Starting phenix.real_space_refine on Sat Jun 21 02:06:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d90_46655/06_2025/9d90_46655.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d90_46655/06_2025/9d90_46655.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9d90_46655/06_2025/9d90_46655.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d90_46655/06_2025/9d90_46655.map" model { file = "/net/cci-nas-00/data/ceres_data/9d90_46655/06_2025/9d90_46655.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d90_46655/06_2025/9d90_46655.cif" } resolution = 3.91 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.027 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 135 5.16 5 C 15460 2.51 5 N 4240 2.21 5 O 4689 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 24524 Number of models: 1 Model: "" Number of chains: 27 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: 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: "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: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1023 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "E" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1034 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 1, 'TRANS': 129} Chain breaks: 1 Chain: "F" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1028 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 1, 'TRANS': 128} Chain breaks: 1 Chain: "G" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 932 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} 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: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 809 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 98} Chain: "Q" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 979 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "R" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 809 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 98} Chain: "S" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 979 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "T" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 809 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 7, 'TRANS': 98} Chain: "U" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 979 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "V" 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 Chain: "a" 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 Chain: "f" 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 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 15.06, per 1000 atoms: 0.61 Number of scatterers: 24524 At special positions: 0 Unit cell: (151.2, 155.52, 141.48, 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 135 16.00 O 4689 8.00 N 4240 7.00 C 15460 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, 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=2.04 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 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=2.04 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 A 501 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.04 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.06 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 331 " distance=2.04 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.04 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=2.02 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=2.05 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=2.03 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=2.02 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.04 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS N 16 " - pdb=" SG CYS N 84 " distance=2.03 Simple disulfide: pdb=" SG CYS O 16 " - pdb=" SG CYS O 84 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 92 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.04 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 92 " distance=2.03 Simple disulfide: pdb=" SG CYS T 23 " - pdb=" SG CYS T 88 " distance=2.04 Simple disulfide: pdb=" SG CYS U 22 " - pdb=" SG CYS U 92 " distance=2.03 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 V 3 " - " MAN V 4 " " BMA a 3 " - " MAN a 4 " " BMA f 3 " - " MAN f 4 " ALPHA1-6 " BMA V 3 " - " MAN V 5 " " BMA a 3 " - " MAN a 5 " " BMA f 3 " - " MAN f 5 " BETA1-4 " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " NAG-ASN " NAG D 701 " - " ASN D 611 " " NAG E 701 " - " ASN E 611 " " NAG F 701 " - " ASN F 611 " " NAG V 1 " - " ASN A 88 " " NAG a 1 " - " ASN B 88 " " NAG f 1 " - " ASN C 88 " Time building additional restraints: 5.79 Conformation dependent library (CDL) restraints added in 2.9 seconds 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5798 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 61 sheets defined 15.0% alpha, 31.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.55 Creating SS restraints... Processing helix chain 'A' and resid 66 through 74 Processing helix chain 'A' and resid 99 through 116 removed outlier: 3.520A pdb=" N GLN A 103 " --> pdb=" O ASN A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.536A pdb=" N THR A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 74 Processing helix chain 'B' and resid 99 through 116 removed outlier: 3.808A pdb=" N THR B 106 " --> pdb=" O GLU B 102 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP B 107 " --> pdb=" O GLN B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 350 Processing helix chain 'B' and resid 475 through 480 removed outlier: 3.513A pdb=" N TRP B 479 " --> pdb=" O MET B 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 71 Processing helix chain 'C' and resid 100 through 116 removed outlier: 3.791A pdb=" N THR C 106 " --> pdb=" O GLU C 102 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP C 107 " --> pdb=" O GLN C 103 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.951A pdb=" N THR C 373 " --> pdb=" O LEU C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 481 removed outlier: 3.806A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 542 Processing helix chain 'D' and resid 565 through 569 removed outlier: 3.514A pdb=" N LEU D 568 " --> pdb=" O LEU D 565 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR D 569 " --> pdb=" O LEU D 566 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 565 through 569' Processing helix chain 'D' and resid 573 through 596 removed outlier: 3.800A pdb=" N TRP D 596 " --> pdb=" O LEU D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 625 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 648 removed outlier: 3.686A pdb=" N ILE D 642 " --> pdb=" O TYR D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 659 removed outlier: 3.721A pdb=" N ASP D 659 " --> pdb=" O LYS D 655 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 534 removed outlier: 3.645A pdb=" N SER E 534 " --> pdb=" O MET E 530 " (cutoff:3.500A) Processing helix