Starting phenix.real_space_refine on Mon Jun 16 20:19:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d98_46670/06_2025/9d98_46670.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d98_46670/06_2025/9d98_46670.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9d98_46670/06_2025/9d98_46670.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d98_46670/06_2025/9d98_46670.map" model { file = "/net/cci-nas-00/data/ceres_data/9d98_46670/06_2025/9d98_46670.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d98_46670/06_2025/9d98_46670.cif" } resolution = 4.19 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= 1.000 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: 4 Type Number sf(0) Gaussians S 113 5.16 5 C 12049 2.51 5 N 3303 2.21 5 O 3635 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 19100 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2781 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 21, 'TRANS': 345} Chain breaks: 4 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 10, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 61 Chain: "B" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2601 Classifications: {'peptide': 330} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 310} Chain breaks: 5 Chain: "C" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2781 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 21, 'TRANS': 345} Chain breaks: 4 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 10, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 61 Chain: "D" Number of atoms: 1076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1076 Classifications: {'peptide': 137} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 135} Chain breaks: 1 Chain: "E" Number of atoms: 1076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1076 Classifications: {'peptide': 137} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 135} Chain breaks: 1 Chain: "F" Number of atoms: 1102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1102 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 138} Chain breaks: 1 Chain: "G" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 925 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "H" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 800 Classifications: {'peptide': 105} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 98} Chain: "I" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 925 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "J" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 800 Classifications: {'peptide': 105} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 98} Chain: "K" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 925 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "L" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 800 Classifications: {'peptide': 105} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 98} Chain: "M" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 775 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "N" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 775 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "O" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 775 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "P" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 11.26, per 1000 atoms: 0.59 Number of scatterers: 19100 At special positions: 0 Unit cell: (108, 150.12, 151.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 113 16.00 O 3635 8.00 N 3303 7.00 C 12049 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.05 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.03 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.08 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 378 " distance=2.04 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS E 605 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.04 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.04 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.05 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS M 16 " - pdb=" SG CYS M 84 " distance=2.04 Simple disulfide: pdb=" SG CYS N 16 " - pdb=" SG CYS N 84 " distance=2.04 Simple disulfide: pdb=" SG CYS O 16 " - pdb=" SG CYS O 84 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Links applied ALPHA1-3 " BMA P 3 " - " MAN P 7 " " MAN P 4 " - " MAN P 5 " " BMA d 3 " - " MAN d 4 " ALPHA1-6 " BMA P 3 " - " MAN P 4 " " MAN P 4 " - " MAN P 6 " " BMA d 3 " - " MAN d 5 " BETA1-4 " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " NAG-ASN " NAG P 1 " - " ASN A 88 " " NAG W 1 " - " ASN B 88 " " NAG d 1 " - " ASN C 88 " Time building additional restraints: 4.78 Conformation dependent library (CDL) restraints added in 2.4 seconds 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4508 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 40 sheets defined 19.0% alpha, 30.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.51 Creating SS restraints... Processing helix chain 'A' and resid 66 through 73 Processing helix chain 'A' and resid 100 through 113 removed outlier: 3.566A pdb=" N ILE A 109 " --> pdb=" O HIS A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 474 through 479 Processing helix chain 'B' and resid 99 through 117 removed outlier: 3.604A pdb=" N GLN B 103 " --> pdb=" O ASN B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 352 Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'B' and resid 475 through 481 removed outlier: 3.645A pdb=" N TRP B 479 " --> pdb=" O MET B 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 74 removed outlier: 3.575A pdb=" N HIS C 72 " --> pdb=" O VAL C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 113 removed outlier: 3.691A pdb=" N ILE C 109 " --> pdb=" O HIS C 105 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU C 111 " --> pdb=" O ASP C 107 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP C 113 " --> pdb=" O ILE C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 474 through 480 Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 546 removed outlier: 3.865A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU D 545 " --> pdb=" O ALA D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 596 removed outlier: 4.295A pdb=" N GLN D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 623 Processing helix chain 'D' and resid 627 through 636 removed outlier: 3.570A pdb=" N TRP D 631 " --> pdb=" O THR D 627 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU D 634 " --> pdb=" O GLN D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 654 removed outlier: 3.937A pdb=" N ILE D 642 " --> pdb=" O TYR D 638 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU D 645 " --> pdb=" O ILE D 641 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N GLN D 650 " --> pdb=" O LEU D 646 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASN D 651 " --> pdb=" O GLU D 647 " (cutoff:3.500A) Processing helix chain 'D' and resid 657 through 662 Processing helix chain 'E' and resid 523 through 527 removed outlier: 3.803A pdb=" N ALA E 526 " --> pdb=" O LEU E 523 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLY E 527 " --> pdb=" O GLY E 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 523 through 527' Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 536 through 543 removed outlier: 4.064A pdb=" N GLN E 540 " --> pdb=" O THR E 536 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASN E 543 " --> pdb=" O VAL E 539 " (cutoff:3.500A) Processing helix chain 'E' and resid 575 through 596 removed outlier: 3.645A pdb=" N ARG E 579 " --> pdb=" O GLN E 575 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TRP E 596 " --> pdb=" O LEU E 592 " (cutoff:3.500A) Processing helix chain 'E' and resid 618 through 626 removed outlier: 3.602A pdb=" N ASP E 624 " --> pdb=" O SER E 620 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN E 625 " --> pdb=" O GLU E 621 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 636 removed outlier: 3.654A pdb=" N TRP E 631 " --> pdb=" O THR E 627 " (cutoff:3.500A) Processing helix chain 'E' and resid 638 through 654 removed outlier: 3.619A pdb=" N LEU E 645 " --> pdb=" O ILE E 641 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N GLN E 650 " --> pdb=" O LEU E 646 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N ASN E 651 " --> pdb=" O GLU E 647 " (cutoff:3.500A) Processing helix chain 'E' and resid 657 through 662 Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 537 through 542 removed outlier: 3.558A pdb=" N ALA F 541 " --> pdb=" O LEU F 537 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG F 542 " --> pdb=" O THR F 538 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 537 through 542' Processing helix chain 'F' and resid 573 through 596 removed outlier: 3.523A pdb=" N TRP F 596 " --> pdb=" O LEU F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 624 Processing helix chain 'F' and resid 627 through 636 removed