Starting phenix.real_space_refine on Fri Jun 28 05:43:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tkp_41356/06_2024/8tkp_41356_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tkp_41356/06_2024/8tkp_41356.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tkp_41356/06_2024/8tkp_41356.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tkp_41356/06_2024/8tkp_41356.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tkp_41356/06_2024/8tkp_41356_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tkp_41356/06_2024/8tkp_41356_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.001 sd= 0.009 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: 6 Type Number sf(0) Gaussians Ca 4 9.91 5 P 10 5.49 5 S 74 5.16 5 C 9731 2.51 5 N 2347 2.21 5 O 2500 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 14666 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 4992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4992 Classifications: {'peptide': 614} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 592} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 1554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1554 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 7, 'TRANS': 179} Chain: "C" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 378 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "D" Number of atoms: 4992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4992 Classifications: {'peptide': 614} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 592} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "E" Number of atoms: 1554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1554 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 7, 'TRANS': 179} Chain: "F" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 378 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 291 Unusual residues: {'CLR': 1, 'NAG': 1, 'PEE': 4, 'R16': 9, 'TWT': 2} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 82 Unusual residues: {'PEE': 1, 'PLM': 2, 'R16': 2, 'TWT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 59 Planarities with less than four sites: {'PLM:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "D" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 320 Unusual residues: {'CLR': 1, 'NAG': 1, 'PEE': 5, 'R16': 9, 'TWT': 2} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 168 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 65 Unusual residues: {'PLM': 2, 'R16': 2, 'TWT': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'PLM:plan-1': 2} Unresolved non-hydrogen planarities: 2 Residues with excluded nonbonded symmetry interactions: 134 residue: pdb=" N LYS A 95 " occ=0.97 ... (7 atoms not shown) pdb=" NZ LYS A 95 " occ=0.94 residue: pdb=" N GLU A 102 " occ=0.97 ... (7 atoms not shown) pdb=" OE2 GLU A 102 " occ=0.56 residue: pdb=" N LYS A 106 " occ=0.95 ... (7 atoms not shown) pdb=" NZ LYS A 106 " occ=0.72 residue: pdb=" N GLU A 132 " occ=0.94 ... (7 atoms not shown) pdb=" OE2 GLU A 132 " occ=0.87 residue: pdb=" N ALA A 133 " occ=0.95 ... (3 atoms not shown) pdb=" CB ALA A 133 " occ=0.91 residue: pdb=" N GLY A 146 " occ=0.93 ... (2 atoms not shown) pdb=" O GLY A 146 " occ=0.91 residue: pdb=" N LEU A 149 " occ=0.89 ... (6 atoms not shown) pdb=" CD2 LEU A 149 " occ=0.93 residue: pdb=" N ASP A 157 " occ=0.91 ... (6 atoms not shown) pdb=" OD2 ASP A 157 " occ=0.83 residue: pdb=" N ASN A 158 " occ=0.78 ... (6 atoms not shown) pdb=" ND2 ASN A 158 " occ=0.85 residue: pdb=" N ASP A 214 " occ=0.98 ... (6 atoms not shown) pdb=" OD2 ASP A 214 " occ=0.69 residue: pdb=" N GLY A 251 " occ=0.98 ... (2 atoms not shown) pdb=" O GLY A 251 " occ=0.89 residue: pdb=" N THR A 268 " occ=0.99 ... (5 atoms not shown) pdb=" CG2 THR A 268 " occ=0.94 ... (remaining 122 not shown) Time building chain proxies: 10.05, per 1000 atoms: 0.69 Number of scatterers: 14666 At special positions: 0 Unit cell: (139.608, 111.354, 112.185, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 4 19.99 S 74 16.00 P 10 15.00 O 2500 8.00 N 2347 7.00 C 9731 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 594 " - pdb=" SG CYS A 743 " distance=2.03 Simple disulfide: pdb=" SG