chain 'E' and resid 541 through 545 removed outlier: 3.724A pdb=" N LEU E 544 " --> pdb=" O ALA E 541 " (cutoff:3.500A) Processing helix chain 'E' and resid 567 through 572 Processing helix chain 'E' and resid 572 through 597 Processing helix chain 'E' and resid 618 through 625 Processing helix chain 'E' and resid 627 through 636 removed outlier: 3.563A pdb=" N SER E 636 " --> pdb=" O ASP E 632 " (cutoff:3.500A) Processing helix chain 'E' and resid 638 through 652 removed outlier: 4.040A pdb=" N GLN E 650 " --> pdb=" O LEU E 646 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 543 removed outlier: 3.961A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 566 through 596 removed outlier: 4.389A pdb=" N GLY F 572 " --> pdb=" O LEU F 568 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE F 573 " --> pdb=" O THR F 569 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS F 574 " --> pdb=" O VAL F 570 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN F 575 " --> pdb=" O TRP F 571 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N TRP F 596 " --> pdb=" O LEU F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 636 removed outlier: 3.549A pdb=" N SER F 636 " --> pdb=" O ASP F 632 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 649 Processing helix chain 'F' and resid 650 through 653 Processing helix chain 'G' and resid 83 through 87 removed outlier: 4.053A pdb=" N THR G 87 " --> pdb=" O SER G 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.671A pdb=" N GLY I 31 " --> pdb=" O THR I 28 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASN I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 28 through 32' Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.518A pdb=" N ASP I 86 " --> pdb=" O THR I 83 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR I 87 " --> pdb=" O SER I 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 83 through 87' Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.836A pdb=" N PHE J 83 " --> pdb=" O PRO J 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 removed outlier: 4.214A pdb=" N ASN K 32 " --> pdb=" O PHE K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 87 removed outlier: 3.616A pdb=" N ASP K 86 " --> pdb=" O THR K 83 " (cutoff:3.500A) removed outlier: 3.725A 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: 4.135A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 59 through 64 removed outlier: 3.755A pdb=" N ASP M 63 " --> pdb=" O SER M 60 " (cutoff:3.500A) Processing helix chain 'M' and resid 75 through 79 removed outlier: 3.632A pdb=" N ASP M 78 " --> pdb=" O LYS M 75 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N SER M 79 " --> pdb=" O ILE M 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 75 through 79' Processing helix chain 'N' and resid 58 through 62 removed outlier: 3.622A pdb=" N LEU N 61 " --> pdb=" O ARG N 58 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TRP N 62 " --> pdb=" O ARG N 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 58 through 62' Processing helix chain 'N' and resid 75 through 79 removed outlier: 3.571A pdb=" N SER N 79 " --> pdb=" O ILE N 76 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 79 removed outlier: 3.636A pdb=" N ASP O 78 " --> pdb=" O LYS O 75 " (cutoff:3.500A) Processing helix chain 'Q' and resid 28 through 30 No H-bonds generated for 'chain 'Q' and resid 28 through 30' Processing helix chain 'Q' and resid 83 through 87 removed outlier: 3.897A pdb=" N THR Q 87 " --> pdb=" O SER Q 84 " (cutoff:3.500A) Processing helix chain 'R' and resid 79 through 83 removed outlier: 3.652A pdb=" N ASP R 82 " --> pdb=" O GLN R 79 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N PHE R 83 " --> pdb=" O SER R 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 79 through 83' Processing helix chain 'S' and resid 28 through 30 No H-bonds generated for 'chain 'S' and resid 28 through 30' Processing helix chain 'S' and resid 83 through 87 removed outlier: 3.672A pdb=" N THR S 87 " --> pdb=" O SER S 84 " (cutoff:3.500A) Processing helix chain 'U' and resid 28 through 30 No H-bonds generated for 'chain 'U' and resid 28 through 30' Processing helix chain 'U' and resid 83 through 87 removed outlier: 3.817A pdb=" N THR U 87 " --> pdb=" O SER U 84 " (cutoff:3.500A) Processing helix chain 'U' and resid 99 through 100C removed outlier: 3.547A pdb=" N GLY U 100C" --> pdb=" O ALA U 100 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 40 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.877A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 93 Processing sheet with id=AA5, first strand: chain 'A' and resid 121 through 122 Processing sheet with id=AA6, first strand: chain 'A' and resid 260 through 261 removed outlier: 6.787A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.448A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 12.057A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 11.978A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.960A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.399A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 11.235A pdb=" N ASP A 457 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 12.954A 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 297 current: chain 'A' and resid 359 through 361 Processing sheet with id=AA7, first strand: chain 'A' and resid 271 through 273 removed outlier: 12.954A pdb=" N ILE A 284 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 11.235A pdb=" N ASP A 457 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 11.399A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.960A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.978A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 12.057A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.448A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 446 through 457 current: chain 'A' and resid 413 through 415 Processing sheet with id=AA8, first strand: chain 'A' and resid 374 through 378 Processing sheet with id=AA9, first strand: chain 'B' and resid 494 through 499 removed outlier: 5.230A pdb=" N VAL B 36 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N CYS E 604 " --> pdb=" O VAL B 38 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 45 through 47 removed outlier: 4.018A pdb=" N ILE B 225 " --> pdb=" O VAL B 245 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 91 through 92 removed outlier: 3.549A pdb=" N GLU B 91 " --> pdb=" O CYS B 239 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 201 through 202 removed outlier: 3.624A pdb=" N VAL B 120 " --> pdb=" O MET B 434 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 260 through 261 removed outlier: 3.781A pdb=" N GLY B 451 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N GLY B 451 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 10.952A pdb=" N THR B 290 " --> pdb=" O GLY B 451 " (cutoff:3.500A) removed