outlier: 3.629A pdb=" N GLU F 634 " --> pdb=" O GLN F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 654 removed outlier: 3.727A pdb=" N ILE F 642 " --> pdb=" O TYR F 638 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N GLN F 650 " --> pdb=" O LEU F 646 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ASN F 651 " --> pdb=" O GLU F 647 " (cutoff:3.500A) Processing helix chain 'F' and resid 657 through 662 Processing helix chain 'G' and resid 28 through 32 removed outlier: 4.039A pdb=" N ASN G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.588A pdb=" N ASP G 86 " --> pdb=" O THR G 83 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR G 87 " --> pdb=" O SER G 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 83 through 87' Processing helix chain 'H' and resid 79 through 83 removed outlier: 3.977A pdb=" N PHE H 83 " --> pdb=" O PRO H 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.656A pdb=" N ASN I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.899A pdb=" N PHE J 83 " --> pdb=" O PRO J 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 removed outlier: 3.986A pdb=" N ASN K 32 " --> pdb=" O PHE K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 64 removed outlier: 3.644A pdb=" N GLN K 64 " --> pdb=" O GLN K 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 61 through 64' Processing helix chain 'K' and resid 83 through 87 removed outlier: 3.667A pdb=" N ASP K 86 " --> pdb=" O THR K 83 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR K 87 " --> pdb=" O SER K 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 83 through 87' Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.955A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 59 through 65 removed outlier: 3.533A pdb=" N TRP M 62 " --> pdb=" O ARG M 59 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP M 63 " --> pdb=" O SER M 60 " (cutoff:3.500A) Processing helix chain 'M' and resid 75 through 79 removed outlier: 3.667A pdb=" N SER M 79 " --> pdb=" O ILE M 76 " (cutoff:3.500A) Processing helix chain 'N' and resid 58 through 65 removed outlier: 3.587A pdb=" N LEU N 61 " --> pdb=" O ARG N 58 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ASP N 63 " --> pdb=" O SER N 60 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY N 65 " --> pdb=" O TRP N 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 59 through 64 removed outlier: 4.244A pdb=" N ASP O 63 " --> pdb=" O SER O 60 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 79 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 3.605A pdb=" N VAL A 38 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N CYS D 604 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 93 Processing sheet with id=AA4, first strand: chain 'A' and resid 201 through 202 Processing sheet with id=AA5, first strand: chain 'A' and resid 259 through 261 removed outlier: 5.916A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N CYS A 445 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N CYS A 296 " --> pdb=" O CYS A 445 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.208A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.977A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 11.967A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.328A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 11.209A pdb=" N ASP A 457 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 12.892A pdb=" N ILE A 284 " --> pdb=" O ASP A 457 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 284 through 298 current: chain 'A' and resid 359 through 361 Processing sheet with id=AA6, first strand: chain 'A' and resid 271 through 273 removed outlier: 3.688A pdb=" N MET A 271 " --> pdb=" O GLN A 287 " (cutoff:3.500A) removed outlier: 12.892A pdb=" N ILE A 284 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 11.209A pdb=" N ASP A 457 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 11.328A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.967A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 11.977A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.208A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N CYS A 296 " --> pdb=" O CYS A 445 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N CYS A 445 " --> pdb=" O CYS A 296 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 443 through 457 current: chain 'A' and resid 413 through 418 Processing sheet with id=AA7, first strand: chain 'A' and resid 374 through 378 Processing sheet with id=AA8, first strand: chain 'B' and resid 83 through 86 removed outlier: 4.224A pdb=" N VAL B 242 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE B 225 " --> pdb=" O VAL B 245 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N VAL B 489 " --> pdb=" O LYS B 46 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LYS B 46 " --> pdb=" O VAL B 489 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ILE B 491 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N VAL B 44 " --> pdb=" O ILE B 491 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLY B 495 " --> pdb=" O TYR B 40 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N TYR B 40 " --> pdb=" O GLY B 495 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ALA B 497 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N VAL B 38 " --> pdb=" O ALA B 497 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N THR B 499 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N VAL B 36 " --> pdb=" O THR B 499 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N VAL E 608 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N VAL B 38 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N THR E 606 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N TYR B 40 " --> pdb=" O CYS E 604 " (cutoff:3.500A) removed outlier: 8.796A pdb=" N CYS E 604 " --> pdb=" O TYR B 40 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 53 through 55 Processing sheet with id=AB1, first strand: chain 'B' and resid 91 through 94 removed outlier: 3.895A pdb=" N GLU B 91 " --> pdb=" O CYS B 239 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 259 through 261 removed outlier: 3.834A pdb=" N GLY B 451 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 10.028A pdb=" N ARG B 444 " --> pdb=" O ILE B 294 " (cutoff:3.500A) removed outlier: 11.364A pdb=" N ILE B 294 " --> pdb=" O ARG B 444 " (cutoff:3.500A) removed outlier: 9.552A pdb=" N VAL B 446 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 10.610A pdb=" N VAL B 292 " --> pdb=" O VAL B 446 " (cutoff:3.500A) removed outlier: 8.890A pdb=" N ASN B 448 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 10.026A pdb=" N THR B 290 " --> pdb=" O ASN B 448 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N THR B 450 " --> pdb=" O PHE B 288 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N GLN B 293 " --> pdb=" O SER B 334 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER B 334 " --> pdb=" O GLN B 293 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 271 through 273 removed outlier: 7.754A pdb=" N THR B 450 " --> pdb=" O PHE B 288 " (cutoff:3.500A) removed outlier: 10.026A pdb=" N THR B 290 " --> pdb=" O ASN B 448 " (cutoff:3.500A) removed outlier: 8.890A pdb=" N ASN B 448 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 10.610A pdb=" N VAL B 292 " --> pdb=" O VAL B 446 " (cutoff:3.500A) removed outlier: 9.552A pdb=" N VAL B 446 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 11.364A pdb=" N ILE B 294 " --> pdb=" O ARG B 444 " (cutoff:3.500A) removed outlier: 10.028A pdb=" N ARG B 444 " --> pdb=" O ILE B 294 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.286A pdb=" N VAL F 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N VAL C 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N THR F 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N TYR C 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N CYS F 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.843A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 91 through 93 Processing sheet with id=AB7, first strand: chain 'C' and resid 201 through 202 Processing sheet with id=AB8, first strand: chain 'C' and resid 260 through 261 removed outlier: 6.586A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N CYS C 445 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N CYS C 296 " --> pdb=" O CYS C 445 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.399A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 12.022A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 11.986A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 10.758A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.351A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 11.311A pdb=" N ASP C 457 " --> pdb=" O ILE C 284 " (cutoff:3.500A) removed outlier: 13.044A pdb=" N ILE C 284 " --> pdb=" O ASP C 457 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 284 through 298 current: chain 'C' and resid 