CYS D 594 " - pdb=" SG CYS D 743 " distance=2.03 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=5, symmetry=0 Links applied BETA1-3 " NAG H 1 " - " NAG H 2 " BETA1-4 " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG A1316 " - " ASN A 748 " " NAG D1316 " - " ASN D 748 " " NAG G 1 " - " ASN A 225 " " NAG H 1 " - " ASN D 225 " Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.26 Conformation dependent library (CDL) restraints added in 2.2 seconds 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3220 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 79 helices and 2 sheets defined 68.5% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.96 Creating SS restraints... Processing helix chain 'A' and resid 90 through 109 removed outlier: 4.540A pdb=" N ARG A 108 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N GLY A 109 " --> pdb=" O GLN A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 130 Processing helix chain 'A' and resid 137 through 163 removed outlier: 4.029A pdb=" N TYR A 162 " --> pdb=" O ASN A 158 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU A 163 " --> pdb=" O LEU A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 176 Processing helix chain 'A' and resid 179 through 205 removed outlier: 3.945A pdb=" N TYR A 184 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE A 185 " --> pdb=" O VAL A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 Processing helix chain 'A' and resid 222 through 231 removed outlier: 5.426A pdb=" N ALA A 229 " --> pdb=" O ASN A 225 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ILE A 230 " --> pdb=" O LYS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 242 removed outlier: 4.836A pdb=" N ASP A 242 " --> pdb=" O ARG A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 248 Processing helix chain 'A' and resid 261 through 263 No H-bonds generated for 'chain 'A' and resid 261 through 263' Processing helix chain 'A' and resid 278 through 307 Processing helix chain 'A' and resid 309 through 311 No H-bonds generated for 'chain 'A' and resid 309 through 311' Processing helix chain 'A' and resid 319 through 324 Processing helix chain 'A' and resid 335 through 354 Processing helix chain 'A' and resid 367 through 394 Processing helix chain 'A' and resid 406 through 429 Proline residue: A 419 - end of helix removed outlier: 3.531A pdb=" N LYS A 427 " --> pdb=" O ASP A 423 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE A 428 " --> pdb=" O LEU A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 470 removed outlier: 3.750A pdb=" N LYS A 470 " --> pdb=" O LEU A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 590 removed outlier: 3.765A pdb=" N GLN A 590 " --> pdb=" O ARG A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 621 Processing helix chain 'A' and resid 623 through 634 removed outlier: 4.135A pdb=" N ASN A 633 " --> pdb=" O CYS A 629 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N LEU A 634 " --> pdb=" O ARG A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 670 Processing helix chain 'A' and resid 676 through 697 Processing helix chain 'A' and resid 714 through 736 removed outlier: 3.694A pdb=" N LEU A 728 " --> pdb=" O PHE A 724 " (cutoff:3.500A) Proline residue: A 729 - end of helix Processing helix chain 'A' and resid 754 through 763 Processing helix chain 'A' and resid 768 through 775 Processing helix chain 'A' and resid 778 through 812 removed outlier: 3.820A pdb=" N ILE A 782 " --> pdb=" O PRO A 778 " (cutoff:3.500A) Proline residue: A 783 - end of helix removed outlier: 3.515A pdb=" N PHE A 794 " --> pdb=" O LEU A 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 31 Processing helix chain 'B' and resid 36 through 49 Processing helix chain 'B' and resid 62 through 65 No H-bonds generated for 'chain 'B' and resid 62 through 65' Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 77 through 80 No H-bonds generated for 'chain 'B' and resid 77 through 80' Processing helix chain 'B' and resid 85 through 92 Processing helix chain 'B' and resid 102 through 111 Processing helix chain 'B' and resid 118 through 129 Processing helix chain 'B' and resid 139 through 150 Processing