.37 Conformation dependent library (CDL) restraints added in 612.9 milliseconds 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. Time building geometry restraints manager: 3.76 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: 3032 17.81 - 35.62: 378 35.62 - 53.44: 135 53.44 - 71.25: 31 71.25 - 89.06: 6 Dihedral angle restraints: 3582 sinusoidal: 2580 harmonic: 1002 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 3579 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: 574 2.03 - 2.67: 13967 2.67 - 3.31: 30979 3.31 - 3.96: 40449 3.96 - 4.60: 59000 Nonbonded interactions: 144969 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 144964 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: 0.050 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: 0.090 Extract box with map and model: 0.510 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 16.460 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 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:0.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:12.760 Internal consistency checks: 0.000 Total: 30.190 ------------------------------------------------------------------------------- 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= 0.125 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. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 48 optimal weight: 8.9990 chunk 56 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 2 optimal weight: 40.0000 chunk 16 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 58 optimal weight: 9.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5111 Z= 0.166 Angle : 0.555 6.472 6939 Z= 0.281 Chirality : 0.052 0.232 759 Planarity : 0.005 0.048 886 Dihedral : 14.594 76.905 1916 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.47 % Allowed : 18.72 % Favored : 79.82 % 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: -1.41 (0.33), residues: 588 helix: -0.82 (0.31), residues: 248 sheet: -2.83 (0.61), residues: 62 loop : -0.37 (0.35), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 41 TYR 0.010 0.001 TYR B 215 PHE 0.010 0.001 PHE B 165 TRP 0.010 0.001 TRP A 118 HIS 0.004 0.001 HIS B 261 *********************** 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. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 50 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 chunk 19 optimal weight: 10.0000 chunk 30 optimal weight: 20.0000 chunk 22 optimal weight: 9.9990 chunk 37 optimal weight: 20.0000 chunk 57 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 chunk 13 optimal weight: 20.0000 chunk 32 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.3058 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= 0.156 Angle : 0.562 6.489 6939 Z= 0.281 Chirality : 0.052 0.199 759 Planarity : 0.005 0.034 886 Dihedral : 14.021 74.208 1916 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 19.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 3.49 % Allowed : 15.78 % Favored : 80.73 % 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: -1.45 (0.33), residues: 588 helix: -1.00 (0.32), residues: 240 sheet: -2.70 (0.69), residues: 55 loop : -0.38 (0.35), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 295 TYR 0.010 0.001 TYR C 191 PHE 0.010 0.001 PHE A 75 TRP 0.012 0.001 TRP A 118 HIS 0.004 0.001 HIS A 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. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 18 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 48 optimal weight: 20.0000 chunk 6 optimal weight: 50.0000 chunk 39 optimal weight: 30.0000 chunk 51 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 58 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5111 Z= 0.112 Angle : 0.491 6.202 6939 Z= 0.240 Chirality : 0.049 0.200 759 Planarity : 0.005 0.036 886 Dihedral : 13.466 71.385 1916 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.02 % Allowed : 15.96 % Favored : 82.02 % 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: -1.18 (0.33), residues: 588 helix: -0.63 (0.32), residues: 238 sheet: -2.69 (0.71), residues: 53 loop : -0.36 (0.34), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 264 TYR 0.009 0.001 TYR B 215 PHE 0.010 0.001 PHE A 75 TRP 0.012 0.001 TRP A 118 HIS 0.004 0.001 HIS A 108 *********************** 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. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 57 optimal weight: 9.9990 chunk 9 optimal weight: 40.0000 chunk 19 optimal weight: 10.0000 chunk 6 optimal weight: 50.0000 chunk 46 optimal weight: 20.0000 chunk 4 optimal weight: 3.9990 chunk 54 optimal weight: 20.0000 chunk 43 optimal weight: 20.0000 chunk 21 optimal weight: 20.0000 chunk 30 optimal weight: 0.8980 chunk 35 optimal weight: 30.0000 overall best weight: 8.9792 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.4193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5111 Z= 0.175 Angle : 0.563 6.415 6939 Z= 0.284 Chirality : 0.052 0.199 759 Planarity : 0.005 0.035 886 Dihedral : 13.571 74.180 1916 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 24.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 2.57 % Allowed : 16.70 % Favored : 80.73 % 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: -1.42 (0.33), residues: 588 helix: -1.01 (0.32), residues: 235 sheet: -2.54 (0.70), residues: 55 loop : -0.38 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 295 TYR 0.012 0.001 TYR C 191 PHE 0.011 0.001 PHE A 75 TRP 0.009 0.001 TRP A 118 HIS 0.004 0.001 HIS B 48 *********************** 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. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 6 optimal weight: 50.0000 chunk 22 optimal weight: 30.0000 chunk 27 optimal weight: 30.0000 chunk 20 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 40 optimal weight: 8.9990 chunk 58 optimal weight: 20.0000 chunk 13 optimal weight: 8.9990 chunk 35 optimal weight: 8.9990 chunk 30 optimal weight: 0.9980 chunk 28 optimal weight: 20.0000 overall best weight: 7.5988 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5111 Z= 0.132 Angle : 0.511 6.302 6939 Z= 0.254 Chirality : 0.050 0.195 759 Planarity : 0.005 0.035 886 Dihedral : 13.297 75.276 1916 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 21.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.12 % Allowed : 15.96 % Favored : 80.92 % 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: -1.24 (0.33), residues: 588 helix: -0.78 (0.33), residues: 233 sheet: -2.53 (0.72), residues: 53 loop : -0.35 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 295 TYR 0.010 0.001 TYR C 191 PHE 0.010 0.001 PHE A 75 TRP 0.012 0.001 TRP A 118 HIS 0.003 0.001 HIS A 108 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 589.54 seconds wall clock time: 10 minutes 39.08 seconds (639.08 seconds total)