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/7un3_26612.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7un3_26612.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=3.5 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7un3_26612.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7un3_26612.pdb" real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7un3_26612.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7un3_26612.map" } resolution = 3.5 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= 0.026 sd= 0.153 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 41 5.16 5 C 6056 2.51 5 N 1605 2.21 5 O 1738 1.98 5 H 9482 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 584": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1256": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 18922 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1193 Classifications: {'peptide': 73} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "A" Number of atoms: 10424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 649, 10424 Inner-chain residues flagged as termini: ['pdbres="HIS A 83 "', 'pdbres="VAL A 122 "', 'pdbres="TYR A 241 "', 'pdbres="PHE A 260 "', 'pdbres="PHE A 313 "', 'pdbres="VAL A 321 "', 'pdbres="LEU A 339 "', 'pdbres="ASP A 343 "', 'pdbres="PRO A 358 "', 'pdbres="ASP A 542 "', 'pdbres="GLY A 663 "', 'pdbres="GLU A 675 "', 'pdbres="ILE A 710 "', 'pdbres="VAL A 928 "', 'pdbres="THR A1046 "', 'pdbres="ARG A1054 "', 'pdbres="LEU A1152 "', 'pdbres="PRO A1252 "'] Classifications: {'peptide': 649} Modifications used: {'COO': 10, 'NH2': 1, 'NH3': 9} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 611} Chain breaks: 9 Chain: "B" Number of atoms: 3686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 3686 Inner-chain residues flagged as termini: ['pdbres="ILE B 121 "', 'pdbres="PRO B 164 "', 'pdbres="VAL B 306 "', 'pdbres="ILE B 319 "'] Classifications: {'peptide': 223} Modifications used: {'COO': 3, 'NH2': 1, 'NH3': 2} Link IDs: {'PTRANS': 12, 'TRANS': 210} Chain breaks: 2 Chain: "C" Number of atoms: 3619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 3619 Inner-chain residues flagged as termini: ['pdbres="ASN C 122 "', 'pdbres="GLY C 166 "', 'pdbres="VAL C 306 "', 'pdbres="ASP C 315 "'] Classifications: {'peptide': 219} Modifications used: {'COO': 3, 'NH3': 3} Link IDs: {'PTRANS': 11, 'TRANS': 207} Chain breaks: 2 Time building chain proxies: 4.73, per 1000 atoms: 0.25 Number of scatterers: 18922 At special positions: 0 Unit cell: (84.975, 114.675, 142.725, 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 41 16.00 O 1738 8.00 N 1605 7.00 C 6056 6.00 H 9482 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: 7.14 Conformation dependent library (CDL) restraints added in 1.1 seconds 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. Time building geometry restraints manager: 8.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.15: 9462 1.15 - 1.31: 1597 1.31 - 1.48: 3812 1.48 - 1.65: 4200 1.65 - 1.82: 62 Bond restraints: 19133 Sorted by residual: bond pdb=" N CYS A1025 " pdb=" H CYS A1025 " ideal model delta sigma weight residual 0.860 1.027 -0.167 2.00e-02 2.50e+03 6.94e+01 bond pdb=" N ASP A 144 " pdb=" H ASP A 144 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.79e+01 bond pdb=" N ARG B 337 " pdb=" H ARG B 337 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.72e+01 bond pdb=" N GLU A1081 " pdb=" H GLU A1081 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.70e+01 bond pdb=" N ASP A 151 " pdb=" H ASP A 151 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.64e+01 ... (remaining 19128 not shown) Histogram of bond angle deviations from ideal: 100.23 - 106.99: 422 106.99 - 113.74: 22868 113.74 - 120.50: 6186 120.50 - 127.25: 5082 127.25 - 134.01: 112 Bond angle restraints: 34670 Sorted by residual: angle pdb=" C ALA A 695 " pdb=" CA ALA A 695 " pdb=" CB ALA A 695 " ideal model delta sigma weight residual 117.23 111.62 5.61 1.36e+00 5.41e-01 1.70e+01 angle pdb=" CA ALA A 695 " pdb=" C ALA A 695 " pdb=" N ASP A 696 " ideal model delta sigma weight residual 119.98 117.43 2.55 8.50e-01 1.38e+00 9.00e+00 angle pdb=" N GLN B 111 " pdb=" CA GLN B 111 " pdb=" C GLN B 111 " ideal model delta sigma weight residual 109.81 114.20 -4.39 2.21e+00 2.05e-01 3.95e+00 angle pdb=" CA GLN B 111 " pdb=" C GLN B 111 " pdb=" N PRO B 112 " ideal model delta sigma weight residual 118.44 121.37 -2.93 1.59e+00 3.96e-01 3.39e+00 angle pdb=" N ASN A 581 " pdb=" CA ASN A 581 " pdb=" CB ASN A 581 " ideal model delta sigma weight residual 114.27 111.25 3.02 1.64e+00 3.72e-01 3.39e+00 ... (remaining 34665 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 5958 17.29 - 34.58: 571 34.58 - 51.87: 172 51.87 - 69.16: 46 69.16 - 86.45: 8 Dihedral angle restraints: 6755 sinusoidal: 4897 harmonic: 1858 Sorted by residual: dihedral pdb=" CA PHE B 224 " pdb=" C PHE B 224 " pdb=" N THR B 225 " pdb=" CA THR B 225 " ideal model delta harmonic sigma weight residual -180.00 -163.31 -16.69 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA ARG