helix chain 'B' and resid 156 through 170 Processing helix chain 'B' and resid 180 through 189 removed outlier: 4.203A pdb=" N ARG B 189 " --> pdb=" O HIS B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 196 No H-bonds generated for 'chain 'B' and resid 193 through 196' Processing helix chain 'C' and resid 24 through 46 removed outlier: 3.648A pdb=" N PHE C 45 " --> pdb=" O ILE C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 61 removed outlier: 4.416A pdb=" N LEU C 59 " --> pdb=" O ARG C 55 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ILE C 60 " --> pdb=" O GLN C 56 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ALA C 61 " --> pdb=" O ILE C 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 109 removed outlier: 3.859A pdb=" N LEU D 94 " --> pdb=" O LYS D 90 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ARG D 108 " --> pdb=" O ILE D 104 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N GLY D 109 " --> pdb=" O GLN D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 132 removed outlier: 5.067A pdb=" N GLU D 132 " --> pdb=" O LEU D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 163 removed outlier: 4.002A pdb=" N TYR D 162 " --> pdb=" O ASN D 158 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU D 163 " --> pdb=" O LEU D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 176 Processing helix chain 'D' and resid 179 through 205 removed outlier: 3.847A pdb=" N TYR D 184 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE D 185 " --> pdb=" O VAL D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 216 Processing helix chain 'D' and resid 222 through 231 removed outlier: 5.213A pdb=" N ALA D 229 " --> pdb=" O ASN D 225 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ILE D 230 " --> pdb=" O LYS D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 240 Processing helix chain 'D' and resid 244 through 248 Processing helix chain 'D' and resid 261 through 263 No H-bonds generated for 'chain 'D' and resid 261 through 263' Processing helix chain 'D' and resid 278 through 305 Processing helix chain 'D' and resid 319 through 325 Processing helix chain 'D' and resid 335 through 354 Processing helix chain 'D' and resid 368 through 395 Processing helix chain 'D' and resid 406 through 428 Proline residue: D 419 - end of helix Processing helix chain 'D' and resid 433 through 470 Processing helix chain 'D' and resid 584 through 589 removed outlier: 3.695A pdb=" N SER D 589 " --> pdb=" O SER D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 621 Processing helix chain 'D' and resid 623 through 631 Processing helix chain 'D' and resid 652 through 669 Processing helix chain 'D' and resid 676 through 697 Processing helix chain 'D' and resid 714 through 736 Proline residue: D 729 - end of helix Processing helix chain 'D' and resid 754 through 763 Processing helix chain 'D' and resid 766 through 775 Processing helix chain 'D' and resid 778 through 812 Proline residue: D 783 - end of helix Processing helix chain 'E' and resid 22 through 31 Processing helix chain 'E' and resid 36 through 49 Processing helix chain 'E' and resid 60 through 65 Proline residue: E 63 - end of helix No H-bonds generated for 'chain 'E' and resid 60 through 65' Processing helix chain 'E' and resid 70 through 74 Processing helix chain 'E' and resid 77 through 80 No H-bonds generated for 'chain 'E' and resid 77 through 80' Processing helix chain 'E' and resid 85 through 92 Processing helix chain 'E' and resid 102 through 111 Processing helix chain 'E' and resid 118 through 129 Processing helix chain 'E' and resid 139 through 149 Processing helix chain 'E' and resid 156 through 168 Processing helix chain 'E' and resid 180 through 189 removed outlier: 4.356A pdb=" N ARG E 189 " --> pdb=" O HIS E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 196 No H-bonds generated for 'chain 'E' and resid 193 through 196' Processing helix chain 'F' and resid 24 through 46 Processing helix chain 'F' and resid 54 through 59 Processing sheet with id= A, first strand: chain 'B' and resid 67 through 69 Processing sheet with id= B, first strand: chain 'E' and resid 67 through 69 800 hydrogen bonds defined for protein. 