outlier: 11.996A pdb=" N ILE B 453 " --> pdb=" O PHE B 288 " (cutoff:3.500A) removed outlier: 12.077A pdb=" N PHE B 288 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 10.655A pdb=" N THR B 455 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 11.133A pdb=" N VAL B 286 " --> pdb=" O THR B 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 284 through 298 current: chain 'B' and resid 359 through 361 Processing sheet with id=AB5, first strand: chain 'B' and resid 271 through 273 removed outlier: 11.133A pdb=" N VAL B 286 " --> pdb=" O THR B 455 " (cutoff:3.500A) removed outlier: 10.655A pdb=" N THR B 455 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 12.077A pdb=" N PHE B 288 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 11.996A pdb=" N ILE B 453 " --> pdb=" O PHE B 288 " (cutoff:3.500A) removed outlier: 10.952A pdb=" N THR B 290 " --> pdb=" O GLY B 451 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N GLY B 451 " --> pdb=" O THR B 290 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 443 through 456 current: chain 'B' and resid 413 through 414 Processing sheet with id=AB6, first strand: chain 'B' and resid 374 through 378 Processing sheet with id=AB7, first strand: chain 'C' and resid 494 through 499 removed outlier: 4.975A pdb=" N VAL C 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL C 38 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N CYS F 604 " --> pdb=" O VAL C 38 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.828A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 91 through 93 removed outlier: 3.673A pdb=" N GLY C 237 " --> pdb=" O PHE C 93 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 198 through 202 removed outlier: 3.612A pdb=" N THR C 123 " --> pdb=" O SER C 199 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE C 201 " --> pdb=" O LYS C 121 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 260 through 261 removed outlier: 3.961A pdb=" N GLY C 451 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.664A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 12.036A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 12.010A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 10.848A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.415A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 11.148A pdb=" N ASP C 457 " --> pdb=" O ILE C 284 " (cutoff:3.500A) removed outlier: 12.836A 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 297 current: chain 'C' and resid 359 through 360 Processing sheet with id=AC3, first strand: chain 'C' and resid 271 through 273 removed outlier: 12.836A pdb=" N ILE C 284 " --> pdb=" O ASP C 457 " (cutoff:3.500A) removed outlier: 11.148A pdb=" N ASP C 457 " --> pdb=" O ILE C 284 " (cutoff:3.500A) removed outlier: 11.415A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.848A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 12.010A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 12.036A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.664A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 446 through 457 current: chain 'C' and resid 413 through 414 Processing sheet with id=AC4, first strand: chain 'C' and resid 374 through 377 Processing sheet with id=AC5, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AC6, first strand: chain 'G' and resid 10 through 11 removed outlier: 6.426A pdb=" N LEU G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N TRP G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 10 through 11 removed outlier: 3.859A pdb=" N VAL G 102 " --> pdb=" O ARG G 94 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AC9, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.843A pdb=" N LEU H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N TYR H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN H 37 " --> pdb=" O ASN H 45 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AD2, first strand: chain 'I' and resid 10 through 11 removed outlier: 6.442A pdb=" N LEU I 34 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N TRP I 50 " --> pdb=" O LEU I 34 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 10 through 11 removed outlier: 3.827A pdb=" N VAL I 102 " --> pdb=" O ARG I 94 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AD5, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.697A pdb=" N LEU J 11 " --> pdb=" O GLU J 105 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AD7, first strand: chain 'K' and resid 10 through 11 removed outlier: 3.609A pdb=" N GLY K 49 " --> pdb=" O TRP K 36 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 10 through 11 removed outlier: 3.909A pdb=" N VAL K 102 " --> pdb=" O ARG K 94 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AE1, first strand: chain 'L' and resid 10 through 12 Processing sheet with id=AE2, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.615A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'M' and resid 2 through 4 removed outlier: 6.759A pdb=" N LYS M 2 " --> pdb=" O GLN M 94 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N TRP M 28 " --> pdb=" O ILE M 36 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 12 through 14 Processing sheet with id=AE5, first strand: chain 'N' and resid 2 through 5 removed outlier: 6.824A pdb=" N LYS N 2 " --> pdb=" O GLN N 94 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N LEU N 96 " --> pdb=" O LYS N 2 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL N 4 " --> pdb=" O LEU N 96 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N PHE N 26 " --> pdb=" O GLY N 38 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N GLY N 38 " --> pdb=" O PHE N 26 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N TRP N 28 " --> pdb=" O ILE N 36 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 12 through 14 Processing sheet with id=AE7, first strand: chain 'O' and resid 2 through 5 removed outlier: 3.782A pdb=" N LYS O 2 " --> pdb=" O GLU O 92 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N TRP O 28 " --> pdb=" O ILE O 36 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'O' and resid 12 through 14 Processing sheet with id=AE9, first strand: chain 'P' and resid 4 through 5 Processing sheet with id=AF1, first strand: chain 'P' and resid 19 through 21 Processing sheet with id=AF2, first strand: chain 'P' and resid 53 through 54 removed outlier: 3.674A pdb=" N THR P 53 " --> pdb=" O TYR P 49 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N LEU P 46 " --> pdb=" O GLN P 37 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLN P 37 " --> pdb=" O LEU P 46 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE P 48 " --> pdb=" O TRP P 35 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Q' and resid 3 through 6 Processing sheet with id=AF4, first strand: chain 'Q' and resid 10 through 11 removed outlier: 3.606A pdb=" N GLY Q 49 " --> pdb=" O TRP Q 36 