B 333 " pdb=" C ARG B 333 " pdb=" N ILE B 334 " pdb=" CA ILE B 334 " ideal model delta harmonic sigma weight residual 180.00 -163.32 -16.68 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CG LYS A 217 " pdb=" CD LYS A 217 " pdb=" CE LYS A 217 " pdb=" NZ LYS A 217 " ideal model delta sinusoidal sigma weight residual 180.00 124.91 55.09 3 1.50e+01 4.44e-03 9.33e+00 ... (remaining 6752 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 924 0.031 - 0.061: 306 0.061 - 0.092: 114 0.092 - 0.123: 81 0.123 - 0.154: 16 Chirality restraints: 1441 Sorted by residual: chirality pdb=" CA ILE A1254 " pdb=" N ILE A1254 " pdb=" C ILE A1254 " pdb=" CB ILE A1254 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.90e-01 chirality pdb=" CA ILE A 660 " pdb=" N ILE A 660 " pdb=" C ILE A 660 " pdb=" CB ILE A 660 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.44e-01 chirality pdb=" CA ILE B 199 " pdb=" N ILE B 199 " pdb=" C ILE B 199 " pdb=" CB ILE B 199 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.05e-01 ... (remaining 1438 not shown) Planarity restraints: 2768 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B 111 " -0.030 5.00e-02 4.00e+02 4.57e-02 3.35e+00 pdb=" N PRO B 112 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 112 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 112 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A1256 " 0.029 5.00e-02 4.00e+02 4.43e-02 3.13e+00 pdb=" N PRO A1257 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A1257 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A1257 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 190 " 0.026 5.00e-02 4.00e+02 3.94e-02 2.48e+00 pdb=" N PRO B 191 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 191 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 191 " 0.022 5.00e-02 4.00e+02 ... (remaining 2765 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.05: 1095 2.05 - 2.69: 27749 2.69 - 3.32: 56693 3.32 - 3.96: 73935 3.96 - 4.60: 108567 Nonbonded interactions: 268039 Sorted by model distance: nonbonded pdb=" HH TYR A 643 " pdb=" OE1 GLU A1102 " model vdw 1.412 1.850 nonbonded pdb=" O TYR A 203 " pdb=" H LEU A 339 " model vdw 1.413 1.850 nonbonded pdb=" H GLY A 263 " pdb=" O VAL A 296 " model vdw 1.481 1.850 nonbonded pdb=" OD1 ASN C 226 " pdb=" H ASP C 261 " model vdw 1.487 1.850 nonbonded pdb=" O VAL B 178 " pdb=" H SER B 182 " model vdw 1.502 1.850 ... (remaining 268034 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 'B' and (resid 73 through 120 or (resid 121 and (name N or name CA or nam \ e C or name O or name CB or name CG1 or name CG2 or name CD1 or name H or name H \ A or name HB or name HG12 or name HG13 or name HG21 or name HG22 or name HG23 or \ name HD11 or name HD12 or name HD13)) or (resid 166 and (name N or name CA or n \ ame C or name O or name HA2 or name HA3)) or resid 167 through 187 or (resid 188 \ 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 o \ r name HD1 or name HD2 or name HE1)) or resid 189 through 306 or (resid 319 and \ (name N or name CA or name C or name O or name CB or name CG1 or name CG2 or nam \ e CD1 or name HA or name HB or name HG12 or name HG13 or name HG21 or name HG22 \ or name HG23 or name HD11 or name HD12 or name HD13)) or resid 320 through 342)) \ selection = (chain 'C' and (resid 73 through 99 or (resid 100 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 N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 101 through 121 or (resid 166 and (name N or name CA or name C or \ name O or name HA2 or name HA3)) or resid 167 through 306 or (resid 319 and (na \ me N or name CA or name C or name O or name CB or name CG1 or name CG2 or name C \ D1 or name HA or name HB or name HG12 or name HG13 or name HG21 or name HG22 or \ name HG23 or name HD11 or name HD12 or name HD13)) or resid 320 through 341 or ( \ resid 342 and (name N or name CA or name C or name O or name CB or name CG or na \ me CD1 or name CD2 or name CE1 or name CE2 or name CZ or name H or name HA or na \ me HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or name HZ )) \ )) } 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: 0.070 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: 0.110 Extract box with map and model: 0.420 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 28.930 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:0.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:25.170 Internal consistency checks: 0.000 Total: 55.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6102 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 : 0.002 0.026 9651 Z= 0.113 Angle : 0.528 5.608 13050 Z= 0.283 Chirality : 0.043 0.154 1441 Planarity : 0.004 0.046 1682 Dihedral : 12.824 86.452 3630 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 0.09 % Allowed : 1.89 % Favored : 98.