Starting phenix.real_space_refine on Mon Apr 8 04:15:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo4_26639/04_2024/7uo4_26639_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo4_26639/04_2024/7uo4_26639.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo4_26639/04_2024/7uo4_26639_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo4_26639/04_2024/7uo4_26639_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo4_26639/04_2024/7uo4_26639_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo4_26639/04_2024/7uo4_26639.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo4_26639/04_2024/7uo4_26639.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo4_26639/04_2024/7uo4_26639_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo4_26639/04_2024/7uo4_26639_neut_updated.pdb" } resolution = 3.38 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= 0.000 sd= 0.032 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 73 5.49 5 Mg 1 5.21 5 S 82 5.16 5 C 7573 2.51 5 N 2096 2.21 5 O 2643 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 922": "OE1" <-> "OE2" Residue "B ASP 99": "OD1" <-> "OD2" Residue "B ASP 175": "OD1" <-> "OD2" Residue "C ASP 5": "OD1" <-> "OD2" Residue "D GLU 60": "OE1" <-> "OE2" Residue "D TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 12470 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 927, 7467 Classifications: {'peptide': 927} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 896} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1416 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 180} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "C" Number of atoms: 559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 559 Classifications: {'peptide': 73} Link IDs: {'TRANS': 72} Chain: "D" Number of atoms: 1417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1417 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 180} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "P" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 719 Classifications: {'RNA': 34} Modifications used: {'rna3p_pur': 15, 'rna3p_pyr': 18} Link IDs: {'rna3p': 33} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 765 Classifications: {'RNA': 36} Modifications used: {'rna3p_pur': 18, 'rna3p_pyr': 18} Link IDs: {'rna3p': 35} Chain: "A" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 104 Unusual residues: {' MG': 1, ' ZN': 2, 'NWX': 1} Classifications: {'undetermined': 4, 'water': 68} Link IDs: {None: 71} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "P" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2451 SG CYS A 301 30.506 90.742 110.832 1.00 11.32 S ATOM 2492 SG CYS A 306 31.486 93.156 111.380 1.00 12.03 S ATOM 2524 SG CYS A 310 31.767 90.452 113.656 1.00 8.37 S ATOM 3932 SG CYS A 487 30.903 88.984 90.661 1.00 15.59 S ATOM 5185 SG CYS A 645 30.725 91.687 91.190 1.00 17.94 S ATOM 5191 SG CYS A 646 29.589 89.986 93.116 1.00 10.61 S Time building chain proxies: 7.09, per 1000 atoms: 0.57 Number of scatterers: 12470 At special positions: 0 Unit cell: (90.525, 125.67, 166.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 82 16.00 P 73 15.00 Mg 1 11.99 O 2643 8.00 N 2096 7.00 C 7573 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 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.77 Conformation dependent library (CDL) restraints added in 2.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1003 " pdb="ZN ZN A1003 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1003 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1003 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1003 " - pdb=" SG CYS A 306 " pdb=" ZN A1004 " pdb="ZN ZN A1004 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1004 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1004 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1004 " - pdb=" SG CYS A 645 " Number of angles added : 6 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2644 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 53 helices and 8 sheets defined 46.9% alpha, 8.4% beta 33 base pairs and 32 stacking pairs defined. Time for finding SS restraints: 6.38 Creating SS restraints... Processing helix chain 'A' and resid 4 through 11 Processing helix chain 'A' and resid 77 through 88 removed outlier: 3.510A pdb=" N THR A 85 " --> pdb=" O GLN A 81 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE A 86 " --> pdb=" O HIS A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 132 Processing helix chain 'A' and resid 140 through 148 removed outlier: 3.503A pdb=" N GLU A 144 " --> pdb=" O ASP A 140 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE A 145 " --> pdb=" O THR