2394 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: 4.06 Time building geometry restraints manager: 6.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2170 1.30 - 1.43: 3945 1.43 - 1.55: 8703 1.55 - 1.68: 20 1.68 - 1.81: 122 Bond restraints: 14960 Sorted by residual: bond pdb=" CA SER A 775 " pdb=" C SER A 775 " ideal model delta sigma weight residual 1.524 1.452 0.072 1.26e-02 6.30e+03 3.26e+01 bond pdb=" C ASN A 770 " pdb=" O ASN A 770 " ideal model delta sigma weight residual 1.237 1.174 0.063 1.17e-02 7.31e+03 2.92e+01 bond pdb=" N LYS A 766 " pdb=" CA LYS A 766 " ideal model delta sigma weight residual 1.456 1.405 0.051 1.23e-02 6.61e+03 1.75e+01 bond pdb=" CA LYS A 766 " pdb=" C LYS A 766 " ideal model delta sigma weight residual 1.524 1.473 0.050 1.26e-02 6.30e+03 1.59e+01 bond pdb=" N GLN A 807 " pdb=" CA GLN A 807 " ideal model delta sigma weight residual 1.459 1.414 0.044 1.16e-02 7.43e+03 1.47e+01 ... (remaining 14955 not shown) Histogram of bond angle deviations from ideal: 100.30 - 107.04: 373 107.04 - 113.79: 8533 113.79 - 120.53: 5882 120.53 - 127.27: 5101 127.27 - 134.01: 141 Bond angle restraints: 20030 Sorted by residual: angle pdb=" N TYR A 774 " pdb=" CA TYR A 774 " pdb=" C TYR A 774 " ideal model delta sigma weight residual 111.28 104.44 6.84 1.09e+00 8.42e-01 3.93e+01 angle pdb=" C VAL A 769 " pdb=" CA VAL A 769 " pdb=" CB VAL A 769 " ideal model delta sigma weight residual 112.14 104.18 7.96 1.35e+00 5.49e-01 3.47e+01 angle pdb=" N GLN A 807 " pdb=" CA GLN A 807 " pdb=" C GLN A 807 " ideal model delta sigma weight residual 111.02 104.02 7.00 1.22e+00 6.72e-01 3.29e+01 angle pdb=" O3P PEE A1311 " pdb=" P PEE A1311 " pdb=" O4P PEE A1311 " ideal model delta sigma weight residual 92.91 109.68 -16.77 3.00e+00 1.11e-01 3.13e+01 angle pdb=" O3P PEE A1302 " pdb=" P PEE A1302 " pdb=" O4P PEE A1302 " ideal model delta sigma weight residual 92.91 109.62 -16.71 3.00e+00 1.11e-01 3.10e+01 ... (remaining 20025 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.57: 8961 35.57 - 71.14: 191 71.14 - 106.71: 43 106.71 - 142.29: 13 142.29 - 177.86: 10 Dihedral angle restraints: 9218 sinusoidal: 4242 harmonic: 4976 Sorted by residual: dihedral pdb=" C ASN A 763 " pdb=" N ASN A 763 " pdb=" CA ASN A 763 " pdb=" CB ASN A 763 " ideal model delta harmonic sigma weight residual -122.60 -138.81 16.21 0 2.50e+00 1.60e-01 4.20e+01 dihedral pdb=" N ASN A 763 " pdb=" C ASN A 763 " pdb=" CA ASN A 763 " pdb=" CB ASN A 763 " ideal model delta harmonic sigma weight residual 122.80 136.16 -13.36 0 2.50e+00 1.60e-01 2.86e+01 dihedral pdb=" C TYR A 774 " pdb=" N TYR A 774 " pdb=" CA TYR A 774 " pdb=" CB TYR A 774 " ideal model delta harmonic sigma weight residual -122.60 -110.09 -12.51 0 2.50e+00 1.60e-01 2.50e+01 ... (remaining 9215 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.158: 2167 0.158 - 0.316: 16 0.316 - 0.473: 4 0.473 - 0.631: 0 0.631 - 0.789: 1 Chirality restraints: 2188 Sorted by residual: chirality pdb=" C1 NAG H 2 " pdb=" O3 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.10e+01 chirality pdb=" CA ASN A 763 " pdb=" N ASN A 763 " pdb=" C ASN A 763 " pdb=" CB ASN A 763 " both_signs ideal model delta sigma weight residual False 2.51 1.72 0.79 2.00e-01 2.50e+01 1.56e+01 chirality pdb=" CA VAL A 799 " pdb=" N VAL A 799 " pdb=" C VAL A 799 " pdb=" CB VAL A 799 " both_signs ideal model delta sigma weight residual False 2.44 2.07 0.37 2.00e-01 2.50e+01 3.45e+00 ... (remaining 2185 not shown) Planarity restraints: 2422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1316 " -0.341 2.00e-02 2.50e+03 2.95e-01 1.09e+03 pdb=" C7 NAG A1316 " 0.079 2.00e-02 2.50e+03 pdb=" C8 NAG A1316 " -0.106 2.00e-02 2.50e+03 pdb=" N2 NAG A1316 " 0.527 2.00e-02 2.50e+03 pdb=" O7 NAG A1316 " -0.159 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 2 " 0.306 2.00e-02 2.50e+03 2.59e-01 8.37e+02 pdb=" C7 NAG H 2 " -0.078 2.00e-02 2.50e+03 pdb=" C8 NAG H 2 " 0.185 2.00e-02 2.50e+03 pdb=" N2 NAG H 2 " -0.447 2.00e-02 2.50e+03 pdb=" O7 NAG H 2 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 1 " 0.259 2.00e-02 2.50e+03 2.19e-01 5.97e+02 pdb=" C7 NAG G 1 " -0.067 