359 through 361 Processing sheet with id=AB9, first strand: chain 'C' and resid 271 through 273 removed outlier: 3.583A pdb=" N MET C 271 " --> pdb=" O GLN C 287 " (cutoff:3.500A) removed outlier: 13.044A pdb=" N ILE C 284 " --> pdb=" O ASP C 457 " (cutoff:3.500A) removed outlier: 11.311A pdb=" N ASP C 457 " --> pdb=" O ILE C 284 " (cutoff:3.500A) removed outlier: 11.351A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.758A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.986A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 12.022A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.399A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N CYS C 296 " --> pdb=" O CYS C 445 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N CYS C 445 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 443 through 457 current: chain 'C' and resid 413 through 414 Processing sheet with id=AC1, first strand: chain 'C' and resid 374 through 378 Processing sheet with id=AC2, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AC3, first strand: chain 'G' and resid 10 through 11 removed outlier: 6.463A pdb=" N LEU G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N TRP G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 10 through 11 removed outlier: 3.974A pdb=" N VAL G 102 " --> pdb=" O ARG G 94 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AC6, first strand: chain 'H' and resid 10 through 12 removed outlier: 7.320A pdb=" N LEU H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N TYR H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AC8, first strand: chain 'I' and resid 10 through 11 removed outlier: 6.839A pdb=" N GLU I 10 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU I 34 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N TRP I 50 " --> pdb=" O LEU I 34 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 10 through 11 removed outlier: 6.839A pdb=" N GLU I 10 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL I 102 " --> pdb=" O ARG I 94 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AD2, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.839A pdb=" N LEU J 11 " --> pdb=" O GLU J 105 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AD4, first strand: chain 'K' and resid 10 through 11 removed outlier: 6.479A pdb=" N LEU K 34 " --> pdb=" O TRP K 50 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N TRP K 50 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N TRP K 36 " --> pdb=" O LEU K 48 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 10 through 11 removed outlier: 3.880A pdb=" N VAL K 102 " --> pdb=" O ARG K 94 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AD7, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.488A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'M' and resid 2 through 5 removed outlier: 6.458A pdb=" N LYS M 2 " --> pdb=" O GLN M 94 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N LEU M 96 " --> pdb=" O LYS M 2 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL M 4 " --> pdb=" O LEU M 96 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N PHE M 26 " --> pdb=" O GLY M 38 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N GLY M 38 " --> pdb=" O PHE M 26 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N TRP M 28 " --> pdb=" O ILE M 36 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'M' and resid 12 through 14 Processing sheet with id=AE1, first strand: chain 'N' and resid 2 through 5 removed outlier: 6.818A pdb=" N TRP N 28 " --> pdb=" O ILE N 36 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'N' and resid 12 through 14 Processing sheet with id=AE3, first strand: chain 'O' and resid 2 through 5 removed outlier: 4.020A pdb=" N LYS O 2 " --> pdb=" O GLU O 92 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N PHE O 26 " --> pdb=" O GLY O 38 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N GLY O 38 " --> pdb=" O PHE O 26 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N TRP O 28 " --> pdb=" O ILE O 36 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'O' and resid 11 through 14 656 hydrogen bonds defined for protein. 1689 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: 6.48 Time building geometry restraints manager: 5.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 6181 1.35 - 1.49: 5094 1.49 - 1.63: 8070 1.63 - 1.77: 1 1.77 - 1.90: 151 Bond restraints: 19497 Sorted by residual: bond pdb=" CA THR B 71 " pdb=" CB THR B 71 " ideal model delta sigma weight residual 1.528 1.625 -0.097 2.61e-02 1.47e+03 1.38e+01 bond pdb=" C3 MAN P 4 " pdb=" O3 MAN P 4 " ideal model delta sigma weight residual 1.408 1.474 -0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" CB CYS B 218 " pdb=" SG CYS B 218 " ideal model delta sigma weight residual 1.808 1.903 -0.095 3.30e-02 9.18e+02 8.34e+00 bond pdb=" CG LEU H 33 " pdb=" CD1 LEU H 33 " ideal model delta sigma weight residual 1.521 1.431 0.090 3.30e-02 9.18e+02 7.47e+00 bond pdb=" C3 MAN P 4 " pdb=" C4 MAN P 4 " ideal model delta sigma weight residual 1.524 1.578 -0.054 2.00e-02 2.50e+03 7.17e+00 ... (remaining 19492 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.51: 26227 4.51 - 9.03: 210 9.03 - 13.54: 26 13.54 - 18.06: 3 18.06 - 22.57: 1 Bond angle restraints: 26467 Sorted by residual: angle pdb=" C ASN B 411 " pdb=" N ASP B 412 " pdb=" CA ASP B 412 " ideal model delta sigma weight residual 121.70 137.60 -15.90 1.80e+00 3.09e-01 7.81e+01 angle pdb=" CD1 LEU H 33 " pdb=" CG LEU H 33 " pdb=" CD2 LEU H 33 " ideal model delta sigma weight residual 110.80 94.17 16.63 2.20e+00 2.07e-01 5.71e+01 angle pdb=" CB LEU H 33 " pdb=" CG LEU H 33 " pdb=" CD2 LEU H 33 " ideal model delta sigma weight residual 110.70 88.13 22.57 3.00e+00 1.11e-01 5.66e+01 angle pdb=" C GLY F 597 " pdb=" N CYS F 598 " pdb=" CA CYS F 598 " ideal model delta sigma weight residual 121.54 133.71 -12.17 1.91e+00 2.74e-01 4.06e+01 angle pdb=" C LYS F 601 " pdb=" N LEU F 602 " pdb=" CA LEU F 602 " ideal model delta sigma weight residual 121.54 133.31 -11.77 1.91e+00 2.74e-01 3.80e+01 ... (remaining 26462 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.57: 10973 21.57 - 43.14: 676 43.14 - 64.72: 111 64.72 - 86.29: 52 86.29 - 107.86: 17 Dihedral angle restraints: 11829 sinusoidal: 4843 harmonic: 6986 Sorted by residual: dihedral pdb=" CB CYS B 218 " pdb=" SG CYS B 218 " pdb=" SG CYS B 247 " pdb=" CB CYS B 247 " ideal model delta sinusoidal sigma weight residual 93.00 3.67 89.33 1 1.00e+01 1.00e-02 9.49e+01 dihedral pdb=" CB CYS B 296 " pdb=" SG CYS B 296 " pdb=" SG CYS B 378 " pdb=" CB CYS B 378 " ideal model delta sinusoidal sigma weight residual -86.00 -1.59 -84.41 1 1.00e+01 1.00e-02 8.66e+01 dihedral pdb=" CB CYS B 54 " pdb=" SG CYS B 54 " pdb=" SG CYS B 74 " pdb=" CB CYS B 74 " ideal model delta sinusoidal sigma weight residual 93.00 164.42 -71.42 1 1.00e+01 1.00e-02 6.54e+01 ... (remaining 11826 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 2829 0.113 - 0.226: 190 0.226 - 0.338: 10 0.338 - 0.451: 3 0.451 - 0.564: 1 Chirality restraints: 3033 Sorted by residual: chirality pdb=" CG LEU H 96 " pdb=" CB LEU H 96 " pdb=" CD1 LEU H 96 " pdb=" CD2 LEU H 96 " both_signs ideal model delta sigma weight residual False -2.59 -2.03 -0.56 2.00e-01 2.50e+01 7.95e+00 chirality pdb=" C1 NAG W 2 " pdb=" O4 NAG W 1 " pdb=" C2 NAG W 2 " pdb=" O5 NAG W 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.45 0.05 2.00e-02 2.50e+03 7.18e+00 chirality pdb=" C1 BMA d 3 " pdb=" O4 NAG d 2 " pdb=" C2 BMA d 3 " pdb=" O5 BMA d 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.44 0.04 2.00e-02 2.50e+03 4.95e+00 ... (remaining 3030 not shown) Planarity restraints: 3352 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE H 71 " 0.040 2.00e-02 2.50e+03 5.15e-02 4.64e+01 pdb=" CG PHE H 71 " -0.115 2.00e-02 2.50e+03 pdb=" CD1 PHE H 71 " 0.052 2.00e-02 2.50e+03 pdb=" CD2 PHE H 71 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE H 71 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE H 71 " 0.016 2.00e-02 2.50e+03 pdb=" CZ PHE H 71 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP I 50 " -0.056 2.00e-02 2.50e+03 4.00e-02 4.00e+01 pdb=" CG TRP I 50 " 0.102 2.00e-02 2.50e+03 pdb=" CD1 TRP I 50 " -0.042 2.00e-02 2.50e+03 pdb=" CD2 TRP I 50 " 0.012 2.00e-02 2.50e+03 pdb=" NE1 TRP I 50 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP I 50 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP I 50 " 0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP I 50 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP I 50 " -0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP I 50 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE I 29 " -0.028 2.00e-02 2.50e+03 3.33e-02 1.94e+01 pdb=" CG PHE I 29 " 0.077 2.00e-02 2.50e+03 pdb=" CD1 PHE I 29 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE I 29 " -0.026 2.00e-02 2.50e+03 pdb=" CE1 PHE I 29 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE I 29 