A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 158 No H-bonds generated for 'chain 'A' and resid 156 through 158' Processing helix chain 'A' and resid 169 through 198 removed outlier: 4.715A pdb=" N GLU A 180 " --> pdb=" O ASN A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 209 No H-bonds generated for 'chain 'A' and resid 207 through 209' Processing helix chain 'A' and resid 243 through 247 Processing helix chain 'A' and resid 252 through 254 No H-bonds generated for 'chain 'A' and resid 252 through 254' Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 276 through 286 Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 304 through 317 removed outlier: 3.708A pdb=" N LEU A 308 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N HIS A 309 " --> pdb=" O ARG A 305 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 376 Processing helix chain 'A' and resid 378 through 383 Processing helix chain 'A' and resid 417 through 425 Processing helix chain 'A' and resid 448 through 458 removed outlier: 4.718A pdb=" N TYR A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ARG A 457 " --> pdb=" O TYR A 453 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N TYR A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 480 removed outlier: 4.234A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE A 480 " --> pdb=" O VAL A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 492 No H-bonds generated for 'chain 'A' and resid 490 through 492' Processing helix chain 'A' and resid 506 through 508 No H-bonds generated for 'chain 'A' and resid 506 through 508' Processing helix chain 'A' and resid 512 through 517 Processing helix chain 'A' and resid 521 through 533 removed outlier: 3.754A pdb=" N PHE A 528 " --> pdb=" O GLN A 524 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 580 removed outlier: 4.316A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 605 removed outlier: 3.598A pdb=" N MET A 601 " --> pdb=" O GLY A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 638 Processing helix chain 'A' and resid 648 through 661 Processing helix chain 'A' and resid 690 through 708 removed outlier: 3.564A pdb=" N PHE A 694 " --> pdb=" O ALA A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 732 removed outlier: 3.617A pdb=" N ASN A 722 " --> pdb=" O LYS A 718 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU A 729 " --> pdb=" O HIS A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 752 Processing helix chain 'A' and resid 768 through 773 Processing helix chain 'A' and resid 779 through 789 removed outlier: 3.877A pdb=" N VAL A 785 " --> pdb=" O ASN A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 798 No H-bonds generated for 'chain 'A' and resid 796 through 798' Processing helix chain 'A' and resid 834 through 842 Processing helix chain 'A' and resid 848 through 851 Processing helix chain 'A' and resid 856 through 871 removed outlier: 4.009A pdb=" N SER A 861 " --> pdb=" O GLU A 857 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP A 865 " --> pdb=" O SER A 861 " (cutoff:3.500A) Proline residue: A 868 - end of helix removed outlier: 4.588A pdb=" N LYS A 871 " --> pdb=" O TYR A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 902 removed outlier: 3.785A pdb=" N VAL A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N TYR A 884 " --> pdb=" O VAL A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 925 removed outlier: 3.867A pdb=" N MET A 924 " --> pdb=" O PHE A 920 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N TYR A 925 " --> pdb=" O TYR A 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 28 removed outlier: 3.939A pdb=" N ALA B 13 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA B 27 " --> pdb=" O GLU B 23 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN B 28 " --> pdb=" O GLN B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 95 removed outlier: 3.624A pdb=" N LYS B 61 " --> pdb=" O ARG B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 108 Processing helix chain 'B' and resid 117 through 124 Proline residue: B 121 - end of helix removed outlier: 3.556A pdb=" N THR B 124 " --> pdb=" O PRO B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 141 Processing helix chain 'C' and resid 6 through 20 removed outlier: 3.853A pdb=" N VAL C 11 " --> pdb=" O LYS C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 40 removed outlier: 3.576A pdb=" N ALA C 30 " --> pdb=" O SER C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 61 Processing helix chain 'C' and resid 68 through 72 Processing helix chain 'D' and resid 10 through 28 removed outlier: 3.737A pdb=" N ALA D 14 " --> pdb=" O PRO