2.00e-02 2.50e+03 pdb=" C8 NAG G 1 " 0.173 2.00e-02 2.50e+03 pdb=" N2 NAG G 1 " -0.370 2.00e-02 2.50e+03 pdb=" O7 NAG G 1 " 0.005 2.00e-02 2.50e+03 ... (remaining 2419 not shown) Histogram of nonbonded interaction distances: 1.15 - 1.90: 8 1.90 - 2.65: 257 2.65 - 3.40: 20990 3.40 - 4.15: 34111 4.15 - 4.90: 63538 Nonbonded interactions: 118904 Sorted by model distance: nonbonded pdb=" CA GLN A 804 " pdb=" OE1 GLN A 807 " model vdw 1.152 3.470 nonbonded pdb=" CA GLN A 804 " pdb=" CD GLN A 807 " model vdw 1.243 3.700 nonbonded pdb=" C GLN A 804 " pdb=" OE1 GLN A 807 " model vdw 1.305 3.270 nonbonded pdb=" CD1 LEU A 809 " pdb=" CD2 LEU D 809 " model vdw 1.586 3.880 nonbonded pdb=" O GLN A 804 " pdb=" OE1 GLN A 807 " model vdw 1.603 3.040 ... (remaining 118899 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 89 through 813 or resid 1301 through 1305 or (resid 1307 a \ nd (name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name \ C38 or name C39 or name C40 or name C41)) or (resid 1308 and (name C31 or name \ C32 or name C33 or name C34 or name C35 or name C36 or name C37)) or resid 1309 \ through 1316)) selection = (chain 'D' and (resid 89 through 813 or (resid 1301 and (name C1 or name C10 or \ name C11 or name C12 or name C2 or name C3 or name C4 or name C5 or name C6 or n \ ame C7 or name C8 or name C9 )) or resid 1302 through 1305 or (resid 1307 and (n \ ame C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 \ or name C39 or name C40 or name C41)) or (resid 1308 and (name C31 or name C32 o \ r name C33 or name C34 or name C35 or name C36 or name C37)) or (resid 1309 and \ (name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C3 \ 8 or name C39 or name C40 or name C41 or name C42)) or (resid 1310 and (name C33 \ or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name \ C40 or name C41 or name C42)) or resid 1311 through 1316)) } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = (chain 'C' and (resid 15 through 62 or resid 201 through 204)) selection = (chain 'F' and (resid 15 through 62 or (resid 201 and (name C1 or name C10 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 o \ r name C18 or name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or \ name C8 or name C9 )) or (resid 202 and (name C30 or name C31 or name C32 or nam \ e C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or \ name C40 or name C41)) or (resid 203 and (name C31 or name C32 or name C33 or n \ ame C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C40 \ or name C41)) or (resid 204 and (name CA or name C1 or name C2 or name C3 or nam \ e C4 or name C5 or name C6 or name C7 or name C8 or name C9 or name O2 )))) } ncs_group { reference = chain 'G' selection = chain 'H' } 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: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.16 max=1.00 mean=0.95 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 10.360 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: 0.010 Extract box with map and model: 19.180 Check model and map are aligned: 0.080 Set scattering table: 0.170 Process input model: 42.250 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.100 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:13.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6182 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 : 0.005 0.074 14960 Z= 0.335 Angle : 0.908 16.771 20030 Z= 0.412 Chirality : 0.048 0.789 2188 Planarity : 0.011 0.295 2418 Dihedral : 16.841 177.858 5992 Min Nonbonded Distance : 1.152 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.94 % Allowed : 6.89 % Favored : 92.17 % Cbeta Deviations : 0.19 % 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: 2.30 (0.21), residues: 1682 helix: 2.40 (0.15), residues: 1181 sheet: None (None), residues: 0 loop : -0.67 (0.29), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 693 HIS 0.003 0.001 HIS A 188 PHE 0.015 0.001 PHE E 105 TYR 0.037 0.001 TYR A 774 ARG 0.003 0.000 ARG E 195 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 243 time to evaluate : 1.