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE I 29 " 0.002 2.00e-02 2.50e+03 ... (remaining 3349 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 4822 2.81 - 3.33: 15815 3.33 - 3.86: 30509 3.86 - 4.38: 33739 4.38 - 4.90: 58764 Nonbonded interactions: 143649 Sorted by model distance: nonbonded pdb=" OG SER B 365 " pdb=" O LYS N 46 " model vdw 2.288 3.040 nonbonded pdb=" OG1 THR K 83 " pdb=" OD1 ASP K 85 " model vdw 2.291 3.040 nonbonded pdb=" O TYR H 49 " pdb=" OG1 THR H 53 " model vdw 2.310 3.040 nonbonded pdb=" O TYR J 49 " pdb=" OG1 THR J 53 " model vdw 2.328 3.040 nonbonded pdb=" OG SER N 79 " pdb=" O LEU N 95 " model vdw 2.335 3.040 ... (remaining 143644 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 58 or resid 68 through 118 or resid 208 through \ 298 or resid 327 through 457 or resid 460 through 503)) selection = (chain 'B' and (resid 33 through 48 or (resid 49 and (name N or name CA or name \ C or name O or name CB )) or resid 50 through 56 or (resid 57 through 58 and (na \ me N or name CA or name C or name O or name CB )) or resid 68 through 86 or (res \ id 87 and (name N or name CA or name C or name O or name CB )) or resid 88 throu \ gh 96 or (resid 97 and (name N or name CA or name C or name O or name CB )) or r \ esid 98 through 116 or (resid 117 and (name N or name CA or name C or name O or \ name CB )) or resid 118 or (resid 208 and (name N or name CA or name C or name O \ or name CB )) or resid 209 through 210 or (resid 211 and (name N or name CA or \ name C or name O or name CB )) or resid 212 through 230 or (resid 231 through 23 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 233 through \ 266 or (resid 267 through 269 and (name N or name CA or name C or name O or name \ CB )) or resid 270 through 274 or (resid 275 and (name N or name CA or name C o \ r name O or name CB )) or resid 276 through 357 or (resid 358 and (name N or nam \ e CA or name C or name O or name CB )) or resid 359 through 369 or (resid 370 an \ d (name N or name CA or name C or name O or name CB )) or resid 371 through 380 \ or (resid 381 and (name N or name CA or name C or name O or name CB )) or resid \ 382 through 395 or (resid 396 and (name N or name CA or name C or name O or name \ CB )) or resid 397 or resid 412 through 439 or (resid 440 and (name N or name C \ A or name C or name O or name CB )) or resid 441 through 456 or (resid 457 and ( \ name N or name CA or name C or name O or name CB )) or resid 463 through 464 or \ (resid 465 and (name N or name CA or name C or name O or name CB or name OG1)) o \ r (resid 466 and (name N or name CA or name C or name O or name CB or name CG )) \ or (resid 467 and (name N or name CA or name C or name O or name CB )) or resid \ 468 through 473 or (resid 474 and (name N or name CA or name C or name O or nam \ e CB )) or resid 475 through 501 or (resid 502 and (name N or name CA or name C \ or name O or name CB )) or resid 503)) selection = (chain 'C' and (resid 33 through 58 or resid 68 through 118 or resid 208 through \ 298 or resid 327 through 457 or resid 460 through 503)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = (chain 'F' and (resid 512 through 550 or resid 567 through 664)) } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' } 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 group one per residue 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: 2.190 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: 0.020 Extract box with map and model: 0.730 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 43.340 Find NCS groups from input model: 0.780 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: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 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 0.097 19549 Z= 0.242 Angle : 1.080 22.573 26586 Z= 0.552 Chirality : 0.060 0.564 3033 Planarity : 0.007 0.070 3349 Dihedral : 15.310 107.860 7210 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.97 % Favored : 93.78 % Rotamer: Outliers : 0.15 % Allowed : 0.39 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.16), residues: 2379 helix: -2.35 (0.22), residues: 350 sheet: -0.22 (0.19), residues: 753 loop : -1.76 (0.16), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.102 0.004 TRP I 50 HIS 0.010 0.002 HIS I 35 PHE 0.115 0.003 PHE H 71 TYR 0.024 0.002 TYR I 90 ARG 0.013 0.001 ARG K 82B Details of bonding type rmsd link_NAG-ASN : bond 0.00359 ( 3) link_NAG-ASN : angle 2.60978 ( 9) link_ALPHA1-6 : bond 0.00220 ( 3) link_ALPHA1-6 : angle 1.32495 ( 9) link_BETA1-4 : bond 0.00616 ( 6) link_BETA1-4 : angle 2.63433 ( 18) link_ALPHA1-3 : bond 0.00644 ( 3) link_ALPHA1-3 : angle 3.59549 ( 9) hydrogen bonds : bond 0.15595 ( 624) hydrogen bonds : angle 7.41442 ( 1689) SS BOND : bond 0.01042 ( 37) SS BOND : angle 2.99808 ( 74) covalent geometry : bond 0.00503 (19497) covalent geometry : angle 1.06471 (26467) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 2119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 504 time to evaluate : 2.097 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: symmetry clash REVERT: A 230 ASP cc_start: 0.8107 (t0) cc_final: 0.7681 (t0) REVERT: A 377 ASN cc_start: 0.8524 (p0) cc_final: 0.8283 (p0) REVERT: A 449 ILE cc_start: 0.8523 (mm) cc_final: 0.8212 (mm) REVERT: A 482 GLU cc_start: 0.8687 (mp0) cc_final: 0.8383 (mp0) REVERT: A 486 TYR cc_start: 0.8237 (m-80) cc_final: 0.7721 (m-10) REVERT: B 115 SER cc_start: 0.6614 (t) cc_final: 0.5981 (p) REVERT: B 270 VAL cc_start: 0.8755 (t) cc_final: 0.8534 (p) REVERT: C 85 HIS cc_start: 0.8082 (m170) cc_final: 0.7455 (m170) REVERT: D 543 ASN cc_start: 0.7130 (OUTLIER) cc_final: 0.6831 (t0) REVERT: D 569 THR cc_start: 0.7448 (t) cc_final: 0.7104 (t) REVERT: D 618 ASN cc_start: 0.6598 (p0) cc_final: 0.6080 (p0) REVERT: E 628 TRP cc_start: 0.8240 (m100) cc_final: 0.7517 (t-100) REVERT: F 530 MET cc_start: 0.8578 (tpt) cc_final: 0.8304 (tpt) REVERT: F 539 VAL cc_start: 0.9314 (m) cc_final: 0.9054 (t) REVERT: G 63 PHE cc_start: 0.8794 (m-10) cc_final: 0.8409 (m-10) REVERT: G 90 TYR cc_start: 0.7343 (m-80) cc_final: 0.6908 (m-80) REVERT: G 100 VAL cc_start: 0.8224 (t) cc_final: 0.7853 (t) REVERT: H 24 ARG cc_start: 0.8444 (tpp80) cc_final: 0.8119 (tpp80) REVERT: I 103 TRP cc_start: 0.7509 (m-10) cc_final: 0.6970 (m-10) REVERT: J 3 GLN cc_start: 0.6840 (mm110) cc_final: 0.6584 (tp40) REVERT: J 82 ASP cc_start: 0.6558 (m-30) cc_final: 0.6231 (m-30) REVERT: K 39 GLN cc_start: 0.8471 (tt0) cc_final: 0.8218 (tt0) REVERT: K 95 ASP cc_start: 0.8828 (t0) cc_final: 0.8478 (t0) REVERT: L 11 LEU cc_start: 0.8557 (tp) cc_final: 0.8356 (tp) REVERT: L 49 TYR cc_start: 0.9030 (p90) cc_final: 0.8746 (p90) REVERT: L 71 PHE cc_start: 0.8149 (m-10) cc_final: 0.7901 (m-10) REVERT: L 83 PHE cc_start: 0.7857 (m-80) cc_final: 0.7509 (m-80) REVERT: M 34 ILE cc_start: 0.8269 (mp) cc_final: 0.8044 (mp) REVERT: M 85 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7893 (mm-30) REVERT: N 35 LYS cc_start: 0.8366 (tttp) cc_final: 0.7810 (tptt) REVERT: N 78 ASP cc_start: 0.7380 (p0) cc_final: 0.6944 (p0) REVERT: O 34 ILE cc_start: 0.8724 (mm) cc_final: 0.8266 (mm) outliers start: 3 outliers final: 0 residues processed: 505 average time/residue: 0.2938 time to fit residues: 231.9757 Evaluate side-chains 391 residues out of total 2119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 390 time to evaluate : 2.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 198 optimal weight: 2.9990 chunk 178 optimal weight: 0.2980 chunk 98 optimal weight: 5.9990 chunk 60 optimal weight: 20.0000 chunk 120 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 184 optimal weight: 10.0000 chunk 71 optimal weight: 8.9990 chunk 112 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 213 optimal weight: 7.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 ASN A 425 ASN C 66 HIS C 374 HIS D 543 ASN D 590 GLN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 575 GLN ** E 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 90 HIS ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 70 HIS M 32 ASN O 40 GLN O 89 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.178501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.160084 restraints weight = 33878.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.158535 restraints weight = 74682.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.156704 restraints weight = 68570.777| |-----------------------------------------------------------------------------| r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 19549 Z= 0.225 Angle : 0.723 10.428 26586 Z= 0.371 Chirality : 0.047 0.273 3033 Planarity : 0.005 0.072 3349 Dihedral : 9.361 85.043 2871 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.93 % Favored : 93.86 % Rotamer: Outliers : 0.24 % Allowed : 5.66 % Favored : 94.