D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 81 removed outlier: 3.675A pdb=" N LYS D 72 " --> pdb=" O THR D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 98 removed outlier: 3.873A pdb=" N GLN D 88 " --> pdb=" O THR D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 112 removed outlier: 3.774A pdb=" N ASP D 112 " --> pdb=" O ASN D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 141 Processing helix chain 'D' and resid 169 through 171 No H-bonds generated for 'chain 'D' and resid 169 through 171' Processing helix chain 'D' and resid 174 through 179 removed outlier: 3.506A pdb=" N SER D 177 " --> pdb=" O MET D 174 " (cutoff:3.500A) Proline residue: D 178 - end of helix No H-bonds generated for 'chain 'D' and resid 174 through 179' Processing sheet with id= A, first strand: chain 'A' and resid 18 through 21 removed outlier: 4.511A pdb=" N ARG A 18 " --> pdb=" O LYS A 59 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE A 104 " --> pdb=" O VAL A 111 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 31 through 38 removed outlier: 3.521A pdb=" N VAL A 31 " --> pdb=" O LYS A 50 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE A 37 " --> pdb=" O GLY A 44 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 541 through 544 Processing sheet with id= D, first strand: chain 'A' and resid 799 through 801 removed outlier: 3.841A pdb=" N PHE A 766 " --> pdb=" O HIS A 613 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TRP A 617 " --> pdb=" O ALA A 762 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA A 762 " --> pdb=" O TRP A 617 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 666 through 668 Processing sheet with id= F, first strand: chain 'A' and resid 816 through 822 Processing sheet with id= G, first strand: chain 'B' and resid 128 through 132 removed outlier: 5.755A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 127 through 132 removed outlier: 3.508A pdb=" N LEU D 189 " --> pdb=" O GLU D 155 " (cutoff:3.500A) 460 hydrogen bonds defined for protein. 1272 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 80 hydrogen bonds 160 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 32 stacking parallelities Total time for adding SS restraints: 4.59 Time building geometry restraints manager: 6.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1874 1.29 - 1.42: 3779 1.42 - 1.55: 6855 1.55 - 1.68: 143 1.68 - 1.81: 129 Bond restraints: 12780 Sorted by residual: bond pdb=" C10 NWX A1001 " pdb=" C11 NWX A1001 " ideal model delta sigma weight residual 1.311 1.552 -0.241 2.00e-02 2.50e+03 1.46e+02 bond pdb=" C10 NWX A1001 " pdb=" O14 NWX A1001 " ideal model delta sigma weight residual 1.626 1.436 0.190 2.00e-02 2.50e+03 9.01e+01 bond pdb=" C13 NWX A1001 " pdb=" O14 NWX A1001 " ideal model delta sigma weight residual 1.300 1.417 -0.117 2.00e-02 2.50e+03 3.41e+01 bond pdb=" C03 NWX A1001 " pdb=" N33 NWX A1001 " ideal model delta sigma weight residual 1.463 1.387 0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C12 NWX A1001 " pdb=" O29 NWX A1001 " ideal model delta sigma weight residual 1.345 1.420 -0.075 2.00e-02 2.50e+03 1.42e+01 ... (remaining 12775 not shown) Histogram of bond angle deviations from ideal: 95.70 - 112.55: 7207 112.55 - 129.40: 10357 129.40 - 146.24: 106 146.24 - 163.09: 0 163.09 - 179.94: 1 Bond angle restraints: 17671 Sorted by residual: angle pdb=" C09 NWX A1001 " pdb=" C08 NWX A1001 " pdb=" C10 NWX A1001 " ideal model delta sigma weight residual 99.10 129.98 -30.88 3.00e+00 1.11e-01 1.06e+02 angle pdb=" C10 NWX A1001 " pdb=" C08 NWX A1001 " pdb=" N07 NWX A1001 " ideal model delta sigma weight residual 152.88 123.40 29.48 3.00e+00 1.11e-01 9.66e+01 angle pdb=" C02 NWX A1001 " pdb=" C03 NWX A1001 " pdb=" N33 NWX A1001 " ideal model delta sigma weight residual 142.45 122.31 20.14 3.00e+00 1.11e-01 4.50e+01 angle pdb=" N04 NWX A1001 " pdb=" C03 NWX A1001 " pdb=" N33 NWX A1001 " ideal model delta sigma weight residual 97.54 115.53 -17.99 3.00e+00 1.11e-01 3.60e+01 angle pdb=" O22 NWX A1001 " pdb=" P21 NWX A1001 " pdb=" O23 NWX A1001 " ideal model delta sigma weight residual 109.57 125.37 -15.80 3.00e+00 1.11e-01 2.77e+01 ... (remaining 17666 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 7516 35.96 - 71.93: 206 71.93 - 107.89: 23 107.89 - 143.85: 2 143.85 - 179.81: 2 Dihedral angle restraints: 7749 sinusoidal: 3665 harmonic: 4084 Sorted by residual: dihedral pdb=" C08 NWX A1001 " pdb=" C10 NWX A1001 " pdb=" C11 NWX A1001 " pdb=" C12 NWX A1001 " ideal model delta sinusoidal sigma weight residual -91.69 88.12 -179.81 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O19 NWX A1001 " pdb=" O20 NWX A1001 " pdb=" P17 NWX A1001 " pdb=" P21 NWX