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 382 MET cc_start: 0.1542 (mtm) cc_final: 0.1256 (mmm) REVERT: A 807 GLN cc_start: 0.7209 (OUTLIER) cc_final: 0.6084 (mt0) REVERT: B 115 MET cc_start: 0.3999 (mmm) cc_final: 0.3544 (pmm) REVERT: C 53 THR cc_start: 0.6565 (p) cc_final: 0.6219 (t) REVERT: D 157 ASP cc_start: 0.8944 (m-30) cc_final: 0.8507 (m-30) REVERT: D 292 PHE cc_start: 0.9182 (t80) cc_final: 0.8944 (t80) REVERT: D 437 LEU cc_start: 0.9460 (tp) cc_final: 0.9238 (tm) REVERT: D 710 ARG cc_start: 0.7765 (mtm-85) cc_final: 0.7554 (pmm150) REVERT: F 54 LYS cc_start: 0.9202 (tptt) cc_final: 0.8781 (tptt) outliers start: 14 outliers final: 3 residues processed: 253 average time/residue: 1.0363 time to fit residues: 291.9656 Evaluate side-chains 139 residues out of total 1514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 135 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 807 GLN Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain E residue 95 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 6.9990 chunk 125 optimal weight: 0.9980 chunk 69 optimal weight: 8.9990 chunk 42 optimal weight: 0.0270 chunk 84 optimal weight: 0.9980 chunk 67 optimal weight: 0.0270 chunk 130 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 79 optimal weight: 30.0000 chunk 96 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 overall best weight: 0.6096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 633 ASN A 655 ASN A 763 ASN ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 GLN ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 GLN D 590 GLN D 655 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6224 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14960 Z= 0.176 Angle : 0.614 10.352 20030 Z= 0.290 Chirality : 0.040 0.319 2188 Planarity : 0.004 0.042 2418 Dihedral : 17.059 176.792 2652 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.54 % Allowed : 13.99 % Favored : 83.47 % 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: 2.27 (0.21), residues: 1682 helix: 2.38 (0.15), residues: 1180 sheet: None (None), residues: 0 loop : -0.70 (0.29), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 25 HIS 0.009 0.001 HIS A 176 PHE 0.017 0.001 PHE A 732 TYR 0.025 0.001 TYR A 774 ARG 0.007 0.000 ARG D 238 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 147 time to evaluate : 1.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 382 MET cc_start: 0.1663 (mtm) cc_final: 0.1380 (mmm) REVERT: A 391 MET cc_start: 0.0936 (OUTLIER) cc_final: 0.0682 (ppp) REVERT: B 115 MET cc_start: 0.3983 (mmm) cc_final: 0.3522 (pmm) REVERT: C 53 THR cc_start: 0.6580 (p) cc_final: 0.6261 (t) REVERT: D 292 PHE cc_start: 0.9191 (t80) cc_final: 0.8905 (t80) REVERT: D 437 LEU cc_start: 0.9479 (tp) cc_final: 0.9273 (tp) REVERT: D 588 MET cc_start: 0.7764 (mmm) cc_final: 0.7431 (mmm) REVERT: D 710 ARG cc_start: 0.7769 (mtm-85) cc_final: 0.7540 (pmm150) REVERT: F 54 LYS cc_start: 0.9135 (tptt) cc_final: 0.8917 (tptt) outliers start: 38 outliers final: 7 residues processed: 170 average time/residue: 0.9289 time to fit residues: 179.6336 Evaluate side-chains 135 residues out of total 1514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 127 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 774 TYR Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain D residue 405 ASN Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 775 SER Chi-restraints excluded: chain F residue 48 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 83 optimal weight: 9.9990 chunk 46 optimal weight: 30.0000 chunk 125 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 41 optimal weight: 8.9990 chunk 151 optimal weight: 1.9990 chunk 163 optimal weight: 0.9980 chunk 134 optimal weight: 0.5980 chunk 149 optimal weight: 0.7980 chunk 51 optimal weight: 9.9990 chunk 121 optimal weight: 0.0270 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 ASN ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 655 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6230 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 14960 Z= 0.167 Angle : 0.590 15.208 20030 Z= 0.277 Chirality : 0.040 0.355 2188 Planarity : 0.004 0.041 2418 Dihedral : 15.644 179.912 2645 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.41 % Allowed : 14.26 % Favored : 83.33 % 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: 2.17 (0.21), residues: 1682 helix: 2.32 (0.15), residues: 1181 sheet: None (None), residues: 0 loop : -0.76 (0.29), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 25 HIS 0.006 0.001 HIS A 176 PHE 0.025 0.001 PHE D 200 TYR 0.022 0.001 TYR A 453 ARG 0.005 0.000 ARG D 238 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 142 time to evaluate : 1.