Starting phenix.real_space_refine (version: 1.20rc4) on Wed Dec 1 20:42:29 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nsk_0499/12_2021/6nsk_0499_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nsk_0499/12_2021/6nsk_0499.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nsk_0499/12_2021/6nsk_0499_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nsk_0499/12_2021/6nsk_0499_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nsk_0499/12_2021/6nsk_0499_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nsk_0499/12_2021/6nsk_0499.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nsk_0499/12_2021/6nsk_0499.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nsk_0499/12_2021/6nsk_0499_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nsk_0499/12_2021/6nsk_0499_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.002 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc4-4434/modules/chem_data/mon_lib" Total number of atoms: 9096 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1449 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 8, 'TRANS': 173} Chain breaks: 1 Chain: "B" Number of atoms: 1449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1449 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 8, 'TRANS': 173} Chain breaks: 1 Chain: "C" Number of atoms: 1449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1449 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 8, 'TRANS': 173} Chain breaks: 1 Chain: "D" Number of atoms: 1449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1449 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 8, 'TRANS': 173} Chain breaks: 1 Chain: "E" Number of atoms: 1449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1449 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 8, 'TRANS': 173} Chain breaks: 1 Chain: "F" Number of atoms: 1449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1449 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 8, 'TRANS': 173} Chain breaks: 1 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'XP4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'XP4:plan-2': 1, 'XP4:plan-1': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {'XP4': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'XP4:plan-2': 1, 'XP4:plan-1': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 107 Unusual residues: {'XP4': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'XP4:plan-2': 1, 'XP4:plan-1': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'XP4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'XP4:plan-2': 1, 'XP4:plan-1': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {'XP4': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'XP4:plan-2': 1, 'XP4:plan-1': 1} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 107 Unusual residues: {'XP4': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'XP4:plan-2': 1, 'XP4:plan-1': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 5.57, per 1000 atoms: 0.61 Number of scatterers: 9096 At special positions: 0 Unit cell: (101.65, 97.37, 62.06, 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 30 16.00 P 6 15.00 O 1494 8.00 N 1332 7.00 C 6234 6.00 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 Amimo 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: 3.70 Conformation dependent library (CDL) restraints added in 1.5 seconds 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2004 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 38 helices and 0 sheets defined 72.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.85 Creating SS restraints... Processing helix chain 'A' and resid 2 through 22 removed outlier: 3.947A pdb=" N LEU A 7 " --> pdb=" O GLY A 3 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N TYR A 8 " --> pdb=" O LEU A 4 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A 21 " --> pdb=" O GLY A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 53 removed outlier: 3.732A pdb=" N VAL A 47 " --> pdb=" O CYS A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 79 No H-bonds generated for 'chain 'A' and resid 76 through 79' Processing helix chain 'A' and resid 82 through 97 Processing helix chain 'A' and resid 102 through 123 Proline residue: A 117 - end of helix removed outlier: 3.665A pdb=" N ILE A 120 " --> pdb=" O VAL A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 160 Processing helix chain 'A' and resid 169 through 190 removed outlier: 4.614A pdb=" N ILE A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Proline residue: A 185 - end of helix Processing helix chain 'B' and resid 2 through 22 removed outlier: 3.904A pdb=" N LEU B 7 " --> pdb=" O GLY B 3 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N TYR B 8 " --> pdb=" O LEU B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 53 removed outlier: 4.339A pdb=" N VAL B 47 " --> pdb=" O CYS