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ARG Q 38 " --> pdb=" O TRP Q 47 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N TRP Q 47 " --> pdb=" O ARG Q 38 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Q' and resid 10 through 11 removed outlier: 3.615A pdb=" N HIS Q 102 " --> pdb=" O GLY Q 94 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'R' and resid 19 through 24 Processing sheet with id=AF7, first strand: chain 'R' and resid 53 through 54 removed outlier: 3.796A pdb=" N THR R 53 " --> pdb=" O TYR R 49 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR R 49 " --> pdb=" O THR R 53 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N TYR R 49 " --> pdb=" O LEU R 33 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEU R 33 " --> pdb=" O TYR R 49 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'S' and resid 3 through 6 Processing sheet with id=AF9, first strand: chain 'S' and resid 10 through 11 removed outlier: 3.521A pdb=" N THR S 110 " --> pdb=" O GLU S 10 " (cutoff:3.500A) removed outlier: 8.810A pdb=" N TYR S 32 " --> pdb=" O ILE S 52 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ILE S 52 " --> pdb=" O TYR S 32 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N PHE S 34 " --> pdb=" O ARG S 50 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ARG S 50 " --> pdb=" O PHE S 34 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N TRP S 36 " --> pdb=" O MET S 48 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'S' and resid 10 through 11 removed outlier: 3.521A pdb=" N THR S 110 " --> pdb=" O GLU S 10 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'T' and resid 4 through 6 Processing sheet with id=AG3, first strand: chain 'T' and resid 45 through 46 Processing sheet with id=AG4, first strand: chain 'T' and resid 48 through 49 Processing sheet with id=AG5, first strand: chain 'U' and resid 3 through 6 Processing sheet with id=AG6, first strand: chain 'U' and resid 10 through 11 removed outlier: 6.605A pdb=" N GLU U 10 " --> pdb=" O THR U 110 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N TYR U 32 " --> pdb=" O ILE U 52 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE U 52 " --> pdb=" O TYR U 32 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N PHE U 34 " --> pdb=" O ARG U 50 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ARG U 50 " --> pdb=" O PHE U 34 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TRP U 36 " --> pdb=" O MET U 48 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'U' and resid 10 through 11 removed outlier: 6.605A pdb=" N GLU U 10 " --> pdb=" O THR U 110 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY U 94 " --> pdb=" O HIS U 102 " (cutoff:3.500A) 858 hydrogen bonds defined for protein. 2148 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: 9.80 Time building geometry restraints manager: 6.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 8002 1.36 - 1.49: 6661 1.49 - 1.63: 10207 1.63 - 1.76: 0 1.76 - 1.90: 180 Bond restraints: 25050 Sorted by residual: bond pdb=" C1 NAG V 1 " pdb=" O5 NAG V 1 " ideal model delta sigma weight residual 1.406 1.502 -0.096 2.00e-02 2.50e+03 2.30e+01 bond pdb=" C1 BMA a 3 " pdb=" C2 BMA a 3 " ideal model delta sigma weight residual 1.519 1.595 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C3 BMA V 3 " pdb=" O3 BMA V 3 " ideal model delta sigma weight residual 1.406 1.474 -0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" C1 BMA a 3 " pdb=" O5 BMA a 3 " ideal model delta sigma weight residual 1.410 1.475 -0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" C1 BMA f 3 " pdb=" C2 BMA f 3 " ideal model delta sigma weight residual 1.519 1.579 -0.060 2.00e-02 2.50e+03 8.96e+00 ... (remaining 25045 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.13: 33383 3.13 - 6.26: 539 6.26 - 9.40: 78 9.40 - 12.53: 23 12.53 - 15.66: 3 Bond angle restraints: 34026 Sorted by residual: angle pdb=" CA ARG K 82B" pdb=" CB ARG K 82B" pdb=" CG ARG K 82B" ideal model delta sigma weight residual 114.10 124.47 -10.37 2.00e+00 2.50e-01 2.69e+01 angle pdb=" C GLU C 64 " pdb=" N LYS C 65 " pdb=" CA LYS C 65 " ideal model delta sigma weight residual 121.54 131.37 -9.83 1.91e+00 2.74e-01 2.65e+01 angle pdb=" CB LYS K 13 " pdb=" CG LYS K 13 " pdb=" CD LYS K 13 " ideal model delta sigma weight residual 111.30 123.05 -11.75 2.30e+00 1.89e-01 2.61e+01 angle pdb=" C GLU M 87 " pdb=" N ASP M 88 " pdb=" CA ASP M 88 " ideal model delta sigma weight residual 121.54 131.07 -9.53 1.91e+00 2.74e-01 2.49e+01 angle pdb=" C LYS O 72 " pdb=" N ASN O 73 " pdb=" CA ASN O 73 " ideal model delta sigma weight residual 121.54 131.06 -9.52 1.91e+00 2.74e-01 2.48e+01 ... (remaining 34021 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.40: 14100 23.40 - 46.79: 864 46.79 - 70.19: 97 70.19 - 93.58: 44 93.58 - 116.98: 28 Dihedral angle restraints: 15133 sinusoidal: 6115 harmonic: 9018 Sorted by residual: dihedral pdb=" CA TRP T 94 " pdb=" C TRP T 94 " pdb=" N PRO T 95 " pdb=" CA PRO T 95 " ideal model delta harmonic sigma weight residual 180.00 117.35 62.65 0 5.00e+00 4.00e-02 1.57e+02 dihedral pdb=" CB CYS B 126 " pdb=" SG CYS B 126 " pdb=" SG CYS B 196 " pdb=" CB CYS B 196 " ideal model delta sinusoidal sigma weight residual 93.00 6.68 86.32 1 1.00e+01 1.00e-02 8.98e+01 dihedral pdb=" CB CYS A 501 " pdb=" SG CYS A 501 " pdb=" SG CYS D 605 " pdb=" CB CYS D 605 " ideal model delta sinusoidal sigma weight residual -86.00 -141.38 55.38 1 1.00e+01 1.00e-02 4.15e+01 ... (remaining 15130 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.205: 3845 0.205 - 0.410: 25 0.410 - 0.616: 4 0.616 - 0.821: 0 0.821 - 1.026: 1 Chirality restraints: 3875 Sorted by residual: chirality pdb=" C1 NAG a 1 " pdb=" ND2 ASN B 88 " pdb=" C2 NAG a 1 " pdb=" O5 NAG a 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.37 -1.03 2.00e-01 2.50e+01 2.63e+01 chirality pdb=" C1 NAG V 1 " pdb=" ND2 ASN A 88 " pdb=" C2 NAG V 1 " pdb=" O5 NAG V 1 " both_signs ideal model delta sigma weight residual False -2.40 -3.00 0.60 2.00e-01 2.50e+01 8.91e+00 chirality pdb=" C4 NAG V 1 " pdb=" C3 NAG V 1 " pdb=" C5 NAG V 1 " pdb=" O4 NAG V 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.09 -0.44 2.00e-01 2.50e+01 4.82e+00 ... (remaining 3872 not shown) Planarity restraints: 4326 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 436 " 0.068 5.00e-02 4.00e+02 1.04e-01 1.73e+01 pdb=" N PRO C 437 " -0.180 5.00e-02 4.00e+02 pdb=" CA PRO C 437 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO C 437 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 112 " 0.027 2.00e-02 2.50e+03 2.33e-02 1.36e+01 pdb=" CG TRP A 112 " -0.063 2.00e-02 2.50e+03 pdb=" CD1 TRP A 112 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP A 112 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 112 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 112 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 