Starting phenix.real_space_refine on Sun May 19 16:31:06 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=False 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 ramachandran_plot_restraints { enabled = 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: 0.00s 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: 1.77, per 1000 atoms: 0.18 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: 2.47 Conformation dependent library (CDL) restraints added in 456.6 milliseconds Time building geometry restraints manager: 2.79 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: 0.020 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: 0.020 Process input model: 9.720 Find NCS groups from input model: 0.120 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:8.230 Internal consistency checks: 0.000 Total: 18.480 ------------------------------------------------------------------------------- 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 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 48 optimal weight: 6.9990 chunk 56 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 16 optimal weight: 8.9990 chunk 32 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5111 Z= 0.159 Angle : 0.546 6.166 6939 Z= 0.272 Chirality : 0.050 0.207 759 Planarity : 0.004 0.048 886 Dihedral : 14.513 79.518 1916 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.51 % Allowed : 11.39 % Favored : 88.10 % Rotamer: Outliers : 1.65 % Allowed : 17.61 % 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: -4.69 (0.27), residues: 588 helix: -3.82 (0.21), residues: 248 sheet: -3.27 (0.63), residues: 53 loop : -2.29 (0.31), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 121 TYR 0.015 0.001 TYR B 215 PHE 0.010 0.001 PHE A 297 TRP 0.007 0.001 TRP B 220 HIS 0.004 0.001 HIS A 108 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 50 optimal weight: 30.0000 chunk 53 optimal weight: 30.0000 chunk 19 optimal weight: 20.0000 chunk 30 optimal weight: 30.0000 chunk 22 optimal weight: 20.0000 chunk 37 optimal weight: 30.0000 chunk 57 optimal weight: 20.0000 chunk 58 optimal weight: 20.0000 chunk 13 optimal weight: 20.0000 chunk 32 optimal weight: 20.0000 chunk 8 optimal weight: 20.0000 overall best weight: 20.0000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.4732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.072 5111 Z= 0.347 Angle : 0.807 7.531 6939 Z= 0.426 Chirality : 0.061 0.286 759 Planarity : 0.007 0.047 886 Dihedral : 15.681 84.564 1916 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 58.88 Ramachandran Plot: Outliers : 7.14 % Allowed : 25.00 % Favored : 67.86 % Rotamer: Outliers : 6.06 % Allowed : 19.82 % Favored : 74.13 % 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: -6.84 (0.23), residues: 588 helix: -5.06 (0.14), residues: 247 sheet: -3.75 (0.66), residues: 50 loop : -4.22 (0.28), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 295 TYR 0.018 0.002 TYR B 215 PHE 0.015 0.002 PHE A 75 TRP 0.010 0.002 TRP A 220 HIS 0.007 0.002 HIS B 48 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 18 optimal weight: 10.0000 chunk 8 optimal weight: 20.0000 chunk 48 optimal weight: 20.0000 chunk 6 optimal weight: 70.0000 chunk 39 optimal weight: 30.0000 chunk 51 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 58 optimal weight: 20.0000 chunk 34 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 overall best weight: 10.0000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.4605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5111 Z= 0.164 Angle : 0.558 5.412 6939 Z= 0.282 Chirality : 0.051 0.214 759 Planarity : 0.005 0.042 886 Dihedral : 14.623 84.615 1916 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 28.03 Ramachandran Plot: Outliers : 1.70 % Allowed : 17.86 % Favored : 80.44 % Rotamer: Outliers : 4.59 % Allowed : 17.06 % Favored : 78.35 % 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: -5.87 (0.25), residues: 588 helix: -4.33 (0.18), residues: 243 sheet: -3.70 (0.62), residues: 46 loop : -3.55 (0.29), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 295 TYR 0.012 0.001 TYR B 215 PHE 0.012 0.001 PHE A 75 TRP 0.009 0.001 TRP A 220 HIS 0.004 0.001 HIS A 108 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 57 optimal weight: 20.0000 chunk 9 optimal weight: 40.0000 chunk 19 optimal weight: 20.0000 chunk 6 optimal weight: 70.0000 chunk 46 optimal weight: 20.0000 chunk 4 optimal weight: 50.0000 chunk 54 optimal weight: 10.0000 chunk 43 optimal weight: 30.0000 chunk 21 optimal weight: 20.0000 chunk 30 optimal weight: 30.0000 chunk 35 optimal weight: 30.0000 overall best weight: 18.0000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.6081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 5111 Z= 0.292 Angle : 0.737 6.555 6939 Z= 0.388 Chirality : 0.057 0.248 759 Planarity : 0.006 0.048 886 Dihedral : 15.130 89.709 1916 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 56.27 Ramachandran Plot: Outliers : 7.48 % Allowed : 25.51 % Favored : 67.01 % Rotamer: Outliers : 7.16 % Allowed : 17.61 % Favored : 75.23 % 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: -7.04 (0.23), residues: 588 helix: -5.20 (0.12), residues: 230 sheet: -3.80 (0.66), residues: 48 loop : -4.50 (0.27), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 295 TYR 0.016 0.002 TYR C 191 PHE 0.016 0.002 PHE A 75 TRP 0.008 0.001 TRP A 220 HIS 0.007 0.002 HIS B 48 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 6 optimal weight: 70.0000 chunk 22 optimal weight: 20.0000 chunk 27 optimal weight: 30.0000 chunk 20 optimal weight: 30.0000 chunk 39 optimal weight: 40.0000 chunk 40 optimal weight: 10.0000 chunk 58 optimal weight: 30.0000 chunk 13 optimal weight: 20.0000 chunk 35 optimal weight: 20.0000 chunk 30 optimal weight: 30.0000 chunk 28 optimal weight: 20.0000 overall best weight: 18.0000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.7063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 5111 Z= 0.248 Angle : 0.651 5.191 6939 Z= 0.339 Chirality : 0.053 0.205 759 Planarity : 0.006 0.050 886 Dihedral : 15.071 87.215 1916 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 44.71 Ramachandran Plot: Outliers : 6.63 % Allowed : 20.24 % Favored : 73.13 % Rotamer: Outliers : 7.52 % Allowed : 18.35 % Favored : 74.13 % 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: -6.91 (0.22), residues: 588 helix: -4.78 (0.16), residues: 230 sheet: -4.64 (0.51), residues: 48 loop : -4.54 (0.26), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 121 TYR 0.011 0.001 TYR C 191 PHE 0.012 0.002 PHE A 75 TRP 0.008 0.002 TRP A 220 HIS 0.005 0.001 HIS B 48 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 270.35 seconds wall clock time: 5 minutes 27.00 seconds (327.00 seconds total)