B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 97 removed outlier: 3.983A pdb=" N LEU B 83 " --> pdb=" O ALA B 79 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N PHE B 84 " --> pdb=" O THR B 80 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY B 85 " --> pdb=" O GLY B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 123 Proline residue: B 117 - end of helix removed outlier: 3.577A pdb=" N ILE B 120 " --> pdb=" O VAL B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 160 Processing helix chain 'B' and resid 169 through 188 removed outlier: 4.669A pdb=" N ILE B 184 " --> pdb=" O LEU B 180 " (cutoff:3.500A) Proline residue: B 185 - end of helix Processing helix chain 'C' and resid 2 through 21 removed outlier: 3.876A pdb=" N LEU C 7 " --> pdb=" O GLY C 3 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N TYR C 8 " --> pdb=" O LEU C 4 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 53 removed outlier: 3.675A pdb=" N VAL C 47 " --> pdb=" O CYS C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 97 removed outlier: 3.938A pdb=" N LEU C 83 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N PHE C 84 " --> pdb=" O THR C 80 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY C 85 " --> pdb=" O GLY C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 123 Proline residue: C 117 - end of helix removed outlier: 3.644A pdb=" N ILE C 120 " --> pdb=" O VAL C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 160 Processing helix chain 'C' and resid 169 through 190 removed outlier: 4.659A pdb=" N ILE C 184 " --> pdb=" O LEU C 180 " (cutoff:3.500A) Proline residue: C 185 - end of helix Processing helix chain 'D' and resid 2 through 22 removed outlier: 3.947A pdb=" N LEU D 7 " --> pdb=" O GLY D 3 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N TYR D 8 " --> pdb=" O LEU D 4 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU D 21 " --> pdb=" O GLY D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 53 removed outlier: 3.745A pdb=" N VAL D 47 " --> pdb=" O CYS D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 79 No H-bonds generated for 'chain 'D' and resid 76 through 79' Processing helix chain 'D' and resid 82 through 97 Processing helix chain 'D' and resid 102 through 123 Proline residue: D 117 - end of helix removed outlier: 3.665A pdb=" N ILE D 120 " --> pdb=" O VAL D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 160 Processing helix chain 'D' and resid 169 through 190 removed outlier: 4.613A pdb=" N ILE D 184 " --> pdb=" O LEU D 180 " (cutoff:3.500A) Proline residue: D 185 - end of helix Processing helix chain 'E' and resid 2 through 22 removed outlier: 3.904A pdb=" N LEU E 7 " --> pdb=" O GLY E 3 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N TYR E 8 " --> pdb=" O LEU E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 53 removed outlier: 4.339A pdb=" N VAL E 47 " --> pdb=" O CYS E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 97 removed outlier: 3.983A pdb=" N LEU E 83 " --> pdb=" O ALA E 79 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N PHE E 84 " --> pdb=" O THR E 80 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY E 85 " --> pdb=" O GLY E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 123 Proline residue: E 117 - end of helix removed outlier: 3.577A pdb=" N ILE E 120 " --> pdb=" O VAL E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 160 Processing helix chain 'E' and resid 169 through 188 removed outlier: 4.669A pdb=" N ILE E 184 " --> pdb=" O LEU E 180 " (cutoff:3.500A) Proline residue: E 185 - end of helix Processing helix chain 'F' and resid 2 through 21 removed outlier: 3.875A pdb=" N LEU F 7 " --> pdb=" O GLY F 3 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N TYR F 8 " --> pdb=" O LEU F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 53 removed outlier: 3.676A pdb=" N VAL F 47 " --> pdb=" O CYS F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 97 removed outlier: 3.938A pdb=" N LEU F 83 " --> pdb=" O ALA F 79 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N PHE F 84 " --> pdb=" O THR F 80 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY F 85 " --> pdb=" O GLY F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 123 Proline residue: F 117 - end of helix removed outlier: 3.644A pdb=" N ILE F 120 " --> pdb=" O VAL F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 160 Processing helix chain 'F' and resid 169 through 190 removed outlier: 4.659A pdb=" N ILE F 184 " --> pdb=" O LEU F 180 " (cutoff:3.500A) Proline residue: F 185 - end of helix 562 hydrogen bonds defined for protein. 1686 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: 2.57 Time building geometry restraints manager: 3.