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -1.64 (0.17), residues: 2379 helix: -1.30 (0.26), residues: 354 sheet: -0.06 (0.20), residues: 711 loop : -1.64 (0.16), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP K 50 HIS 0.006 0.002 HIS K 35 PHE 0.054 0.002 PHE H 71 TYR 0.015 0.002 TYR A 39 ARG 0.004 0.001 ARG B 350 Details of bonding type rmsd link_NAG-ASN : bond 0.00657 ( 3) link_NAG-ASN : angle 2.58316 ( 9) link_ALPHA1-6 : bond 0.00563 ( 3) link_ALPHA1-6 : angle 2.38457 ( 9) link_BETA1-4 : bond 0.00601 ( 6) link_BETA1-4 : angle 2.80510 ( 18) link_ALPHA1-3 : bond 0.00301 ( 3) link_ALPHA1-3 : angle 2.99723 ( 9) hydrogen bonds : bond 0.05011 ( 624) hydrogen bonds : angle 5.95297 ( 1689) SS BOND : bond 0.00429 ( 37) SS BOND : angle 1.89624 ( 74) covalent geometry : bond 0.00522 (19497) covalent geometry : angle 0.70891 (26467) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 469 time to evaluate : 2.269 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 279 ASN cc_start: 0.8397 (OUTLIER) cc_final: 0.8106 (t0) REVERT: A 486 TYR cc_start: 0.8576 (m-80) cc_final: 0.8284 (m-80) REVERT: B 103 GLN cc_start: 0.8305 (tm-30) cc_final: 0.7990 (tm-30) REVERT: B 115 SER cc_start: 0.7026 (t) cc_final: 0.6758 (p) REVERT: B 331 CYS cc_start: 0.6024 (m) cc_final: 0.5671 (m) REVERT: C 85 HIS cc_start: 0.8449 (m170) cc_final: 0.7906 (m170) REVERT: D 618 ASN cc_start: 0.6850 (p0) cc_final: 0.6642 (p0) REVERT: F 530 MET cc_start: 0.9205 (tpt) cc_final: 0.8765 (tpt) REVERT: F 636 SER cc_start: 0.9067 (p) cc_final: 0.8865 (t) REVERT: G 4 LEU cc_start: 0.8581 (mm) cc_final: 0.8229 (mt) REVERT: G 47 TRP cc_start: 0.8379 (t60) cc_final: 0.7603 (t60) REVERT: G 62 LYS cc_start: 0.7816 (ptmt) cc_final: 0.7320 (ptmm) REVERT: G 63 PHE cc_start: 0.7722 (m-10) cc_final: 0.7331 (m-10) REVERT: H 35 TRP cc_start: 0.8247 (m100) cc_final: 0.7628 (m100) REVERT: H 71 PHE cc_start: 0.5061 (m-10) cc_final: 0.4691 (m-10) REVERT: H 82 ASP cc_start: 0.8052 (p0) cc_final: 0.7632 (p0) REVERT: H 91 MET cc_start: 0.5706 (pmm) cc_final: 0.4733 (ptp) REVERT: I 103 TRP cc_start: 0.6955 (m-10) cc_final: 0.6702 (m-10) REVERT: K 95 ASP cc_start: 0.8782 (t0) cc_final: 0.8119 (t0) outliers start: 5 outliers final: 1 residues processed: 473 average time/residue: 0.2768 time to fit residues: 204.8964 Evaluate side-chains 379 residues out of total 2119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 377 time to evaluate : 2.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 40 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 178 optimal weight: 0.8980 chunk 19 optimal weight: 8.9990 chunk 13 optimal weight: 0.0470 chunk 189 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 203 optimal weight: 2.9990 chunk 12 optimal weight: 0.0000 chunk 220 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 overall best weight: 0.5682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 246 GLN A 258 GLN A 279 ASN D 577 GLN D 590 GLN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 590 GLN E 630 GLN G 32 ASN H 89 GLN I 43 GLN K 100 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.183136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.165429 restraints weight = 33260.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.164284 restraints weight = 68141.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.163570 restraints weight = 62564.581| |-----------------------------------------------------------------------------| r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19549 Z= 0.116 Angle : 0.625 12.157 26586 Z= 0.315 Chirality : 0.045 0.254 3033 Planarity : 0.004 0.058 3349 Dihedral : 8.675 78.765 2871 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.88 % Favored : 94.91 % Rotamer: Outliers : 0.19 % Allowed : 2.95 % Favored : 96.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.29 (0.17), residues: 2379 helix: -0.68 (0.27), residues: 353 sheet: 0.22 (0.20), residues: 733 loop : -1.59 (0.17), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP O 62 HIS 0.008 0.001 HIS L 90 PHE 0.042 0.001 PHE H 71 TYR 0.021 0.002 TYR L 94 ARG 0.009 0.000 ARG I 82B Details of bonding type rmsd link_NAG-ASN : bond 0.00239 ( 3) link_NAG-ASN : angle 2.04382 ( 9) link_ALPHA1-6 : bond 0.00716 ( 3) link_ALPHA1-6 : angle 1.87904 ( 9) link_BETA1-4 : bond 0.00334 ( 6) link_BETA1-4 : angle 2.30675 ( 18) link_ALPHA1-3 : bond 0.00612 ( 3) link_ALPHA1-3 : angle 2.46855 ( 9) hydrogen bonds : bond 0.03932 ( 624) hydrogen bonds : angle 5.48185 ( 1689) SS BOND : bond 0.00453 ( 37) SS BOND : angle 1.75810 ( 74) covalent geometry : bond 0.00262 (19497) covalent geometry : angle 0.61317 (26467) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 2119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 479 time to evaluate : 2.150 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 486 TYR cc_start: 0.8273 (m-80) cc_final: 0.7868 (m-80) REVERT: B 102 GLU cc_start: 0.7751 (mp0) cc_final: 0.7334 (tp30) REVERT: B 331 CYS cc_start: 0.5244 (m) cc_final: 0.5008 (m) REVERT: B 338 TRP cc_start: 0.7657 (t-100) cc_final: 0.7438 (t60) REVERT: B 390 LEU cc_start: 0.8435 (mt) cc_final: 0.7078 (mt) REVERT: C 85 HIS cc_start: 0.8506 (m170) cc_final: 0.7896 (m170) REVERT: C 104 MET cc_start: 0.8630 (ttp) cc_final: 0.7900 (ttp) REVERT: D 543 ASN cc_start: 0.7055 (t0) cc_final: 0.6777 (t0) REVERT: D 618 ASN cc_start: 0.6608 (p0) cc_final: 0.6228 (p0) REVERT: D 642 ILE cc_start: 0.6172 (tp) cc_final: 0.5943 (tp) REVERT: E 649 SER cc_start: 0.8284 (t) cc_final: 0.8017 (m) REVERT: F 530 MET cc_start: 0.9013 (tpt) cc_final: 0.8600 (tpt) REVERT: F 539 VAL cc_start: 0.9280 (m) cc_final: 0.9059 (t) REVERT: F 647 GLU cc_start: 0.8674 (tp30) cc_final: 0.8330 (tp30) REVERT: G 1 GLN cc_start: 0.7262 (mm110) cc_final: 0.7017 (mm-40) REVERT: G 4 LEU cc_start: 0.8571 (mm) cc_final: 0.8190 (mt) REVERT: G 62 LYS cc_start: 0.7713 (ptmt) cc_final: 0.7290 (ptmm) REVERT: G 63 PHE cc_start: 0.7577 (m-10) cc_final: 0.7247 (m-10) REVERT: H 82 ASP cc_start: 0.7859 (p0) cc_final: 0.7457 (p0) REVERT: H 89 GLN cc_start: 0.7836 (OUTLIER) cc_final: 0.7590 (pp30) REVERT: H 91 MET cc_start: 0.5684 (pmm) cc_final: 0.3533 (ptp) REVERT: K 95 ASP cc_start: 0.8739 (t0) cc_final: 0.8139 (t0) outliers start: 4 outliers final: 2 residues processed: 482 average time/residue: 0.2784 time to fit residues: 210.8567 Evaluate side-chains 373 residues out of total 2119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 370 time to evaluate : 1.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 111 optimal weight: 0.8980 chunk 78 optimal weight: 6.9990 chunk 231 optimal weight: 9.9990 chunk 61 optimal weight: 9.9990 chunk 98 optimal weight: 4.9990 chunk 64 optimal weight: 9.9990 chunk 138 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 169 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 170 optimal weight: 7.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 279 ASN B 85 HIS B 295 ASN B 330 HIS C 99 ASN C 422 GLN D 577 GLN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 40 GLN O 89 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.174478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.152880 restraints weight = 33916.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.150159 restraints weight = 79530.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.148312 restraints weight = 54186.203| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.097 19549 Z= 0.298 Angle : 0.807 11.757 26586 Z= 0.411 Chirality : 0.050 0.271 3033 Planarity : 0.005 0.067 3349 Dihedral : 8.764 80.940 2871 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.36 % Favored : 92.35 % Rotamer: Outliers : 0.15 % Allowed : 4.89 % Favored : 94.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -1.55 (0.17), residues: 2379 helix: -0.90 (0.27), residues: 357 sheet: -0.01 (0.20), residues: 737 loop : -1.72 (0.17), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.085 0.003 TRP K 50 HIS 0.012 0.002 HIS H 90 PHE 0.045 0.002 PHE H 71 TYR 0.028 0.002 TYR D 638 ARG 0.004 0.001 ARG F 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00993 ( 3) link_NAG-ASN : angle 3.08152 ( 9) link_ALPHA1-6 : bond 0.00426 ( 3) link_ALPHA1-6 : angle 2.51906 ( 9) link_BETA1-4 : bond 0.00551 ( 6) link_BETA1-4 : angle 2.80727 ( 18) link_ALPHA1-3 : bond 0.00224 ( 3) link_ALPHA1-3 : angle 2.97937 ( 9) hydrogen bonds : bond 0.05377 ( 624) hydrogen bonds : angle 5.88193 ( 1689) SS BOND : bond 0.00882 ( 37) SS BOND : angle 1.91469 ( 74) covalent geometry : bond 0.00694 (19497) covalent geometry : angle 0.79356 (26467) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 445 time to evaluate : 1.978 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 107 ASP cc_start: 0.7268 (p0) cc_final: 0.6369 (p0) REVERT: A 377 ASN cc_start: 0.7576 (p0) cc_final: 0.7364 (p0) REVERT: A 486 TYR cc_start: 0.8710 (m-80) cc_final: 0.8375 (m-10) REVERT: B 102 GLU cc_start: 0.7858 (mp0) cc_final: 0.7574 (tp30) REVERT: B 331 CYS cc_start: 0.5994 (m) cc_final: 0.5777 (m) REVERT: B 338 TRP cc_start: 0.7996 (t-100) cc_final: 0.7659 (t60) REVERT: B 390 LEU cc_start: 0.8669 (mt) cc_final: 0.7375 (mt) REVERT: C 271 MET cc_start: 0.8175 (mmm) cc_final: 0.7929 (mmm) REVERT: D 543 ASN cc_start: 0.7363 (t0) cc_final: 0.7112 (t0) REVERT: D 617 ARG cc_start: 0.8012 (mtt180) cc_final: 0.7188 (mtt180) REVERT: D 618 ASN cc_start: 0.6414 (p0) cc_final: 0.6180 (p0) REVERT: E 617 ARG cc_start: 0.7011 (mtm-85) cc_final: 0.6767 (ttp-110) REVERT: E 649 SER cc_start: 0.8436 (t) cc_final: 0.8165 (m) REVERT: G 4 LEU cc_start: 0.8625 (mm) cc_final: 0.8217 (mt) REVERT: G 62 LYS cc_start: 0.8084 (ptmt) cc_final: 0.7527 (ptmm) REVERT: G 63 PHE cc_start: 0.8040 (m-10) cc_final: 0.7695 (m-10) REVERT: G 73 LYS cc_start: 0.7452 (mtmt) cc_final: 0.6877 (mttt) REVERT: G 82 VAL cc_start: 0.8119 (t) cc_final: 0.7863 (t) REVERT: H 32 GLU cc_start: 0.7027 (mt-10) cc_final: 0.6485 (mt-10) REVERT: H 50 TYR cc_start: 0.8756 (m-10) cc_final: 0.8357 (m-80) REVERT: H 82 ASP cc_start: 0.8011 (p0) cc_final: 0.7713 (p0) REVERT: H 91 MET cc_start: 0.6512 (pmm) cc_final: 0.4640 (ptp) REVERT: I 103 TRP cc_start: 0.7096 (m-10) cc_final: 0.6752 (m-10) REVERT: J 49 TYR cc_start: 0.6854 (p90) cc_final: 0.6588 (p90) REVERT: M 34 ILE cc_start: 0.6874 (mp) cc_final: 0.6336 (mp) REVERT: O 26 PHE cc_start: 0.7116 (p90) cc_final: 0.6865 (p90) REVERT: O 34 ILE cc_start: 0.8023 (mm) cc_final: 0.7803 (mm) outliers start: 3 outliers final: 2 residues processed: 448 average time/residue: 0.2823 time to fit residues: 197.3700 Evaluate side-chains 346 residues out of total 2119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 344 time to evaluate : 1.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 115 optimal weight: 0.9980 chunk 182 optimal weight: 5.9990 chunk 201 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 186 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 212 optimal weight: 4.9990 chunk 172 optimal weight: 10.0000 chunk 86 optimal weight: 4.9990 chunk 198 optimal weight: 5.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN C 33 ASN ** D 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 GLN H 31 ASN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 32 ASN O 89 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.176126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.154558 restraints weight = 32528.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.153904 restraints weight = 69685.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.152322 restraints weight = 46797.477| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 19549 Z= 0.197 Angle : 0.706 11.732 26586 Z= 0.358 Chirality : 0.047 0.268 3033 Planarity : 0.005 0.079 3349 Dihedral : 8.387 75.948 2871 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.73 % Favored : 93.11 % Rotamer: Outliers : 0.05 % Allowed : 3.10 % Favored : 96.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.59 (0.17), residues: 2379 helix: -0.93 (0.26), residues: 379 sheet: -0.14 (0.19), residues: 763 loop : -1.71 (0.17), residues: 1237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP K 50 HIS 0.007 0.001 HIS A 72 PHE 0.039 0.002 PHE H 71 TYR 0.014 0.002 TYR D 638 ARG 0.009 0.001 ARG I 82B Details of bonding type rmsd link_NAG-ASN : bond 0.00685 ( 3) link_NAG-ASN : angle 2.47865 ( 9) link_ALPHA1-6 : bond 0.00787 ( 3) link_ALPHA1-6 : angle 2.02963 ( 9) link_BETA1-4 : bond 0.00494 ( 6) link_BETA1-4 : angle 2.29148 ( 18) link_ALPHA1-3 : bond 0.00337 ( 3) link_ALPHA1-3 : angle 2.54477 ( 9) hydrogen bonds : bond 0.04404 ( 624) hydrogen bonds : angle 5.64501 ( 1689) SS BOND : bond 0.00430 ( 37) SS BOND : angle 1.87943 ( 74) covalent geometry : bond 0.00458 (19497) covalent geometry : angle 0.69362 (26467) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 455 time to evaluate : 2.270 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 107 ASP cc_start: 0.7023 (p0) cc_final: 0.6046 (p0) REVERT: A 444 ARG cc_start: 0.6255 (mmm-85) cc_final: 0.5885 (ttp80) REVERT: A 486 TYR cc_start: 0.8628 (m-80) cc_final: 0.8152 (m-10) REVERT: B 102 GLU cc_start: 0.7883 (mp0) cc_final: 0.7512 (tp30) REVERT: B 280 ASN cc_start: 0.6274 (p0) cc_final: 0.5951 (p0) REVERT: B 486 TYR cc_start: 0.8995 (m-10) cc_final: 0.8527 (m-10) REVERT: C 85 HIS cc_start: 0.8484 (m170) cc_final: 0.8011 (m170) REVERT: D 540 GLN cc_start: 0.7457 (tm-30) cc_final: 0.7243 (tm-30) REVERT: D 543 ASN cc_start: 0.7328 (t0) cc_final: 0.6971 (t0) REVERT: D 617 ARG cc_start: 0.8079 (mtt180) cc_final: 0.7584 (mtt180) REVERT: D 618 ASN cc_start: 0.6175 (p0) cc_final: 0.5903 (p0) REVERT: E 617 ARG cc_start: 0.6919 (mtm-85) cc_final: 0.6660 (ttp-110) REVERT: E 628 TRP cc_start: 0.8733 (m100) cc_final: 0.8494 (m100) REVERT: G 4 LEU cc_start: 0.8543 (mm) cc_final: 0.8095 (mt) REVERT: H 50 TYR cc_start: 0.8583 (m-10) cc_final: 0.8308 (m-10) REVERT: H 82 ASP cc_start: 0.8004 (p0) cc_final: 0.7715 (p0) REVERT: H 91 MET cc_start: 0.6423 (pmm) cc_final: 0.4674 (ptp) REVERT: I 80 LEU cc_start: 0.7135 (tt) cc_final: 0.6928 (tt) REVERT: J 71 PHE cc_start: 0.6054 (m-80) cc_final: 0.5844 (m-80) REVERT: O 26 PHE cc_start: 0.6984 (p90) cc_final: 0.6684 (p90) REVERT: O 62 TRP cc_start: 0.8812 (m-10) cc_final: 0.8566 (m-90) outliers start: 1 outliers final: 1 residues processed: 456 average time/residue: 0.2944 time to fit residues: 210.9239 Evaluate side-chains 356 residues out of total 2119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 355 time to evaluate : 2.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 36 optimal weight: 2.9990 chunk 60 optimal weight: 9.9990 chunk 12 optimal weight: 8.9990 chunk 225 optimal weight: 8.9990 chunk 147 optimal weight: 0.9990 chunk 153 optimal weight: 10.0000 chunk 28 optimal weight: 0.8980 chunk 182 optimal weight: 9.9990 chunk 85 optimal weight: 3.9990 chunk 209 optimal weight: 9.9990 chunk 94 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 279 ASN ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN O 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.175375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.152726 restraints weight = 32891.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.153257 restraints weight = 76862.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.152265 restraints weight = 51219.958| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 19549 Z= 0.205 Angle : 0.716 11.971 26586 Z= 0.363 Chirality : 0.048 0.375 3033 Planarity : 0.005 0.065 3349 Dihedral : 8.229 72.740 2871 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.69 % Favored : 92.10 % Rotamer: Outliers : 0.05 % Allowed : 2.27 % Favored : 97.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.58 (0.17), residues: 2379 helix: -0.84 (0.26), residues: 375 sheet: -0.14 (0.19), residues: 764 loop : -1.71 (0.17), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.080 0.003 TRP K 50 HIS 0.009 0.001 HIS C 66 PHE 0.032 0.002 PHE H 71 TYR 0.025 0.002 TYR G 90 ARG 0.006 0.000 ARG K 82B Details of bonding type rmsd link_NAG-ASN : bond 0.00727 ( 3) link_NAG-ASN : angle 2.50936 ( 9) link_ALPHA1-6 : bond 0.00705 ( 3) link_ALPHA1-6 : angle 2.15050 ( 9) link_BETA1-4 : bond 0.00466 ( 6) link_BETA1-4 : angle 2.25786 ( 18) link_ALPHA1-3 : bond 0.00203 ( 3) link_ALPHA1-3 : angle 2.62118 ( 9) hydrogen bonds : bond 0.04416 ( 624) hydrogen bonds : angle 5.60547 ( 1689) SS BOND : bond 0.00554 ( 37) SS BOND : angle 1.88598 ( 74) covalent geometry : bond 0.00481 (19497) covalent geometry : angle 0.70356 (26467) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 453 time to evaluate : 2.043 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 377 ASN cc_start: 0.7390 (p0) cc_final: 0.7107 (p0) REVERT: A 486 TYR cc_start: 0.8622 (m-80) cc_final: 0.8226 (m-10) REVERT: B 102 GLU cc_start: 0.7867 (mp0) cc_final: 0.7529 (tp30) REVERT: B 338 TRP cc_start: 0.8014 (t-100) cc_final: 0.7805 (t-100) REVERT: B 486 TYR cc_start: 0.9049 (m-80) cc_final: 0.8491 (m-10) REVERT: C 78 ASP cc_start: 0.7236 (t0) cc_final: 0.6902 (t0) REVERT: C 85 HIS cc_start: 0.8605 (m170) cc_final: 0.8046 (m170) REVERT: D 543 ASN cc_start: 0.7389 (t0) cc_final: 0.6986 (t0) REVERT: D 617 ARG cc_start: 0.8062 (mtt180) cc_final: 0.7400 (mtt180) REVERT: D 618 ASN cc_start: 0.6184 (p0) cc_final: 0.5902 (p0) REVERT: E 628 TRP cc_start: 0.8729 (m100) cc_final: 0.8413 (m100) REVERT: F 647 GLU cc_start: 0.9040 (tp30) cc_final: 0.8772 (tp30) REVERT: G 4 LEU cc_start: 0.8620 (mm) cc_final: 0.8353 (mt) REVERT: G 73 LYS cc_start: 0.7705 (mtmt) cc_final: 0.7043 (mttt) REVERT: G 82 VAL cc_start: 0.8080 (t) cc_final: 0.7811 (t) REVERT: H 50 TYR cc_start: 0.8636 (m-10) cc_final: 0.8318 (m-80) REVERT: H 82 ASP cc_start: 0.8047 (p0) cc_final: 0.7741 (p0) REVERT: I 103 TRP cc_start: 0.6779 (m-10) cc_final: 0.6344 (m-10) REVERT: J 49 TYR cc_start: 0.6575 (p90) cc_final: 0.6197 (p90) REVERT: J 53 THR cc_start: 0.7050 (p) cc_final: 0.6772 (p) REVERT: L 71 PHE cc_start: 0.7901 (m-10) cc_final: 0.7336 (m-10) REVERT: O 62 TRP cc_start: 0.8856 (m-10) cc_final: 0.8561 (m-90) outliers start: 1 outliers final: 1 residues processed: 454 average time/residue: 0.2995 time to fit residues: 217.9003 Evaluate side-chains 345 residues out of total 2119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 344 time to evaluate : 2.