A1001 " ideal model delta sinusoidal sigma weight residual 41.64 -151.40 -166.96 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" CA VAL A 609 " pdb=" C VAL A 609 " pdb=" N GLU A 610 " pdb=" CA GLU A 610 " ideal model delta harmonic sigma weight residual -180.00 -161.91 -18.09 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 7746 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.057: 2049 1.057 - 2.113: 0 2.113 - 3.170: 0 3.170 - 4.227: 0 4.227 - 5.284: 1 Chirality restraints: 2050 Sorted by residual: chirality pdb=" C10 NWX A1001 " pdb=" C08 NWX A1001 " pdb=" C11 NWX A1001 " pdb=" O14 NWX A1001 " both_signs ideal model delta sigma weight residual False 2.51 -2.78 5.28 2.00e-01 2.50e+01 6.98e+02 chirality pdb=" C11 NWX A1001 " pdb=" C10 NWX A1001 " pdb=" C12 NWX A1001 " pdb=" O30 NWX A1001 " both_signs ideal model delta sigma weight residual False -2.39 -2.55 0.16 2.00e-01 2.50e+01 6.47e-01 chirality pdb=" CA ILE B 185 " pdb=" N ILE B 185 " pdb=" C ILE B 185 " pdb=" CB ILE B 185 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.99e-01 ... (remaining 2047 not shown) Planarity restraints: 1998 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP D 182 " -0.023 5.00e-02 4.00e+02 3.48e-02 1.94e+00 pdb=" N PRO D 183 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO D 183 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 183 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 56 " 0.006 2.00e-02 2.50e+03 1.30e-02 1.68e+00 pdb=" C GLN B 56 " -0.022 2.00e-02 2.50e+03 pdb=" O GLN B 56 " 0.008 2.00e-02 2.50e+03 pdb=" N ARG B 57 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 168 " -0.020 5.00e-02 4.00e+02 3.04e-02 1.47e+00 pdb=" N PRO A 169 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 169 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 169 " -0.017 5.00e-02 4.00e+02 ... (remaining 1995 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.49: 88 2.49 - 3.09: 9516 3.09 - 3.69: 19408 3.69 - 4.30: 28770 4.30 - 4.90: 47397 Nonbonded interactions: 105179 Sorted by model distance: nonbonded pdb="ZN ZN A1003 " pdb=" O HOH A1160 " model vdw 1.885 2.230 nonbonded pdb=" OD1 ASP D 101 " pdb=" OG SER D 151 " model vdw 1.900 2.440 nonbonded pdb=" O ILE B 120 " pdb=" OG1 THR B 124 " model vdw 1.975 2.440 nonbonded pdb=" OG1 THR A 540 " pdb=" OE1 GLU A 665 " model vdw 2.075 2.440 nonbonded pdb=" O GLY A 25 " pdb=" OG1 THR A 26 " model vdw 2.086 2.440 ... (remaining 105174 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B' and (resid 6 through 7 or (resid 8 and (name N or name CA or name C o \ r name O or name CB )) or resid 9 through 22 or (resid 23 through 28 and (name N \ or name CA or name C or name O or name CB )) or resid 29 through 39 or (resid 4 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 41 or (resid \ 42 through 43 and (name N or name CA or name C or name O or name CB )) or resid \ 44 through 192)) selection = (chain 'D' and (resid 6 through 25 or (resid 26 through 28 and (name N or name C \ A or name C or name O or name CB )) or resid 29 through 31 or (resid 32 and (nam \ e N or name CA or name C or name O or name CB )) or resid 33 through 34 or (resi \ d 35 and (name N or name CA or name C or name O or name CB )) or resid 36 throug \ h 38 or (resid 39 through 40 and (name N or name CA or name C or name O or name \ CB )) or resid 41 through 192)) } 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=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 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: 3.320 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: 12.950 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 43.520 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.060 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:3.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 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 0.241 12780 Z= 0.309 Angle : 0.686 30.876 17671 Z= 0.314 Chirality : 0.122 5.284 2050 Planarity : 0.003 0.035 1998 Dihedral : 15.381 179.815 5105 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 1.27 % Allowed : 7.35 % Favored : 91.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -1.06 (0.23), residues: 1366 helix: 0.57 (0.21), residues: 658 sheet: -2.50 (0.40), residues: 154 loop : -1.67 (0.25), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 916 HIS 0.005 0.001 HIS C 36 PHE 0.011 0.001 PHE A 694 TYR 0.013 0.001 TYR A 788 ARG 0.003 0.000 ARG A 836 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 96 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 903 TYR cc_start: 0.6943 (OUTLIER) cc_final: 0.6591 (m-80) outliers start: 15 outliers final: 4 residues processed: 111 average time/residue: 0.2840 time to fit residues: 45.1109 Evaluate side-chains 76 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 71 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 734 ASN Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 903 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 110 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 128 optimal weight: 5.