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1266 1.31 - 1.43: 2876 1.43 - 1.56: 5200 1.56 - 1.68: 6 1.68 - 1.81: 48 Bond restraints: 9396 Sorted by residual: bond pdb=" N TRP D 183 " pdb=" CA TRP D 183 " ideal model delta sigma weight residual 1.459 1.493 -0.033 1.20e-02 6.94e+03 7.72e+00 bond pdb=" N TRP A 183 " pdb=" CA TRP A 183 " ideal model delta sigma weight residual 1.459 1.493 -0.033 1.20e-02 6.94e+03 7.72e+00 bond pdb=" N TRP C 183 " pdb=" CA TRP C 183 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.23e-02 6.61e+03 7.36e+00 bond pdb=" N TRP F 183 " pdb=" CA TRP F 183 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.23e-02 6.61e+03 7.36e+00 bond pdb=" N TRP B 183 " pdb=" CA TRP B 183 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.23e-02 6.61e+03 7.13e+00 ... (remaining 9391 not shown) Histogram of bond angle deviations from ideal: 99.84 - 106.78: 328 106.78 - 113.72: 5407 113.72 - 120.66: 4052 120.66 - 127.60: 2805 127.60 - 134.54: 212 Bond angle restraints: 12804 Sorted by residual: angle pdb=" C PHE C 169 " pdb=" N THR C 170 " pdb=" CA THR C 170 " ideal model delta sigma weight residual 120.09 125.21 -5.12 1.25e+00 6.40e-01 1.67e+01 angle pdb=" C PHE F 169 " pdb=" N THR F 170 " pdb=" CA THR F 170 " ideal model delta sigma weight residual 120.09 125.21 -5.12 1.25e+00 6.40e-01 1.67e+01 angle pdb=" C THR D 181 " pdb=" N ALA D 182 " pdb=" CA ALA D 182 " ideal model delta sigma weight residual 122.15 112.59 9.56 2.83e+00 1.25e-01 1.14e+01 angle pdb=" C THR A 181 " pdb=" N ALA A 182 " pdb=" CA ALA A 182 " ideal model delta sigma weight residual 122.15 112.59 9.56 2.83e+00 1.25e-01 1.14e+01 angle pdb=" CA TYR F 90 " pdb=" CB TYR F 90 " pdb=" CG TYR F 90 " ideal model delta sigma weight residual 113.90 119.82 -5.92 1.80e+00 3.09e-01 1.08e+01 ... (remaining 12799 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.95: 4421 11.95 - 23.91: 483 23.91 - 35.86: 138 35.86 - 47.82: 48 47.82 - 59.77: 88 Dihedral angle restraints: 5178 sinusoidal: 2046 harmonic: 3132 Sorted by residual: dihedral pdb=" CA LEU F 128 " pdb=" C LEU F 128 " pdb=" N ASP F 129 " pdb=" CA ASP F 129 " ideal model delta harmonic sigma weight residual -180.00 -156.63 -23.37 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA LEU C 128 " pdb=" C LEU C 128 " pdb=" N ASP C 129 " pdb=" CA ASP C 129 " ideal model delta harmonic sigma weight residual -180.00 -156.70 -23.30 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA LEU D 128 " pdb=" C LEU D 128 " pdb=" N ASP D 129 " pdb=" CA ASP D 129 " ideal model delta harmonic sigma weight residual 180.00 -159.13 -20.87 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 5175 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 604 0.034 - 0.068: 460 0.068 - 0.102: 241 0.102 - 0.136: 94 0.136 - 0.169: 41 Chirality restraints: 1440 Sorted by residual: chirality pdb=" CA TRP F 183 " pdb=" N TRP F 183 " pdb=" C TRP F 183 " pdb=" CB TRP F 183 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.18e-01 chirality pdb=" CA ARG A 102 " pdb=" N ARG A 102 " pdb=" C ARG A 102 " pdb=" CB ARG A 102 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.04e-01 chirality pdb=" CA ARG D 102 " pdb=" N ARG D 102 " pdb=" C ARG D 102 " pdb=" CB ARG D 102 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.04e-01 ... (remaining 1437 not shown) Planarity restraints: 1470 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 90 " 0.037 2.00e-02 2.50e+03 3.05e-02 1.86e+01 pdb=" CG TYR D 90 " -0.073 2.00e-02 2.50e+03 pdb=" CD1 TYR D 90 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR D 90 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR D 90 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR D 90 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR D 90 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR D 90 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 90 " 0.037 2.00e-02 2.50e+03 3.05e-02 1.86e+01 pdb=" CG TYR A 90 " -0.073 2.00e-02 2.50e+03 pdb=" CD1 TYR A 90 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR A 90 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR A 90 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR A 90 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR A 90 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 90 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 90 " 0.037 2.00e-02 2.50e+03 3.01e-02 1.82e+01 pdb=" CG TYR E 90 " -0.073 2.00e-02 2.50e+03 pdb=" CD1 TYR E 90 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR E 90 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR E 90 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR E 90 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR E 90 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR E 90 " 0.005 2.00e-02 2.50e+03 ... (remaining 1467 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1074 2.75 - 3.29: 8453 3.29 - 3.83: 14923 3.83 - 4.36: 18182 4.36 - 4.90: 32205 Nonbonded interactions: 74837 Sorted by model distance: nonbonded pdb=" O GLU B 177 " pdb=" OG1 THR B 181 " model vdw 2.213 2.440 nonbonded pdb=" O GLU E 177 " pdb=" OG1 THR E 181 " model vdw 2.213 2.440 nonbonded pdb=" O GLU F 177 " pdb=" OG1 THR F 181 " model vdw 2.219 2.440 nonbonded pdb=" O GLU C 177 " pdb=" OG1 THR C 181 " model vdw 2.219 2.440 nonbonded pdb=" O GLU D 177 " pdb=" OG1 THR D 181 " model vdw 2.230 2.440 ... (remaining 74832 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 1 through 195 or resid 201)) selection = (chain 'B' and (resid 1 through 195 or (resid 201 and (name C18 or name C19 or n \ ame C2 or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 o \ r name C26 or name C27 or name C28 or name C29 or name C30 or name C31 or name O \ 7 or name O8 )))) selection = (chain 'C' and (resid 1 through 195 or (resid 201 and (name C18 or name C19 or n \ ame C2 or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 o \ r name C26 or name C27 or name C28 or name C29 or name C30 or name C31 or name O \ 7 or name O8 )))) selection = (chain 'D' and (resid 1 through 195 or resid 201)) selection = (chain 'E' and (resid 1 through 195 or (resid 201 and (name C18 or name C19 or n \ ame C2 or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 o \ r name C26 or name C27 or name C28 or name C29 or name C30 or name C31 or name O \ 7 or name O8 )))) selection = (chain 'F' and (resid 1 through 195 or (resid 201 and (name C18 or name C19 or n \ ame C2 or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 o \ r name C26 or name C27 or name C28 or name C29 or name C30 or name C31 or name O \ 7 or name O8 )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 30 5.16 5 C 6234 2.51 5 N 1332 2.21 5 O 1494 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Write .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: 0.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.760 Check model and map are aligned: 0.130 Convert atoms to be neutral: 0.080 Process input model: 26.280 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:10.720 Set ADP refinement strategy: 0.000 Write .geo file: 0.000 Internal consistency checks: 0.000 Total: 39.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 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 : 0.008 0.069 9396 Z= 0.543 Angle : 1.114 9.557 12804 Z= 0.577 Chirality : 0.060 0.169 1440 Planarity : 0.008 0.045 1470 Dihedral : 14.473 59.771 3174 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.23 (0.20), residues: 1068 helix: -1.94 (0.14), residues: 810 sheet: None (None), residues: 0 loop : -2.09 (0.35), residues: 258 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.097 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.8861 time to fit residues: 146.9898 Evaluate side-chains 106 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 1.066 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.7980 chunk 81 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 84 optimal weight: 6.9990 chunk 32 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 HIS A 114 ASN B 114 ASN C 95 HIS D 95 HIS D 114 ASN E 114 ASN F 95 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 9396 Z= 0.163 Angle : 0.561 6.820 12804 Z= 0.292 Chirality : 0.042 0.174 1440 Planarity : 0.005 0.035 1470 Dihedral : 15.087 59.681 1410 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer Outliers : 1.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.31 (0.25), residues: 1068 helix: 0.30 (0.17), residues: 834 sheet: None (None), residues: 0 loop : -1.75 (0.39), residues: 234 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 130 time to evaluate : 0.995 Fit side-chains outliers start: 12 outliers final: 2 residues processed: 132 average time/residue: 0.7185 time to fit residues: 105.8082 Evaluate side-chains 110 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 108 time to evaluate : 1.002 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 1.2896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 98 optimal weight: 7.9990 chunk 106 optimal weight: 0.9990 chunk 87 optimal weight: 0.0770 chunk 97 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 78 optimal weight: 10.0000 overall best weight: 0.6940 ------------------------------------------------------------------------------- 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: 0.7539 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 9396 Z= 0.142 Angle : 0.508 6.902 12804 Z= 0.258 Chirality : 0.040 0.166 1440 Planarity : 0.004 0.036 1470 Dihedral : 13.562 59.121 1410 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer Outliers : 2.