112 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 112 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 112 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 112 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE O 67 " -0.022 2.00e-02 2.50e+03 2.61e-02 1.19e+01 pdb=" CG PHE O 67 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE O 67 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE O 67 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE O 67 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE O 67 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE O 67 " -0.001 2.00e-02 2.50e+03 ... (remaining 4323 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4988 2.79 - 3.32: 20060 3.32 - 3.84: 39164 3.84 - 4.37: 43203 4.37 - 4.90: 76224 Nonbonded interactions: 183639 Sorted by model distance: nonbonded pdb=" O TYR P 49 " pdb=" OG1 THR P 53 " model vdw 2.258 3.040 nonbonded pdb=" O TYR T 49 " pdb=" OG1 THR T 53 " model vdw 2.260 3.040 nonbonded pdb=" O TYR L 49 " pdb=" OG1 THR L 53 " model vdw 2.297 3.040 nonbonded pdb=" OE1 GLN B 328 " pdb=" NH1 ARG B 419 " model vdw 2.325 3.120 nonbonded pdb=" O GLY D 516 " pdb=" OH TYR G 97 " model vdw 2.332 3.040 ... (remaining 183634 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' selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and (resid 512 through 543 or resid 565 through 659 or resid 701)) selection = (chain 'E' and (resid 512 through 543 or resid 565 through 659 or resid 701)) selection = (chain 'F' and (resid 512 through 543 or resid 565 through 659 or resid 701)) } ncs_group { reference = (chain 'G' and resid 1 through 110) 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' } ncs_group { reference = chain 'P' selection = chain 'R' selection = chain 'T' } ncs_group { reference = chain 'Q' selection = chain 'S' selection = chain 'U' } ncs_group { reference = chain 'V' selection = chain 'a' selection = chain 'f' } 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: 2.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.050 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 56.670 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.160 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 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 0.096 25113 Z= 0.228 Angle : 1.016 19.625 34170 Z= 0.499 Chirality : 0.061 1.026 3875 Planarity : 0.007 0.105 4320 Dihedral : 15.812 116.975 9200 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.72 % Favored : 94.22 % Rotamer: Outliers : 0.11 % Allowed : 0.42 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.20 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.14), residues: 3079 helix: -1.88 (0.23), residues: 374 sheet: 0.03 (0.17), residues: 950 loop : -1.84 (0.13), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.003 TRP A 112 HIS 0.009 0.001 HIS A 105 PHE 0.060 0.002 PHE O 67 TYR 0.036 0.002 TYR J 49 ARG 0.023 0.001 ARG J 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00882 ( 6) link_NAG-ASN : angle 8.66610 ( 18) link_ALPHA1-6 : bond 0.00561 ( 3) link_ALPHA1-6 : angle 1.66678 ( 9) link_BETA1-4 : bond 0.02124 ( 6) link_BETA1-4 : angle 6.23680 ( 18) link_ALPHA1-3 : bond 0.00487 ( 3) link_ALPHA1-3 : angle 3.16396 ( 9) hydrogen bonds : bond 0.14142 ( 809) hydrogen bonds : angle 7.10852 ( 2148) SS BOND : bond 0.00679 ( 45) SS BOND : angle 2.04732 ( 90) covalent geometry : bond 0.00483 (25050) covalent geometry : angle 0.98073 (34026) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 698 time to evaluate : 2.911 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9185 (tpp) cc_final: 0.8968 (tpt) REVERT: A 230 ASP cc_start: 0.9049 (t0) cc_final: 0.8712 (t0) REVERT: B 359 ILE cc_start: 0.8792 (mm) cc_final: 0.8565 (mm) REVERT: C 295 ASN cc_start: 0.7278 (t160) cc_final: 0.7002 (t0) REVERT: C 368 ASP cc_start: 0.8877 (m-30) cc_final: 0.8620 (m-30) REVERT: G 2 GLU cc_start: 0.7889 (pm20) cc_final: 0.7452 (pm20) REVERT: H 91 MET cc_start: 0.8685 (pmm) cc_final: 0.8477 (pmm) REVERT: I 82 VAL cc_start: 0.7975 (t) cc_final: 0.7730 (t) REVERT: J 79 GLN cc_start: 0.8140 (mm110) cc_final: 0.7836 (mm110) REVERT: J 91 MET cc_start: 0.7852 (ptp) cc_final: 0.7408 (ptp) REVERT: K 47 TRP cc_start: 0.7822 (t60) cc_final: 0.7133 (t60) REVERT: K 81 ASP cc_start: 0.6863 (m-30) cc_final: 0.6029 (p0) REVERT: K 100 VAL cc_start: 0.8254 (t) cc_final: 0.8012 (t) REVERT: M 52 ASN cc_start: 0.9112 (p0) cc_final: 0.8562 (p0) REVERT: N 53 ASP cc_start: 0.8160 (p0) cc_final: 0.7895 (p0) REVERT: N 95 LEU cc_start: 0.8873 (tp) cc_final: 0.8588 (tp) REVERT: O 96 LEU cc_start: 0.8105 (mm) cc_final: 0.7854 (mm) REVERT: P 4 MET cc_start: 0.7245 (tpp) cc_final: 0.7033 (tpt) REVERT: P 71 PHE cc_start: 0.6840 (m-10) cc_final: 0.6516 (m-10) REVERT: Q 47 TRP cc_start: 0.7339 (t60) cc_final: 0.7089 (t60) REVERT: Q 81 GLU cc_start: 0.6945 (tm-30) cc_final: 0.6492 (tm-30) REVERT: Q 82 ASN cc_start: 0.8318 (t0) cc_final: 0.7762 (t0) REVERT: S 48 MET cc_start: 0.7525 (mtm) cc_final: 0.7175 (mtm) REVERT: S 99 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7589 (mm-30) REVERT: T 82 ASP cc_start: 0.8734 (m-30) cc_final: 0.8298 (m-30) REVERT: U 19 LYS cc_start: 0.8945 (tmtt) cc_final: 0.8621 (tmtt) REVERT: U 100 ASN cc_start: 0.7877 (m-40) cc_final: 0.7673 (m-40) outliers start: 3 outliers final: 1 residues processed: 700 average time/residue: 0.3407 time to fit residues: 379.9229 Evaluate side-chains 567 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 566 time to evaluate : 2.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 465 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 255 optimal weight: 9.9990 chunk 229 optimal weight: 0.4980 chunk 127 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 154 optimal weight: 9.9990 chunk 122 optimal weight: 2.9990 chunk 237 optimal weight: 8.9990 chunk 91 optimal weight: 6.9990 chunk 144 optimal weight: 3.9990 chunk 176 optimal weight: 10.0000 chunk 275 optimal weight: 10.0000 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN B 283 ASN C 67 ASN ** C 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 ASN D 543 ASN E 607 ASN E 658 GLN ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 35 HIS ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 100 ASN L 3 GLN L 38 GLN L 70 HIS M 20 GLN M 32 ASN N 25 GLN ** O 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 38 GLN Q 62 HIS R 37 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.136125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.101132 restraints weight = 46590.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.098587 restraints weight = 37151.