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 ASN A 572 HIS B 56 GLN C 19 GLN C 36 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12780 Z= 0.261 Angle : 0.660 30.338 17671 Z= 0.309 Chirality : 0.063 2.239 2050 Planarity : 0.003 0.057 1998 Dihedral : 15.664 161.087 2597 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.60 % Allowed : 10.98 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.70 (0.23), residues: 1366 helix: 0.82 (0.21), residues: 661 sheet: -2.28 (0.39), residues: 163 loop : -1.43 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 916 HIS 0.007 0.001 HIS C 36 PHE 0.017 0.001 PHE D 92 TYR 0.013 0.001 TYR A 289 ARG 0.004 0.000 ARG D 75 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 75 time to evaluate : 1.362 Fit side-chains outliers start: 19 outliers final: 9 residues processed: 91 average time/residue: 0.2664 time to fit residues: 36.7682 Evaluate side-chains 78 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 69 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 729 GLU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 903 TYR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain D residue 106 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 71 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 87 optimal weight: 0.0170 chunk 35 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 114 optimal weight: 0.9980 chunk 127 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12780 Z= 0.176 Angle : 0.593 26.547 17671 Z= 0.276 Chirality : 0.062 2.274 2050 Planarity : 0.003 0.036 1998 Dihedral : 15.504 150.034 2590 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.77 % Allowed : 12.08 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.38 (0.23), residues: 1366 helix: 1.03 (0.21), residues: 656 sheet: -1.98 (0.43), residues: 141 loop : -1.28 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 916 HIS 0.004 0.001 HIS A 309 PHE 0.011 0.001 PHE D 92 TYR 0.015 0.001 TYR D 12 ARG 0.008 0.000 ARG D 51 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 74 time to evaluate : 1.342 Fit side-chains outliers start: 21 outliers final: 11 residues processed: 93 average time/residue: 0.2526 time to fit residues: 35.4749 Evaluate side-chains 80 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 69 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 729 GLU Chi-restraints excluded: chain A residue 903 TYR Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 186 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 86 optimal weight: 0.8980 chunk 128 optimal weight: 3.9990 chunk 136 optimal weight: 10.0000 chunk 67 optimal weight: 0.6980 chunk 122 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN A 790 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 12780 Z= 0.302 Angle : 0.641 27.225 17671 Z= 0.300 Chirality : 0.062 2.196 2050 Planarity : 0.003 0.026 1998 Dihedral : 15.593 140.958 2590 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.11 % Allowed : 12.58 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.34 (0.24), residues: 1366 helix: 1.06 (0.21), residues: 660 sheet: -2.16 (0.38), residues: 165 loop : -1.14 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 182 HIS 0.004 0.001 HIS C 36 PHE 0.011 0.001 PHE A 694 TYR 0.018 0.001 TYR B 135 ARG 0.007 0.000 ARG D 51 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 67 time to evaluate : 1.310 Fit side-chains outliers start: 25 outliers final: 18 residues processed: 87 average time/residue: 0.2437 time to fit residues: 32.1079 Evaluate side-chains 82 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 64 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 729 GLU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 903 TYR Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 186 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 113 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 101 optimal weight: 0.0470 chunk 56 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 94 optimal weight: 0.0980 chunk 0 optimal weight: 7.9990 chunk 69 optimal weight: 0.5980 chunk 122 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 650 HIS A 790 ASN C 19 GLN C 34 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 12780 Z= 0.155 Angle : 0.598 25.971 17671 Z= 0.275 