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.26), residues: 1068 helix: 1.34 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -1.20 (0.44), residues: 228 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 125 time to evaluate : 0.917 Fit side-chains outliers start: 20 outliers final: 8 residues processed: 133 average time/residue: 0.7730 time to fit residues: 114.0647 Evaluate side-chains 125 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 117 time to evaluate : 1.043 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 1.3468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 65 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN B 95 HIS D 160 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 9396 Z= 0.246 Angle : 0.561 7.222 12804 Z= 0.287 Chirality : 0.043 0.164 1440 Planarity : 0.004 0.037 1470 Dihedral : 13.311 59.074 1410 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer Outliers : 3.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.40 (0.26), residues: 1068 helix: 1.51 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -1.17 (0.43), residues: 228 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 107 time to evaluate : 0.987 Fit side-chains outliers start: 28 outliers final: 16 residues processed: 123 average time/residue: 0.7717 time to fit residues: 105.2784 Evaluate side-chains 115 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 99 time to evaluate : 1.025 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 14 residues processed: 2 average time/residue: 0.1431 time to fit residues: 1.7827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 1 optimal weight: 0.5980 chunk 77 optimal weight: 9.9990 chunk 43 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 0 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN D 160 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 9396 Z= 0.172 Angle : 0.514 6.821 12804 Z= 0.261 Chirality : 0.041 0.129 1440 Planarity : 0.004 0.037 1470 Dihedral : 12.819 59.398 1410 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer Outliers : 3.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.91 (0.27), residues: 1068 helix: 1.82 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -0.79 (0.45), residues: 228 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 106 time to evaluate : 0.998 Fit side-chains outliers start: 28 outliers final: 17 residues processed: 120 average time/residue: 0.7846 time to fit residues: 104.2766 Evaluate side-chains 123 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 106 time to evaluate : 1.057 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 14 residues processed: 3 average time/residue: 0.0975 time to fit residues: 1.8623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.5980 chunk 94 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 104 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN B 44 ASN D 160 ASN E 44 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 9396 Z= 0.202 Angle : 0.530 6.995 12804 Z= 0.269 Chirality : 0.041 0.131 1440 Planarity : 0.004 0.037 1470 Dihedral : 12.357 59.553 1410 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer Outliers : 2.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.03 (0.27), residues: 1068 helix: 1.88 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -0.64 (0.45), residues: 228 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 111 time to evaluate : 0.945 Fit side-chains outliers start: 27 outliers final: 18 residues processed: 128 average time/residue: 0.7477 time to fit residues: 106.3572 Evaluate side-chains 125 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 107 time to evaluate : 1.009 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 14 residues processed: 4 average time/residue: 0.1105 time to fit residues: 2.0252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.0570 chunk 11 optimal weight: 9.9990 chunk 59 optimal weight: 6.9990 chunk 76 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 65 optimal weight: 0.3980 chunk 63 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 64 optimal weight: 0.0020 overall best weight: 0.4908 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN B 44 ASN D 160 ASN E 44 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 9396 Z= 0.126 Angle : 0.479 6.596 12804 Z= 0.240 Chirality : 0.039 0.128 1440 Planarity : 0.004 0.034 1470 Dihedral : 11.579 59.651 1410 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer Outliers : 2.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.57 (0.27), residues: 1068 helix: 2.24 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -0.32 (0.47), residues: 228 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 128 time to evaluate : 0.991 Fit side-chains outliers start: 25 outliers final: 15 residues processed: 143 average time/residue: 0.7012 time to fit residues: 112.1601 Evaluate side-chains 132 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 117 time to evaluate : 1.062 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 14 residues processed: 1 average time/residue: 0.1341 time to fit residues: 1.5593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 51 optimal weight: 0.0050 chunk 9 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 overall best weight: 0.