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 382 MET cc_start: 0.1784 (mtm) cc_final: 0.1532 (mmm) REVERT: B 115 MET cc_start: 0.4090 (mmm) cc_final: 0.3616 (pmm) REVERT: C 46 MET cc_start: 0.4130 (ptt) cc_final: 0.2246 (pp-130) REVERT: C 53 THR cc_start: 0.6341 (p) cc_final: 0.6037 (t) REVERT: D 292 PHE cc_start: 0.9195 (t80) cc_final: 0.8914 (t80) REVERT: D 588 MET cc_start: 0.7822 (mmm) cc_final: 0.7465 (mmm) REVERT: D 710 ARG cc_start: 0.7706 (mtm-85) cc_final: 0.7455 (pmm150) REVERT: F 35 LEU cc_start: 0.9426 (mm) cc_final: 0.9135 (tm) outliers start: 36 outliers final: 11 residues processed: 161 average time/residue: 1.0052 time to fit residues: 185.4669 Evaluate side-chains 135 residues out of total 1514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 124 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 730 VAL Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 405 ASN Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 703 SER Chi-restraints excluded: chain D residue 775 SER Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 48 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 149 optimal weight: 0.3980 chunk 113 optimal weight: 0.7980 chunk 78 optimal weight: 50.0000 chunk 16 optimal weight: 50.0000 chunk 72 optimal weight: 0.5980 chunk 101 optimal weight: 0.5980 chunk 151 optimal weight: 0.6980 chunk 160 optimal weight: 2.9990 chunk 79 optimal weight: 0.0470 chunk 143 optimal weight: 0.8980 chunk 43 optimal weight: 0.0980 overall best weight: 0.3478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6214 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14960 Z= 0.151 Angle : 0.590 11.812 20030 Z= 0.277 Chirality : 0.039 0.310 2188 Planarity : 0.003 0.043 2418 Dihedral : 14.992 175.948 2645 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.41 % Allowed : 15.26 % Favored : 82.33 % 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: 2.11 (0.21), residues: 1682 helix: 2.28 (0.15), residues: 1181 sheet: None (None), residues: 0 loop : -0.79 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 25 HIS 0.004 0.000 HIS A 176 PHE 0.017 0.001 PHE A 283 TYR 0.015 0.001 TYR D 261 ARG 0.013 0.000 ARG E 165 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 145 time to evaluate : 1.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 382 MET cc_start: 0.1835 (mtm) cc_final: 0.1578 (mmm) REVERT: B 115 MET cc_start: 0.4077 (mmm) cc_final: 0.3613 (pmm) REVERT: C 46 MET cc_start: 0.3951 (ptt) cc_final: 0.2147 (pp-130) REVERT: C 53 THR cc_start: 0.6381 (p) cc_final: 0.6139 (t) REVERT: D 292 PHE cc_start: 0.9173 (t80) cc_final: 0.8938 (t80) REVERT: D 304 ASN cc_start: 0.9394 (t0) cc_final: 0.9098 (t0) REVERT: D 588 MET cc_start: 0.7804 (mmm) cc_final: 0.7436 (mmm) REVERT: D 710 ARG cc_start: 0.7656 (mtm-85) cc_final: 0.7366 (pmm150) REVERT: F 35 LEU cc_start: 0.9435 (mm) cc_final: 0.9130 (tm) outliers start: 36 outliers final: 8 residues processed: 168 average time/residue: 0.9220 time to fit residues: 175.5864 Evaluate side-chains 134 residues out of total 1514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 126 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain D residue 160 LYS Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 405 ASN Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 48 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 133 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 136 optimal weight: 0.7980 chunk 110 optimal weight: 6.9990 chunk 0 optimal weight: 50.0000 chunk 81 optimal weight: 6.9990 chunk 144 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6272 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14960 Z= 0.232 Angle : 0.619 14.846 20030 Z= 0.291 Chirality : 0.040 0.311 2188 Planarity : 0.004 0.047 2418 Dihedral : 14.377 171.862 2645 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.95 % Allowed : 15.80 % Favored : 81.26 % 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: 2.02 (0.21), residues: 1682 helix: 2.18 (0.15), residues: 1191 sheet: None (None), residues: 0 loop : -0.80 (0.29), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A 190 HIS 0.004 0.001 HIS E 198 PHE 0.024 0.001 PHE D 200 TYR 0.030 0.001 TYR D 261 ARG 0.004 0.000 ARG D 223 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 132 time to evaluate : 1.