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.099891 restraints weight = 43113.331| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.097 25113 Z= 0.314 Angle : 0.813 21.684 34170 Z= 0.399 Chirality : 0.052 0.913 3875 Planarity : 0.006 0.077 4320 Dihedral : 10.169 114.023 3713 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.82 % Favored : 93.15 % Rotamer: Outliers : 2.62 % Allowed : 13.54 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.20 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.15), residues: 3079 helix: -0.90 (0.25), residues: 395 sheet: 0.06 (0.17), residues: 946 loop : -1.70 (0.14), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP G 50 HIS 0.007 0.002 HIS B 105 PHE 0.018 0.002 PHE A 53 TYR 0.023 0.002 TYR H 49 ARG 0.007 0.001 ARG K 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00345 ( 6) link_NAG-ASN : angle 7.92860 ( 18) link_ALPHA1-6 : bond 0.00323 ( 3) link_ALPHA1-6 : angle 2.54547 ( 9) link_BETA1-4 : bond 0.01409 ( 6) link_BETA1-4 : angle 5.62221 ( 18) link_ALPHA1-3 : bond 0.00305 ( 3) link_ALPHA1-3 : angle 3.23623 ( 9) hydrogen bonds : bond 0.04744 ( 809) hydrogen bonds : angle 5.73571 ( 2148) SS BOND : bond 0.00492 ( 45) SS BOND : angle 2.05947 ( 90) covalent geometry : bond 0.00733 (25050) covalent geometry : angle 0.77356 (34026) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 575 time to evaluate : 2.743 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 MET cc_start: 0.7988 (mmm) cc_final: 0.7767 (mmm) REVERT: A 434 MET cc_start: 0.8146 (tpt) cc_final: 0.7615 (tpt) REVERT: A 435 TYR cc_start: 0.9019 (m-80) cc_final: 0.8778 (m-10) REVERT: B 74 CYS cc_start: 0.6488 (m) cc_final: 0.6202 (m) REVERT: B 359 ILE cc_start: 0.8787 (mm) cc_final: 0.8449 (mm) REVERT: C 62 GLU cc_start: 0.8073 (tp30) cc_final: 0.7324 (tt0) REVERT: C 83 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7304 (tt0) REVERT: C 295 ASN cc_start: 0.7523 (t160) cc_final: 0.7106 (t0) REVERT: E 648 GLU cc_start: 0.8365 (tm-30) cc_final: 0.8098 (tm-30) REVERT: F 543 ASN cc_start: 0.8906 (m110) cc_final: 0.8287 (t0) REVERT: F 621 GLU cc_start: 0.8288 (pt0) cc_final: 0.8085 (pt0) REVERT: G 2 GLU cc_start: 0.8576 (pm20) cc_final: 0.8270 (pm20) REVERT: H 47 LEU cc_start: 0.9321 (mm) cc_final: 0.8876 (mm) REVERT: H 82 ASP cc_start: 0.8059 (m-30) cc_final: 0.7822 (m-30) REVERT: J 78 LEU cc_start: 0.8692 (mp) cc_final: 0.8341 (mp) REVERT: J 79 GLN cc_start: 0.8101 (mm110) cc_final: 0.7731 (mm110) REVERT: K 47 TRP cc_start: 0.8393 (t60) cc_final: 0.8025 (t60) REVERT: L 61 ARG cc_start: 0.8772 (ptp90) cc_final: 0.8235 (ptt180) REVERT: L 62 PHE cc_start: 0.8075 (m-80) cc_final: 0.7738 (m-10) REVERT: M 52 ASN cc_start: 0.9345 (p0) cc_final: 0.8781 (p0) REVERT: M 53 ASP cc_start: 0.9113 (p0) cc_final: 0.8746 (p0) REVERT: N 10 ASP cc_start: 0.8597 (t0) cc_final: 0.8370 (t70) REVERT: N 53 ASP cc_start: 0.8509 (p0) cc_final: 0.8264 (p0) REVERT: N 60 SER cc_start: 0.9213 (p) cc_final: 0.8892 (p) REVERT: P 46 LEU cc_start: 0.8847 (tt) cc_final: 0.8612 (pt) REVERT: P 71 PHE cc_start: 0.6693 (m-10) cc_final: 0.6204 (m-10) REVERT: Q 47 TRP cc_start: 0.7423 (t60) cc_final: 0.6596 (t60) REVERT: Q 81 GLU cc_start: 0.6924 (tm-30) cc_final: 0.6297 (tm-30) REVERT: Q 82 ASN cc_start: 0.8519 (t0) cc_final: 0.7882 (t0) REVERT: R 4 MET cc_start: 0.7541 (tpt) cc_final: 0.7336 (tpp) REVERT: R 27 GLU cc_start: 0.9042 (pm20) cc_final: 0.8603 (pm20) REVERT: R 95 ARG cc_start: 0.6584 (mmp80) cc_final: 0.6298 (mmp80) REVERT: S 32 TYR cc_start: 0.8418 (m-80) cc_final: 0.8093 (m-80) REVERT: S 46 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8301 (mm-30) REVERT: T 39 LYS cc_start: 0.8548 (mppt) cc_final: 0.8166 (mptt) REVERT: T 81 GLU cc_start: 0.8779 (pm20) cc_final: 0.8563 (pm20) REVERT: T 82 ASP cc_start: 0.8820 (m-30) cc_final: 0.8378 (m-30) outliers start: 69 outliers final: 54 residues processed: 609 average time/residue: 0.3462 time to fit residues: 333.6636 Evaluate side-chains 589 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 535 time to evaluate : 2.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain I residue 2 GLU Chi-restraints excluded: chain I residue 76 ASN Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain J residue 10 PHE Chi-restraints excluded: chain J residue 17 ASP Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain L residue 3 GLN Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain M residue 32 ASN Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 71 ILE Chi-restraints excluded: chain M residue 80 ASP Chi-restraints excluded: chain M residue 86 VAL Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 15 THR Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 42 SER Chi-restraints excluded: chain N residue 61 LEU Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain O residue 11 THR Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 86 VAL Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain Q residue 111 VAL Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain S residue 81 GLU Chi-restraints excluded: chain S residue 100 GLU Chi-restraints excluded: chain T residue 48 ILE Chi-restraints excluded: chain T residue 53 THR Chi-restraints excluded: chain U residue 74 SER Chi-restraints excluded: chain U residue 108 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 290 optimal weight: 5.9990 chunk 167 optimal weight: 7.9990 chunk 16 optimal weight: 0.7980 chunk 292 optimal weight: 20.0000 chunk 263 optimal weight: 10.0000 chunk 288 optimal weight: 9.9990 chunk 43 optimal weight: 0.6980 chunk 183 optimal weight: 7.9990 chunk 121 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 275 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 67 ASN E 607 ASN G 76 ASN H 89 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN L 38 GLN M 20 GLN M 32 ASN S 64 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.138352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.103369 restraints weight = 45983.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.100487 restraints weight = 34486.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.101135 restraints weight = 42054.047| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 25113 Z= 0.155 Angle : 0.674 19.097 34170 Z= 0.326 Chirality : 0.048 0.782 3875 Planarity : 0.004 0.074 4320 Dihedral : 8.647 110.433 3712 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.03 % Favored : 94.93 % Rotamer: Outliers : 3.04 % Allowed : 16.32 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.20 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.15), residues: 3079 helix: -0.19 (0.27), residues: 385 sheet: 0.20 (0.17), residues: 961 loop : -1.54 (0.14), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP G 50 HIS 0.004 0.001 HIS B 105 PHE 0.023 0.001 PHE R 71 TYR 0.025 0.002 TYR H 49 ARG 0.013 0.001 ARG R 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00524 ( 6) link_NAG-ASN : angle 7.14483 ( 18) link_ALPHA1-6 : bond 0.00498 ( 3) link_ALPHA1-6 : angle 2.14019 ( 9) link_BETA1-4 : bond 0.01375 ( 6) link_BETA1-4 : angle 5.11361 ( 18) link_ALPHA1-3 : bond 0.00292 ( 3) link_ALPHA1-3 : angle 3.20350 ( 9) hydrogen bonds : bond 