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 22 optimal weight: 0.9980 chunk 57 optimal weight: 9.9990 chunk 9 optimal weight: 20.0000 chunk 178 optimal weight: 9.9990 chunk 84 optimal weight: 1.9990 chunk 131 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 chunk 155 optimal weight: 3.9990 chunk 149 optimal weight: 10.0000 chunk 156 optimal weight: 5.9990 chunk 220 optimal weight: 8.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 279 ASN B 295 ASN D 577 GLN ** D 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 90 HIS ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 89 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.175648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.157749 restraints weight = 32342.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.156388 restraints weight = 70451.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.154286 restraints weight = 52202.085| |-----------------------------------------------------------------------------| r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 19549 Z= 0.184 Angle : 0.698 12.063 26586 Z= 0.353 Chirality : 0.047 0.259 3033 Planarity : 0.005 0.070 3349 Dihedral : 7.911 67.676 2871 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.23 % Favored : 92.52 % Rotamer: Outliers : 0.05 % Allowed : 1.74 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.55 (0.17), residues: 2379 helix: -0.76 (0.27), residues: 374 sheet: -0.19 (0.19), residues: 759 loop : -1.66 (0.17), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP K 50 HIS 0.007 0.001 HIS L 90 PHE 0.020 0.002 PHE H 71 TYR 0.013 0.002 TYR L 49 ARG 0.004 0.000 ARG B 503 Details of bonding type rmsd link_NAG-ASN : bond 0.00581 ( 3) link_NAG-ASN : angle 2.36149 ( 9) link_ALPHA1-6 : bond 0.00733 ( 3) link_ALPHA1-6 : angle 2.02047 ( 9) link_BETA1-4 : bond 0.00492 ( 6) link_BETA1-4 : angle 2.07633 ( 18) link_ALPHA1-3 : bond 0.00396 ( 3) link_ALPHA1-3 : angle 2.59822 ( 9) hydrogen bonds : bond 0.04255 ( 624) hydrogen bonds : angle 5.51824 ( 1689) SS BOND : bond 0.00458 ( 37) SS BOND : angle 1.97388 ( 74) covalent geometry : bond 0.00431 (19497) covalent geometry : angle 0.68586 (26467) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 440 time to evaluate : 2.134 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 104 MET cc_start: 0.6946 (mmm) cc_final: 0.6667 (mmm) REVERT: A 107 ASP cc_start: 0.6695 (p0) cc_final: 0.5974 (p0) REVERT: A 486 TYR cc_start: 0.8591 (m-80) cc_final: 0.8193 (m-10) REVERT: B 102 GLU cc_start: 0.7909 (mp0) cc_final: 0.7535 (tp30) REVERT: B 486 TYR cc_start: 0.9108 (m-80) cc_final: 0.8508 (m-10) REVERT: C 78 ASP cc_start: 0.7192 (t0) cc_final: 0.6832 (t0) REVERT: C 85 HIS cc_start: 0.8780 (m170) cc_final: 0.8296 (m170) REVERT: D 543 ASN cc_start: 0.7420 (t0) cc_final: 0.7072 (t0) REVERT: D 617 ARG cc_start: 0.8024 (mtt180) cc_final: 0.7411 (mtt180) REVERT: G 4 LEU cc_start: 0.8566 (mm) cc_final: 0.8357 (mt) REVERT: G 73 LYS cc_start: 0.7703 (mtmt) cc_final: 0.7053 (mttt) REVERT: H 23 CYS cc_start: 0.3715 (t) cc_final: 0.2312 (t) REVERT: H 50 TYR cc_start: 0.8602 (m-10) cc_final: 0.8316 (m-80) REVERT: I 4 LEU cc_start: 0.8528 (mm) cc_final: 0.8324 (mt) REVERT: I 103 TRP cc_start: 0.6885 (m-10) cc_final: 0.6484 (m-10) REVERT: J 49 TYR cc_start: 0.6643 (p90) cc_final: 0.6234 (p90) REVERT: J 53 THR cc_start: 0.7110 (p) cc_final: 0.6793 (p) REVERT: J 70 HIS cc_start: 0.7741 (p-80) cc_final: 0.7116 (t-90) REVERT: K 95 ASP cc_start: 0.8667 (t0) cc_final: 0.8213 (t0) REVERT: L 71 PHE cc_start: 0.7930 (m-10) cc_final: 0.7359 (m-10) REVERT: O 62 TRP cc_start: 0.8773 (m-10) cc_final: 0.8536 (m-90) outliers start: 1 outliers final: 1 residues processed: 441 average time/residue: 0.2886 time to fit residues: 201.2866 Evaluate side-chains 349 residues out of total 2119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 348 time to evaluate : 2.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 186 optimal weight: 3.9990 chunk 92 optimal weight: 0.0470 chunk 94 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 146 optimal weight: 8.9990 chunk 221 optimal weight: 9.9990 chunk 142 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 179 optimal weight: 8.9990 chunk 181 optimal weight: 5.9990 overall best weight: 2.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 279 ASN A 422 GLN ** D 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN O 89 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.173246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.154363 restraints weight = 33739.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.148038 restraints weight = 71321.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.145117 restraints weight = 64107.033| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 19549 Z= 0.217 Angle : 0.726 12.164 26586 Z= 0.369 Chirality : 0.048 0.261 3033 Planarity : 0.005 0.070 3349 Dihedral : 7.771 60.767 2871 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.24 % Favored : 91.51 % Rotamer: Outliers : 0.05 % Allowed : 1.60 % Favored : 98.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.62 (0.17), residues: 2379 helix: -0.89 (0.26), residues: 376 sheet: -0.10 (0.20), residues: 723 loop : -1.74 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.003 TRP C 45 HIS 0.007 0.001 HIS L 90 PHE 0.023 0.002 PHE H 71 TYR 0.014 0.002 TYR G 97 ARG 0.005 0.000 ARG B 503 Details of bonding type rmsd link_NAG-ASN : bond 0.00705 ( 3) link_NAG-ASN : angle 2.60535 ( 9) link_ALPHA1-6 : bond 0.00682 ( 3) link_ALPHA1-6 : angle 1.91819 ( 9) link_BETA1-4 : bond 0.00516 ( 6) link_BETA1-4 : angle 2.22058 ( 18) link_ALPHA1-3 : bond 0.00279 ( 3) link_ALPHA1-3 : angle 2.69330 ( 9) hydrogen bonds : bond 0.04528 ( 624) hydrogen bonds : angle 5.60761 ( 1689) SS BOND : bond 0.00464 ( 37) SS BOND : angle 2.02513 ( 74) covalent geometry : bond 0.00513 (19497) covalent geometry : angle 0.71302 (26467) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 431 time to evaluate : 2.164 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 435 TYR cc_start: 0.6109 (t80) cc_final: 0.5826 (t80) REVERT: A 486 TYR cc_start: 0.8675 (m-80) cc_final: 0.8287 (m-10) REVERT: B 102 GLU cc_start: 0.7874 (mp0) cc_final: 0.7629 (tp30) REVERT: C 78 ASP cc_start: 0.7171 (t0) cc_final: 0.6925 (t0) REVERT: C 258 GLN cc_start: 0.7902 (mt0) cc_final: 0.7638 (mt0) REVERT: D 543 ASN cc_start: 0.7435 (t0) cc_final: 0.6998 (t0) REVERT: D 617 ARG cc_start: 0.8010 (mtt180) cc_final: 0.5991 (mpt180) REVERT: D 638 TYR cc_start: 0.6240 (m-80) cc_final: 0.5965 (m-80) REVERT: E 623 TRP cc_start: 0.7354 (m100) cc_final: 0.7130 (m100) REVERT: G 4 LEU cc_start: 0.8423 (mm) cc_final: 0.8207 (mt) REVERT: G 62 LYS cc_start: 0.7763 (ptmm) cc_final: 0.7503 (ptmm) REVERT: G 73 LYS cc_start: 0.7790 (mtmt) cc_final: 0.7179 (mttt) REVERT: H 23 CYS cc_start: 0.3738 (t) cc_final: 0.2351 (t) REVERT: H 86 TYR cc_start: 0.8355 (m-80) cc_final: 0.8084 (m-10) REVERT: I 4 LEU cc_start: 0.8534 (mm) cc_final: 0.8324 (mt) REVERT: J 49 TYR cc_start: 0.6652 (p90) cc_final: 0.6280 (p90) REVERT: J 53 THR cc_start: 0.7231 (p) cc_final: 0.6872 (p) REVERT: J 70 HIS cc_start: 0.7903 (p-80) cc_final: 0.7147 (t-90) REVERT: L 71 PHE cc_start: 0.7938 (m-80) cc_final: 0.7304 (m-10) outliers start: 1 outliers final: 1 residues processed: 432 average time/residue: 0.3220 time to fit residues: 222.2835 Evaluate side-chains 337 residues out of total 2119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 336 time to evaluate : 2.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 140 optimal weight: 0.5980 chunk 139 optimal weight: 4.9990 chunk 224 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 167 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 184 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 85 HIS A 279 ASN ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 30 ASN O 89 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.180739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.140666 restraints weight = 33815.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.141573 restraints weight = 58714.