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 382 MET cc_start: 0.1725 (mtm) cc_final: 0.1479 (mmm) REVERT: B 58 MET cc_start: -0.1155 (mmp) cc_final: -0.1923 (mtp) REVERT: B 115 MET cc_start: 0.4155 (mmm) cc_final: 0.3669 (pmm) REVERT: C 46 MET cc_start: 0.3931 (ptt) cc_final: 0.2158 (pp-130) REVERT: C 53 THR cc_start: 0.6392 (p) cc_final: 0.6153 (t) REVERT: D 292 PHE cc_start: 0.9219 (t80) cc_final: 0.8982 (t80) REVERT: D 304 ASN cc_start: 0.9407 (t0) cc_final: 0.9117 (t0) REVERT: D 588 MET cc_start: 0.7766 (mmm) cc_final: 0.7404 (mmm) REVERT: D 613 MET cc_start: 0.8880 (mmm) cc_final: 0.8191 (mtm) REVERT: D 710 ARG cc_start: 0.7489 (mtm-85) cc_final: 0.7203 (pmm150) REVERT: F 35 LEU cc_start: 0.9444 (mm) cc_final: 0.9140 (tm) outliers start: 44 outliers final: 18 residues processed: 156 average time/residue: 0.8800 time to fit residues: 156.9737 Evaluate side-chains 140 residues out of total 1514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 122 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 PHE Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain A residue 730 VAL Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain D residue 160 LYS Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 382 MET Chi-restraints excluded: chain D residue 405 ASN Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 460 MET Chi-restraints excluded: chain D residue 643 THR Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 173 ASP Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain F residue 18 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.2822 > 50: distance: 43 - 49: 13.599 distance: 44 - 67: 23.491 distance: 49 - 50: 36.515 distance: 49 - 55: 34.080 distance: 50 - 51: 8.673 distance: 50 - 53: 26.829 distance: 51 - 52: 24.079 distance: 51 - 56: 23.038 distance: 52 - 78: 45.734 distance: 53 - 54: 26.990 distance: 54 - 55: 35.185 distance: 56 - 57: 12.850 distance: 57 - 58: 23.757 distance: 57 - 60: 15.561 distance: 58 - 59: 18.276 distance: 58 - 63: 23.741 distance: 59 - 85: 19.059 distance: 60 - 61: 26.199 distance: 60 - 62: 21.184 distance: 64 - 65: 41.607 distance: 65 - 66: 30.992 distance: 65 - 67: 33.975 distance: 66 - 93: 26.903 distance: 67 - 68: 35.543 distance: 68 - 69: 33.828 distance: 68 - 71: 23.037 distance: 69 - 70: 32.112 distance: 69 - 78: 54.605 distance: 70 - 98: 38.658 distance: 71 - 72: 28.061 distance: 72 - 73: 11.388 distance: 72 - 74: 9.184 distance: 73 - 75: 27.358 distance: 74 - 76: 16.251 distance: 75 - 77: 26.793 distance: 76 - 77: 28.361 distance: 78 - 79: 33.778 distance: 79 - 80: 34.726 distance: 79 - 82: 33.231 distance: 80 - 81: 16.544 distance: 80 - 85: 9.410 distance: 82 - 83: 19.958 distance: 82 - 84: 40.045 distance: 85 - 86: 18.990 distance: 86 - 87: 41.544 distance: 86 - 89: 36.618 distance: 87 - 88: 32.833 distance: 87 - 93: 26.233 distance: 89 - 90: 22.008 distance: 89 - 91: 23.111 distance: 90 - 92: 27.028 distance: 93 - 94: 43.016 distance: 94 - 95: 28.219 distance: 94 - 97: 48.071 distance: 95 - 96: 12.570 distance: 95 - 98: 17.106 distance: 98 - 99: 12.894 distance: 99 - 100: 29.015 distance: 99 - 102: 21.318 distance: 100 - 101: 48.198 distance: 100 - 104: 39.943 distance: 102 - 103: 10.688 distance: 104 - 105: 8.063 distance: 105 - 106: 6.621 distance: 106 - 107: 52.633 distance: 106 - 113: 17.593 distance: 109 - 110: 40.140 distance: 111 - 112: 40.753 distance: 113 - 114: 30.399 distance: 114 - 115: 27.027 distance: 114 - 117: 33.022 distance: 115 - 116: 37.601 distance: 115 - 120: 8.440 distance: 117 - 118: 41.151 distance: 117 - 119: 29.441