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % 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 (0.24), residues: 1130 helix: 0.05 (0.28), residues: 308 sheet: -0.86 (0.32), residues: 248 loop : -1.51 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 72 TYR 0.013 0.001 TYR A1100 PHE 0.011 0.001 PHE A 622 TRP 0.008 0.001 TRP B 171 HIS 0.004 0.001 HIS B 328 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 7.9990 chunk 113 optimal weight: 10.0000 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 chunk 100 optimal weight: 8.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6435 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 9651 Z= 0.272 Angle : 0.622 7.022 13050 Z= 0.331 Chirality : 0.061 0.257 1441 Planarity : 0.005 0.041 1682 Dihedral : 12.327 85.220 3630 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.28 % Allowed : 2.65 % Favored : 97.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % 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: -1.27 (0.24), residues: 1130 helix: 0.48 (0.29), residues: 291 sheet: -1.04 (0.32), residues: 244 loop : -1.43 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 154 TYR 0.013 0.002 TYR A 604 PHE 0.027 0.002 PHE B 212 TRP 0.013 0.002 TRP A 278 HIS 0.006 0.001 HIS B 328 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 9.9990 chunk 38 optimal weight: 8.9990 chunk 61 optimal weight: 30.0000 chunk 45 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 64 optimal weight: 7.9990 chunk 17 optimal weight: 0.0870 chunk 36 optimal weight: 2.9990 chunk 96 optimal weight: 9.9990 chunk 12 optimal weight: 8.9990 overall best weight: 5.8166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6480 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9651 Z= 0.181 Angle : 0.530 5.999 13050 Z= 0.277 Chirality : 0.056 0.203 1441 Planarity : 0.004 0.041 1682 Dihedral : 11.905 86.098 3630 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 0.38 % Allowed : 3.88 % Favored : 95.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % 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: -1.05 (0.25), residues: 1130 helix: 0.83 (0.31), residues: 294 sheet: -1.04 (0.32), residues: 242 loop : -1.33 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A1107 TYR 0.015 0.001 TYR B 233 PHE 0.019 0.002 PHE A 292 TRP 0.007 0.001 TRP A 278 HIS 0.005 0.001 HIS B 328 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 79 optimal weight: 8.9990 chunk 102 optimal weight: 8.9990 chunk 32 optimal weight: 7.9990 chunk 68 optimal weight: 20.0000 chunk 90 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6534 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9651 Z= 0.197 Angle : 0.525 6.034 13050 Z= 0.275 Chirality : 0.057 0.208 1441 Planarity : 0.004 0.040 1682 Dihedral : 11.703 85.939 3630 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 0.57 % Allowed : 4.17 % Favored : 95.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % 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 (0.25), residues: 1130 helix: 0.54 (0.30), residues: 296 sheet: -1.15 (0.33), residues: 225 loop : -1.29 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 569 TYR 0.010 0.001 TYR B 233 PHE 0.022 0.002 PHE B 212 TRP 0.012 0.001 TRP A 278 HIS 0.006 0.001 HIS B 328 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 9 optimal weight: 10.0000 chunk 108 optimal weight: 20.0000 chunk 87 optimal weight: 10.0000 chunk 42 optimal weight: 7.9990 chunk 60 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6640 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 9651 Z= 0.239 Angle : 0.588 6.864 13050 Z= 0.313 Chirality : 0.059 0.223 1441 Planarity : 0.005 0.044 1682 Dihedral : 12.182 86.362 3630 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.41 % Favored : 91.50 % Rotamer: Outliers : 1.70 % Allowed : 5.68 % Favored : 92.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % 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: -1.74 (0.24), residues: 1130 helix: -0.19 (0.30), residues: 291 sheet: -1.48 (0.33), residues: 218 loop : -1.49 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 150 TYR 0.014 0.002 TYR B 233 PHE 0.021 0.002 PHE B 212 TRP 0.012 0.001 TRP A 278 HIS 0.005 0.001 HIS A 155 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 81 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 70 optimal weight: 10.0000 chunk 61 optimal weight: 30.0000 chunk 56 optimal weight: 9.9990 chunk 110 optimal weight: 40.0000 chunk 66 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6632 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9651 Z= 0.198 Angle : 0.530 5.694 13050 Z= 0.277 Chirality : 0.057 0.207 1441 Planarity : 0.004 0.043 1682 Dihedral : 11.986 85.220 3630 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 1.80 % Allowed : 5.49 % Favored : 92.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % 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: -1.73 (0.24), residues: 1130 helix: -0.15 (0.30), residues: 291 sheet: -1.49 (0.33), residues: 220 loop : -1.49 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 569 TYR 0.010 0.001 TYR B 110 PHE 0.020 0.001 PHE B 212 TRP 0.013 0.001 TRP A 278 HIS 0.004 0.001 HIS B 328 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 724.28 seconds wall clock time: 13 minutes 6.08 seconds (786.08 seconds total)