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.143160 restraints weight = 47185.744| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 19549 Z= 0.212 Angle : 0.738 12.204 26586 Z= 0.374 Chirality : 0.047 0.263 3033 Planarity : 0.005 0.071 3349 Dihedral : 7.419 59.394 2871 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.73 % Favored : 92.01 % Rotamer: Outliers : 0.05 % Allowed : 0.53 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.66 (0.17), residues: 2379 helix: -0.95 (0.26), residues: 381 sheet: -0.10 (0.20), residues: 708 loop : -1.77 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.003 TRP K 50 HIS 0.007 0.001 HIS K 35 PHE 0.022 0.002 PHE H 71 TYR 0.025 0.002 TYR A 217 ARG 0.004 0.000 ARG G 82B Details of bonding type rmsd link_NAG-ASN : bond 0.00721 ( 3) link_NAG-ASN : angle 2.61417 ( 9) link_ALPHA1-6 : bond 0.00832 ( 3) link_ALPHA1-6 : angle 1.37270 ( 9) link_BETA1-4 : bond 0.00567 ( 6) link_BETA1-4 : angle 2.23611 ( 18) link_ALPHA1-3 : bond 0.00314 ( 3) link_ALPHA1-3 : angle 2.61321 ( 9) hydrogen bonds : bond 0.04489 ( 624) hydrogen bonds : angle 5.59216 ( 1689) SS BOND : bond 0.00421 ( 37) SS BOND : angle 1.99003 ( 74) covalent geometry : bond 0.00501 (19497) covalent geometry : angle 0.72581 (26467) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 421 time to evaluate : 2.040 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 107 ASP cc_start: 0.6849 (p0) cc_final: 0.6486 (p0) REVERT: A 426 MET cc_start: 0.6521 (mmm) cc_final: 0.6095 (mtp) REVERT: A 434 MET cc_start: 0.7386 (pmm) cc_final: 0.6980 (pmm) REVERT: A 486 TYR cc_start: 0.8743 (m-80) cc_final: 0.8327 (m-10) REVERT: B 102 GLU cc_start: 0.8067 (mp0) cc_final: 0.7547 (tp30) REVERT: B 331 CYS cc_start: 0.7134 (m) cc_final: 0.6826 (m) REVERT: C 78 ASP cc_start: 0.7368 (t0) cc_final: 0.7049 (t0) REVERT: C 258 GLN cc_start: 0.8017 (mt0) cc_final: 0.7719 (mt0) REVERT: D 543 ASN cc_start: 0.7558 (t0) cc_final: 0.7145 (t0) REVERT: D 617 ARG cc_start: 0.7933 (mtt180) cc_final: 0.6171 (mmp80) REVERT: F 647 GLU cc_start: 0.8793 (tp30) cc_final: 0.8585 (tp30) REVERT: G 4 LEU cc_start: 0.8614 (mm) cc_final: 0.8282 (mt) REVERT: G 62 LYS cc_start: 0.8061 (ptmm) cc_final: 0.7739 (ptmm) REVERT: G 73 LYS cc_start: 0.7860 (mtmt) cc_final: 0.7100 (mttt) REVERT: H 23 CYS cc_start: 0.4155 (t) cc_final: 0.2808 (t) REVERT: H 35 TRP cc_start: 0.8486 (m100) cc_final: 0.7803 (m100) REVERT: H 86 TYR cc_start: 0.8355 (m-80) cc_final: 0.8058 (m-10) REVERT: I 50 TRP cc_start: 0.7660 (p-90) cc_final: 0.7384 (p-90) REVERT: J 49 TYR cc_start: 0.6964 (p90) cc_final: 0.6745 (p90) REVERT: J 53 THR cc_start: 0.7700 (p) cc_final: 0.7318 (p) REVERT: J 70 HIS cc_start: 0.8432 (p-80) cc_final: 0.7393 (t-90) REVERT: L 71 PHE cc_start: 0.8126 (m-80) cc_final: 0.7531 (m-10) REVERT: O 4 VAL cc_start: 0.7479 (t) cc_final: 0.7214 (p) REVERT: O 34 ILE cc_start: 0.8366 (mm) cc_final: 0.8159 (mm) outliers start: 1 outliers final: 1 residues processed: 422 average time/residue: 0.3222 time to fit residues: 215.4759 Evaluate side-chains 337 residues out of total 2119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 336 time to evaluate : 2.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 126 optimal weight: 0.9980 chunk 231 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 209 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 3 optimal weight: 0.0000 chunk 38 optimal weight: 0.9980 chunk 167 optimal weight: 6.9990 chunk 128 optimal weight: 0.9980 chunk 212 optimal weight: 9.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 279 ASN B 246 GLN ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 90 HIS ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN O 89 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.183850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.146567 restraints weight = 33535.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.149124 restraints weight = 58844.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.149714 restraints weight = 44614.417| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.3963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 19549 Z= 0.138 Angle : 0.679 12.457 26586 Z= 0.343 Chirality : 0.046 0.254 3033 Planarity : 0.004 0.065 3349 Dihedral : 6.750 59.368 2871 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.68 % Favored : 93.11 % Rotamer: Outliers : 0.05 % Allowed : 0.58 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.51 (0.17), residues: 2379 helix: -0.80 (0.26), residues: 381 sheet: -0.01 (0.21), residues: 705 loop : -1.67 (0.17), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP K 50 HIS 0.005 0.001 HIS K 35 PHE 0.014 0.001 PHE H 71 TYR 0.036 0.002 TYR A 217 ARG 0.005 0.000 ARG G 82B Details of bonding type rmsd link_NAG-ASN : bond 0.00432 ( 3) link_NAG-ASN : angle 2.11583 ( 9) link_ALPHA1-6 : bond 0.01005 ( 3) link_ALPHA1-6 : angle 1.43652 ( 9) link_BETA1-4 : bond 0.00504 ( 6) link_BETA1-4 : angle 1.83095 ( 18) link_ALPHA1-3 : bond 0.00634 ( 3) link_ALPHA1-3 : angle 2.34637 ( 9) hydrogen bonds : bond 0.03826 ( 624) hydrogen bonds : angle 5.37290 ( 1689) SS BOND : bond 0.00401 ( 37) SS BOND : angle 1.86218 ( 74) covalent geometry : bond 0.00323 (19497) covalent geometry : angle 0.66876 (26467) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 433 time to evaluate : 2.704 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 426 MET cc_start: 0.6393 (mmm) cc_final: 0.6094 (mtp) REVERT: A 434 MET cc_start: 0.7169 (pmm) cc_final: 0.6767 (pmm) REVERT: A 435 TYR cc_start: 0.6305 (t80) cc_final: 0.6042 (t80) REVERT: A 486 TYR cc_start: 0.8561 (m-80) cc_final: 0.8030 (m-10) REVERT: B 102 GLU cc_start: 0.8058 (mp0) cc_final: 0.7447 (tp30) REVERT: B 331 CYS cc_start: 0.6899 (m) cc_final: 0.6639 (m) REVERT: B 338 TRP cc_start: 0.8453 (t-100) cc_final: 0.8004 (t60) REVERT: B 486 TYR cc_start: 0.8887 (m-10) cc_final: 0.8374 (m-10) REVERT: C 78 ASP cc_start: 0.7248 (t0) cc_final: 0.6882 (t0) REVERT: C 85 HIS cc_start: 0.8493 (m170) cc_final: 0.8045 (m170) REVERT: C 258 GLN cc_start: 0.8018 (mt0) cc_final: 0.7723 (mt0) REVERT: D 543 ASN cc_start: 0.7401 (t0) cc_final: 0.6559 (m-40) REVERT: G 4 LEU cc_start: 0.8517 (mm) cc_final: 0.8237 (mt) REVERT: G 62 LYS cc_start: 0.7954 (ptmm) cc_final: 0.7688 (ptmm) REVERT: H 23 CYS cc_start: 0.4089 (t) cc_final: 0.2741 (t) REVERT: H 35 TRP cc_start: 0.8438 (m100) cc_final: 0.7734 (m100) REVERT: H 86 TYR cc_start: 0.8330 (m-80) cc_final: 0.8031 (m-10) REVERT: I 50 TRP cc_start: 0.7612 (p-90) cc_final: 0.6979 (p-90) REVERT: J 49 TYR cc_start: 0.6965 (p90) cc_final: 0.6695 (p90) REVERT: J 53 THR cc_start: 0.7457 (p) cc_final: 0.7092 (p) REVERT: J 70 HIS cc_start: 0.8196 (p-80) cc_final: 0.7209 (t-90) REVERT: K 74 SER cc_start: 0.8882 (p) cc_final: 0.8594 (t) REVERT: K 75 ILE cc_start: 0.8190 (pt) cc_final: 0.7876 (pt) REVERT: K 95 ASP cc_start: 0.8853 (t0) cc_final: 0.8480 (t0) REVERT: L 71 PHE cc_start: 0.8200 (m-80) cc_final: 0.7606 (m-10) REVERT: M 28 TRP cc_start: 0.3798 (m100) cc_final: 0.3354 (m100) outliers start: 1 outliers final: 1 residues processed: 434 average time/residue: 0.3154 time to fit residues: 221.5142 Evaluate side-chains 353 residues out of total 2119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 352 time to evaluate : 2.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 142 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 158 optimal weight: 20.0000 chunk 133 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 219 optimal weight: 0.9990 chunk 208 optimal weight: 20.0000 chunk 101 optimal weight: 0.9990 chunk 78 optimal weight: 0.0060 overall best weight: 0.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 216 HIS A 279 ASN ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 652 GLN H 31 ASN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN O 89 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.188195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.151950 restraints weight = 33844.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.155701 restraints weight = 55493.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.156081 restraints weight = 38603.787| |-----------------------------------------------------------------------------| r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 19549 Z= 0.139 Angle : 0.673 11.873 26586 Z= 0.341 Chirality : 0.046 0.259 3033 Planarity : 0.004 0.064 3349 Dihedral : 6.506 59.106 2871 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.77 % Favored : 93.02 % Rotamer: Outliers : 0.10 % Allowed : 0.53 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.17), residues: 2379 helix: -0.64 (0.27), residues: 366 sheet: -0.02 (0.20), residues: 718 loop : -1.60 (0.17), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.003 TRP K 47 HIS 0.004 0.001 HIS K 35 PHE 0.023 0.001 PHE L 98 TYR 0.048 0.002 TYR A 217 ARG 0.005 0.000 ARG I 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00404 ( 3) link_NAG-ASN : angle 2.08977 ( 9) link_ALPHA1-6 : bond 0.00913 ( 3) link_ALPHA1-6 : angle 1.50276 ( 9) link_BETA1-4 : bond 0.00507 ( 6) link_BETA1-4 : angle 1.78460 ( 18) link_ALPHA1-3 : bond 0.00557 ( 3) link_ALPHA1-3 : angle 2.36513 ( 9) hydrogen bonds : bond 0.03785 ( 624) hydrogen bonds : angle 5.33278 ( 1689) SS BOND : bond 0.00417 ( 37) SS BOND : angle 1.87446 ( 74) covalent geometry : bond 0.00324 (19497) covalent geometry : angle 0.66288 (26467) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5969.98 seconds wall clock time: 107 minutes 15.24 seconds (6435.24 seconds total)