Chirality : 0.061 2.200 2050 Planarity : 0.003 0.025 1998 Dihedral : 15.532 134.188 2590 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.11 % Allowed : 13.51 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.10 (0.24), residues: 1366 helix: 1.20 (0.21), residues: 659 sheet: -1.81 (0.42), residues: 141 loop : -1.08 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 916 HIS 0.004 0.000 HIS A 309 PHE 0.010 0.001 PHE A 694 TYR 0.015 0.001 TYR A 903 ARG 0.005 0.000 ARG D 51 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 65 time to evaluate : 1.461 Fit side-chains revert: symmetry clash REVERT: C 62 MET cc_start: 0.7350 (mtt) cc_final: 0.7006 (mtt) outliers start: 25 outliers final: 15 residues processed: 86 average time/residue: 0.2504 time to fit residues: 33.0278 Evaluate side-chains 79 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 64 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 729 GLU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 903 TYR Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 186 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 45 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 chunk 33 optimal weight: 0.0010 chunk 136 optimal weight: 9.9990 chunk 113 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 131 optimal weight: 0.9980 overall best weight: 0.6786 ------------------------------------------------------------------------------- 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: 0.7798 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12780 Z= 0.172 Angle : 0.600 25.563 17671 Z= 0.275 Chirality : 0.060 2.167 2050 Planarity : 0.003 0.024 1998 Dihedral : 15.455 130.476 2590 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.11 % Allowed : 13.85 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.03 (0.24), residues: 1366 helix: 1.34 (0.21), residues: 650 sheet: -1.65 (0.41), residues: 148 loop : -1.03 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 916 HIS 0.004 0.001 HIS A 309 PHE 0.010 0.001 PHE A 694 TYR 0.012 0.001 TYR A 903 ARG 0.003 0.000 ARG D 51 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 68 time to evaluate : 1.446 Fit side-chains revert: symmetry clash REVERT: C 62 MET cc_start: 0.7314 (mtt) cc_final: 0.6986 (mtt) outliers start: 25 outliers final: 21 residues processed: 86 average time/residue: 0.2475 time to fit residues: 32.5948 Evaluate side-chains 86 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 65 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 729 GLU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 186 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 15 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 135 optimal weight: 10.0000 chunk 85 optimal weight: 0.2980 chunk 82 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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: 0.7817 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12780 Z= 0.209 Angle : 0.612 25.926 17671 Z= 0.283 Chirality : 0.060 2.125 2050 Planarity : 0.003 0.024 1998 Dihedral : 15.462 131.748 2588 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.20 % Allowed : 14.27 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.07 (0.24), residues: 1366 helix: 1.35 (0.21), residues: 658 sheet: -1.65 (0.41), residues: 148 loop : -1.02 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 154 HIS 0.004 0.001 HIS A 309 PHE 0.011 0.001 PHE A 694 TYR 0.016 0.001 TYR A 903 ARG 0.003 0.000 ARG D 51 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 65 time to evaluate : 1.295 Fit side-chains revert: symmetry clash REVERT: C 62 MET cc_start: 0.7325 (mtt) cc_final: 0.6997 (mtt) outliers start: 26 outliers final: 18 residues processed: 85 average time/residue: 0.2456 time to fit residues: 31.9402 Evaluate side-chains 83 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 65 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 729 GLU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 186 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 81 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 92 optimal weight: 0.0470 chunk 67 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 118 optimal weight: 9.9990 overall best weight: 0.8880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN A 468 GLN ** A 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12780 Z= 0.204 Angle : 0.626 26.547 17671 Z= 0.286 Chirality : 0.060 2.100 2050 Planarity : 0.003 0.023 1998 Dihedral : 15.486 133.283 2588 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.77 % Allowed : 14.78 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.09 (0.24), residues: 1366 helix: 1.40 (0.21), residues: 651 