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN D 160 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 9396 Z= 0.144 Angle : 0.496 6.646 12804 Z= 0.250 Chirality : 0.042 0.203 1440 Planarity : 0.004 0.037 1470 Dihedral : 11.262 59.556 1410 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer Outliers : 2.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.71 (0.27), residues: 1068 helix: 2.33 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -0.24 (0.47), residues: 228 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 113 time to evaluate : 0.976 Fit side-chains outliers start: 22 outliers final: 16 residues processed: 127 average time/residue: 0.7163 time to fit residues: 101.4623 Evaluate side-chains 129 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 113 time to evaluate : 1.028 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 14 residues processed: 2 average time/residue: 1.0783 time to fit residues: 3.6294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 6.9990 chunk 97 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 91 optimal weight: 0.5980 chunk 96 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN D 160 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 9396 Z= 0.172 Angle : 0.514 6.906 12804 Z= 0.261 Chirality : 0.043 0.201 1440 Planarity : 0.004 0.040 1470 Dihedral : 11.083 59.703 1410 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer Outliers : 2.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.69 (0.27), residues: 1068 helix: 2.30 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -0.20 (0.46), residues: 228 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 110 time to evaluate : 1.073 Fit side-chains outliers start: 20 outliers final: 14 residues processed: 124 average time/residue: 0.7823 time to fit residues: 107.4973 Evaluate side-chains 122 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 108 time to evaluate : 1.099 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 14 residues processed: 0 time to fit residues: 1.4137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 71 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN D 160 ASN E 95 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 9396 Z= 0.217 Angle : 0.546 7.154 12804 Z= 0.278 Chirality : 0.044 0.189 1440 Planarity : 0.004 0.040 1470 Dihedral : 11.190 59.221 1410 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer Outliers : 2.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.48 (0.27), residues: 1068 helix: 2.14 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -0.22 (0.46), residues: 228 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 109 time to evaluate : 0.917 Fit side-chains outliers start: 21 outliers final: 16 residues processed: 125 average time/residue: 0.7563 time to fit residues: 105.0366 Evaluate side-chains 115 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 99 time to evaluate : 0.982 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 14 residues processed: 2 average time/residue: 1.1623 time to fit residues: 3.8374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 88 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 75 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN D 160 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.149763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.119052 restraints weight = 10409.435| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.67 r_work: 0.3430 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3418 rms_B_bonded: 1.54 restraints_weight: 0.2500 r_work: 0.3406 rms_B_bonded: 1.62 restraints_weight: 0.1250 r_work: 0.3392 rms_B_bonded: 1.76 restraints_weight: 0.0625 r_work: 0.3378 rms_B_bonded: 1.93 restraints_weight: 0.0312 r_work: 0.3363 rms_B_bonded: 2.15 restraints_weight: 0.0156 r_work: 0.3347 rms_B_bonded: 2.41 restraints_weight: 0.0078 r_work: 0.3329 rms_B_bonded: 2.71 restraints_weight: 0.0039 r_work: 0.3310 rms_B_bonded: 3.06 restraints_weight: 0.0020 r_work: 0.3290 rms_B_bonded: 3.46 restraints_weight: 0.0010 r_work: 0.3267 rms_B_bonded: 3.91 restraints_weight: 0.0005 r_work: 0.3243 rms_B_bonded: 4.42 restraints_weight: 0.0002 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 9396 Z= 0.150 Angle : 0.502 6.963 12804 Z= 0.255 Chirality : 0.042 0.183 1440 Planarity : 0.004 0.041 1470 Dihedral : 10.785 59.455 1410 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer Outliers : 1.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.76 (0.27), residues: 1068 helix: 2.34 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -0.09 (0.47), residues: 228 =============================================================================== Job complete usr+sys time: 2300.50 seconds wall clock time: 42 minutes 27.83 seconds (2547.83 seconds total)