sheet: -1.69 (0.41), residues: 148 loop : -1.01 (0.27), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 916 HIS 0.004 0.001 HIS A 309 PHE 0.009 0.001 PHE D 92 TYR 0.015 0.001 TYR A 903 ARG 0.003 0.000 ARG D 51 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 66 time to evaluate : 1.580 Fit side-chains revert: symmetry clash REVERT: C 62 MET cc_start: 0.7322 (mtt) cc_final: 0.6995 (mtt) outliers start: 21 outliers final: 20 residues processed: 82 average time/residue: 0.2436 time to fit residues: 30.9325 Evaluate side-chains 84 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 64 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 729 GLU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 186 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 55 optimal weight: 8.9990 chunk 99 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 114 optimal weight: 0.6980 chunk 119 optimal weight: 5.9990 chunk 83 optimal weight: 0.8980 chunk 133 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12780 Z= 0.190 Angle : 0.622 26.738 17671 Z= 0.285 Chirality : 0.059 2.089 2050 Planarity : 0.003 0.025 1998 Dihedral : 15.483 134.688 2588 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.69 % Allowed : 15.20 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.14 (0.24), residues: 1366 helix: 1.43 (0.21), residues: 653 sheet: -1.64 (0.41), residues: 148 loop : -0.97 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 916 HIS 0.004 0.001 HIS A 309 PHE 0.009 0.001 PHE A 741 TYR 0.015 0.001 TYR A 903 ARG 0.003 0.000 ARG D 51 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 65 time to evaluate : 1.487 Fit side-chains revert: symmetry clash REVERT: C 62 MET cc_start: 0.7320 (mtt) cc_final: 0.6993 (mtt) outliers start: 20 outliers final: 20 residues processed: 80 average time/residue: 0.2557 time to fit residues: 31.3785 Evaluate side-chains 83 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 63 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 729 GLU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 186 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 63 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 140 optimal weight: 8.9990 chunk 129 optimal weight: 0.5980 chunk 111 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12780 Z= 0.259 Angle : 0.649 27.374 17671 Z= 0.298 Chirality : 0.059 2.058 2050 Planarity : 0.003 0.025 1998 Dihedral : 15.559 136.423 2588 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.69 % Allowed : 15.37 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.19 (0.24), residues: 1366 helix: 1.45 (0.21), residues: 660 sheet: -1.64 (0.41), residues: 148 loop : -0.94 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 916 HIS 0.004 0.001 HIS C 36 PHE 0.011 0.001 PHE A 741 TYR 0.013 0.001 TYR A 903 ARG 0.003 0.000 ARG D 51 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 64 time to evaluate : 1.377 Fit side-chains revert: symmetry clash REVERT: C 62 MET cc_start: 0.7378 (mtt) cc_final: 0.7043 (mtt) outliers start: 20 outliers final: 18 residues processed: 79 average time/residue: 0.2453 time to fit residues: 29.9345 Evaluate side-chains 79 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 61 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 729 GLU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 186 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 103 optimal weight: 0.3980 chunk 16 optimal weight: 0.0980 chunk 31 optimal weight: 1.9990 chunk 112 optimal weight: 0.4980 chunk 46 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 20 optimal weight: 0.0770 chunk 98 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 80 optimal weight: 0.4980 overall best weight: 0.3138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.055368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.038663 restraints weight = 60289.594| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 3.20 r_work: 0.2813 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12780 Z= 0.137 Angle : 0.612 26.670 17671 Z= 0.278 Chirality : 0.059 2.088 2050 Planarity : 0.003 0.026 1998 Dihedral : 15.486 137.881 2588 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.60 % Allowed : 15.54 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.25 (0.24), residues: 1366 helix: 1.50 (0.21), residues: 651 sheet: -1.58 (0.41), residues: 148 loop : -0.88 (0.27), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 916 HIS 0.003 0.000 HIS A 309 PHE 0.007 0.001 PHE A 471 TYR 0.015 0.001 TYR A 903 ARG 0.002 0.000 ARG D 51 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2381.93 seconds wall clock time: 46 minutes 16.16 seconds (2776.16 seconds total)