0.03761 ( 809) hydrogen bonds : angle 5.37396 ( 2148) SS BOND : bond 0.00405 ( 45) SS BOND : angle 1.49048 ( 90) covalent geometry : bond 0.00359 (25050) covalent geometry : angle 0.63651 (34026) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 591 time to evaluate : 2.967 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 74 CYS cc_start: 0.6518 (m) cc_final: 0.6203 (m) REVERT: B 359 ILE cc_start: 0.8749 (mm) cc_final: 0.8546 (mm) REVERT: C 62 GLU cc_start: 0.8027 (tp30) cc_final: 0.7208 (tt0) REVERT: C 83 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7242 (tt0) REVERT: C 104 MET cc_start: 0.8679 (tpp) cc_final: 0.8472 (ttt) REVERT: E 648 GLU cc_start: 0.8429 (tm-30) cc_final: 0.8079 (tm-30) REVERT: F 543 ASN cc_start: 0.8847 (m110) cc_final: 0.8382 (t0) REVERT: G 2 GLU cc_start: 0.8614 (pm20) cc_final: 0.8281 (pm20) REVERT: G 100 MET cc_start: 0.8436 (mmm) cc_final: 0.8214 (mmt) REVERT: H 47 LEU cc_start: 0.9309 (mm) cc_final: 0.8916 (mm) REVERT: J 49 TYR cc_start: 0.8438 (p90) cc_final: 0.8139 (p90) REVERT: J 78 LEU cc_start: 0.8422 (mp) cc_final: 0.8142 (mp) REVERT: J 79 GLN cc_start: 0.8067 (mm110) cc_final: 0.7655 (mm110) REVERT: J 82 ASP cc_start: 0.8514 (m-30) cc_final: 0.8272 (m-30) REVERT: K 47 TRP cc_start: 0.8410 (t60) cc_final: 0.7979 (t60) REVERT: L 4 LEU cc_start: 0.8255 (mt) cc_final: 0.7986 (mt) REVERT: L 61 ARG cc_start: 0.8826 (ptp90) cc_final: 0.8197 (ptt180) REVERT: L 62 PHE cc_start: 0.8110 (m-80) cc_final: 0.7814 (m-10) REVERT: M 52 ASN cc_start: 0.9348 (p0) cc_final: 0.8777 (p0) REVERT: M 53 ASP cc_start: 0.9148 (p0) cc_final: 0.8770 (p0) REVERT: N 10 ASP cc_start: 0.8655 (t0) cc_final: 0.8394 (t70) REVERT: N 53 ASP cc_start: 0.8472 (p0) cc_final: 0.8225 (p0) REVERT: O 24 ILE cc_start: 0.9269 (mm) cc_final: 0.8744 (mt) REVERT: P 33 LEU cc_start: 0.7990 (tp) cc_final: 0.7757 (mt) REVERT: P 46 LEU cc_start: 0.8849 (tt) cc_final: 0.8638 (pt) REVERT: P 71 PHE cc_start: 0.6947 (m-10) cc_final: 0.6433 (m-10) REVERT: Q 81 GLU cc_start: 0.6749 (tm-30) cc_final: 0.6180 (tm-30) REVERT: R 27 GLU cc_start: 0.9020 (pm20) cc_final: 0.8506 (pm20) REVERT: S 32 TYR cc_start: 0.8427 (m-80) cc_final: 0.8096 (m-80) REVERT: S 46 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8339 (mm-30) REVERT: S 100 PHE cc_start: 0.8637 (p90) cc_final: 0.8327 (p90) REVERT: T 39 LYS cc_start: 0.8623 (mppt) cc_final: 0.8273 (mmtm) REVERT: T 81 GLU cc_start: 0.8833 (pm20) cc_final: 0.8502 (pm20) REVERT: T 82 ASP cc_start: 0.8781 (m-30) cc_final: 0.8233 (m-30) REVERT: T 94 TRP cc_start: 0.8215 (t-100) cc_final: 0.7692 (t-100) REVERT: U 10 GLU cc_start: 0.7927 (tt0) cc_final: 0.7596 (tt0) REVERT: U 12 LYS cc_start: 0.9079 (tptt) cc_final: 0.8719 (tptt) outliers start: 80 outliers final: 59 residues processed: 628 average time/residue: 0.3456 time to fit residues: 343.7813 Evaluate side-chains 603 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 544 time to evaluate : 2.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain E residue 603 ILE Chi-restraints excluded: chain E residue 607 ASN Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain I residue 2 GLU Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain J residue 10 PHE Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 63 ASP Chi-restraints excluded: chain M residue 80 ASP Chi-restraints excluded: chain M residue 86 VAL Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 42 SER Chi-restraints excluded: chain N residue 61 LEU Chi-restraints excluded: chain N residue 86 VAL Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 86 VAL Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain Q residue 53 ILE Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 39 LYS Chi-restraints excluded: chain R residue 53 THR Chi-restraints excluded: chain S residue 100 GLU Chi-restraints excluded: chain T residue 48 ILE Chi-restraints excluded: chain T residue 53 THR Chi-restraints excluded: chain T residue 102 THR Chi-restraints excluded: chain U residue 63 LEU Chi-restraints excluded: chain U residue 74 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 117 optimal weight: 2.9990 chunk 172 optimal weight: 5.9990 chunk 120 optimal weight: 0.3980 chunk 260 optimal weight: 30.0000 chunk 299 optimal weight: 10.0000 chunk 6 optimal weight: 0.1980 chunk 3 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 190 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 106 optimal weight: 0.0770 overall best weight: 1.5342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 6 GLN ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 ASN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN L 38 GLN S 64 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.138019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.102767 restraints weight = 46599.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.100691 restraints weight = 36682.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.102151 restraints weight = 40301.594| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 25113 Z= 0.162 Angle : 0.680 17.166 34170 Z= 0.325 Chirality : 0.046 0.394 3875 Planarity : 0.004 0.071 4320 Dihedral : 8.175 107.290 3712 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.91 % Favored : 94.06 % Rotamer: Outliers : 3.54 % Allowed : 18.60 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.20 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.15), residues: 3079 helix: -0.02 (0.28), residues: 390 sheet: 0.26 (0.17), residues: 961 loop : -1.47 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP G 50 HIS 0.005 0.001 HIS L 90 PHE 0.018 0.001 PHE R 71 TYR 0.025 0.002 TYR H 49 ARG 0.007 0.000 ARG K 38 Details of bonding type rmsd link_NAG-ASN : bond 0.01221 ( 6) link_NAG-ASN : angle 7.81308 ( 18) link_ALPHA1-6 : bond 0.00491 ( 3) link_ALPHA1-6 : angle 2.15037 ( 9) link_BETA1-4 : bond 0.01291 ( 6) link_BETA1-4 : angle 4.91818 ( 18) link_ALPHA1-3 : bond 0.00159 ( 3) link_ALPHA1-3 : angle 3.27715 ( 9) hydrogen bonds : bond 0.03563 ( 809) hydrogen bonds : angle 5.18898 ( 2148) SS BOND : bond 0.00405 ( 45) SS BOND : angle 1.66099 ( 90) covalent geometry : bond 0.00377 (25050) covalent geometry : angle 0.63879 (34026) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 574 time to evaluate : 2.753 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: B 74 CYS cc_start: 0.6479 (m) cc_final: 0.6233 (m) REVERT: C 62 GLU cc_start: 0.8015 (tp30) cc_final: 0.7244 (tt0) REVERT: C 83 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7695 (tm-30) REVERT: C 475 MET cc_start: 0.8599 (mmm) cc_final: 0.8392 (mmm) REVERT: E 540 GLN cc_start: 0.7786 (OUTLIER) cc_final: 0.7190 (mt0) REVERT: E 648 GLU cc_start: 0.8491 (tm-30) cc_final: 0.8064 (tm-30) REVERT: F 543 ASN cc_start: 0.8868 (m110) cc_final: 0.8305 (t0) REVERT: G 2 GLU cc_start: 0.8631 (pm20) cc_final: 0.8303 (pm20) REVERT: G 97 TYR cc_start: 0.8927 (t80) cc_final: 0.8574 (t80) REVERT: G 100 MET cc_start: 0.8456 (mmm) cc_final: 0.8020 (mmt) REVERT: H 47 LEU cc_start: 0.9331 (mm) cc_final: 0.8946 (mm) REVERT: H 61 ARG cc_start: 0.8344 (ptp-170) cc_final: 0.8089 (ptp-170) REVERT: I 47 TRP cc_start: 0.8568 (t60) cc_final: 0.8264 (t60) REVERT: J 49 TYR cc_start: 0.8383 (p90) cc_final: 0.8074 (p90) REVERT: J 78 LEU cc_start: 0.8586 (mp) cc_final: 0.8349 (mp) REVERT: J 79 GLN cc_start: 0.8108 (mm110) cc_final: 0.7458 (mm110) REVERT: J 82 ASP cc_start: 0.8618 (m-30) cc_final: 0.8408 (m-30) REVERT: K 47 TRP cc_start: 0.8289 (t60) cc_final: 0.7834 (t60) REVERT: K 50 TRP cc_start: 0.8193 (p-90) cc_final: 0.7931 (p-90) REVERT: L 4 LEU cc_start: 0.8284 (mt) cc_final: 0.8069 (mt) REVERT: L 82 ASP cc_start: 0.8190 (m-30) cc_final: 0.7819 (m-30) REVERT: M 52 ASN cc_start: 0.9304 (p0) cc_final: 0.8724 (p0) REVERT: M 53 ASP cc_start: 0.9107 (p0) cc_final: 0.8728 (p0) REVERT: N 53 ASP cc_start: 0.8431 (p0) cc_final: 0.8166 (p0) REVERT: O 24 ILE cc_start: 0.9240 (mm) cc_final: 0.8777 (mt) REVERT: P 33 LEU cc_start: 0.7914 (tp) cc_final: 0.7655 (mt) REVERT: P 46 LEU cc_start: 0.8814 (tt) cc_final: 0.8578 (pt) REVERT: P 71 PHE cc_start: 0.6814 (m-10) cc_final: 0.6238 (m-10) REVERT: Q 47 TRP cc_start: 0.7608 (t60) cc_final: 0.6913 (t60) REVERT: Q 81 GLU cc_start: 0.6816 (tm-30) cc_final: 0.6223 (tm-30) REVERT: R 27 GLU cc_start: 0.9053 (pm20) cc_final: 0.8851 (pm20) REVERT: S 46 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8262 (mm-30) REVERT: S 82 ASN cc_start: 0.8600 (t0) cc_final: 0.8294 (t0) REVERT: S 100 PHE cc_start: 0.8595 (p90) cc_final: 0.8256 (p90) REVERT: S 105 GLN cc_start: 0.8685 (pm20) cc_final: 0.8336 (pm20) REVERT: T 39 LYS cc_start: 0.8773 (mppt) cc_final: 0.8194 (mmtm) REVERT: T 81 GLU cc_start: 0.8801 (pm20) cc_final: 0.8494 (pm20) REVERT: T 82 ASP cc_start: 0.8790 (m-30) cc_final: 0.8303 (m-30) REVERT: T 94 TRP cc_start: 0.8101 (t-100) cc_final: 0.7736 (t-100) REVERT: U 10 GLU cc_start: 0.7738 (tt0) cc_final: 0.7386 (tt0) REVERT: U 12 LYS cc_start: 0.9000 (tptt) cc_final: 0.8659 (tptt) REVERT: U 99 GLU cc_start: 0.7987 (mp0) cc_final: 0.7768 (mp0) outliers start: 93 outliers final: 68 residues processed: 619 average time/residue: 0.3371 time to fit residues: 330.7047 Evaluate side-chains 619 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 550 time to evaluate : 3.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain E residue 540 GLN Chi-restraints excluded: chain E residue 603 ILE Chi-restraints excluded: chain E residue 604 CYS Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain I residue 2 GLU Chi-restraints excluded: chain I residue 20 VAL Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain J residue 10 PHE Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 63 ASP Chi-restraints excluded: chain M residue 80 ASP Chi-restraints excluded: chain M residue 86 VAL Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 42 SER Chi-restraints excluded: chain N residue 61 LEU Chi-restraints excluded: chain N residue 86 VAL Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain O residue 11 THR Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 86 VAL Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain Q residue 53 ILE Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 53 THR Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain S residue 100 GLU Chi-restraints excluded: chain T residue 48 ILE Chi-restraints excluded: chain T residue 53 THR Chi-restraints excluded: chain T residue 102 THR Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 63 LEU Chi-restraints excluded: chain U residue 74 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 6 optimal weight: 0.0980 chunk 92 optimal weight: 9.9990 chunk 53 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 142 optimal weight: 0.8980 chunk 167 optimal weight: 5.9990 chunk 199 optimal weight: 0.9990 chunk 286 optimal weight: 20.0000 chunk 139 optimal weight: 0.6980 chunk 253 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN L 38 GLN R 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.138977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.104434 restraints weight = 46498.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.101771 restraints weight = 35442.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.102955 restraints weight = 39859.514| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 25113 Z= 0.135 Angle : 0.662 17.577 34170 Z= 0.315 Chirality : 0.045 0.392 3875 Planarity : 0.004 0.072 4320 Dihedral : 7.728 106.674 3712 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.87 % Favored : 95.10 % Rotamer: Outliers : 3.27 % Allowed : 20.01 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.20 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.15), residues: 3079 helix: 0.16 (0.28), residues: 390 sheet: 0.32 (0.18), residues: 961 loop : -1.39 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP G 50 HIS 0.004 0.001 HIS L 90 PHE 0.017 0.001 PHE R 71 TYR 0.027 0.001 TYR H 49 ARG 0.006 0.000 ARG K 38 Details of bonding type rmsd link_NAG-ASN : bond 0.01170 ( 6) link_NAG-ASN : angle 7.65003 ( 18) link_ALPHA1-6 : bond 0.00555 ( 3) link_ALPHA1-6 : angle 2.13766 ( 9) link_BETA1-4 : bond 0.01268 ( 6) link_BETA1-4 : angle 4.67094 ( 18) link_ALPHA1-3 : bond 0.00365 ( 3) link_ALPHA1-3 : angle 3.33157 ( 9) hydrogen bonds : bond 0.03303 ( 809) hydrogen bonds : angle 5.03676 ( 2148) SS BOND : bond 0.00415 ( 45) SS BOND : angle 1.61510 ( 90) covalent geometry : bond 0.00314 (25050) covalent geometry : angle 0.62191 (34026) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 580 time to evaluate : 2.845 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: symmetry clash REVERT: B 74 CYS cc_start: 0.6477 (m) cc_final: 0.6219 (m) REVERT: C 62 GLU cc_start: 0.8010 (tp30) cc_final: 0.7254 (tt0) REVERT: C 83 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7566 (tm-30) REVERT: C 475 MET cc_start: 0.8592 (mmm) cc_final: 0.8380 (mmm) REVERT: E 540 GLN cc_start: 0.7709 (OUTLIER) cc_final: 0.7277 (mt0) REVERT: E 648 GLU cc_start: 0.8483 (tm-30) cc_final: 0.7721 (tm-30) REVERT: F 543 ASN cc_start: 0.8832 (m110) cc_final: 0.8304 (t0) REVERT: G 2 GLU cc_start: 0.8619 (pm20) cc_final: 0.8304 (pm20) REVERT: G 97 TYR cc_start: 0.8927 (t80) cc_final: 0.8511 (t80) REVERT: G 100 MET cc_start: 0.8496 (mmm) cc_final: 0.7921 (mmt) REVERT: H 47 LEU cc_start: 0.9271 (mm) cc_final: 0.8956 (mm) REVERT: H 61 ARG cc_start: 0.8450 (ptp-170) cc_final: 0.8171 (ptp-170) REVERT: I 47 TRP cc_start: 0.8601 (t60) cc_final: 0.8285 (t60) REVERT: I 105 GLN cc_start: 0.8789 (pm20) cc_final: 0.8564 (pm20) REVERT: J 49 TYR cc_start: 0.8352 (p90) cc_final: 0.8071 (p90) REVERT: J 79 GLN cc_start: 0.8106 (mm110) cc_final: 0.7423 (mm110) REVERT: J 82 ASP cc_start: 0.8494 (m-30) cc_final: 0.8280 (m-30) REVERT: K 47 TRP cc_start: 0.8368 (t60) cc_final: 0.7961 (t60) REVERT: L 32 GLU cc_start: 0.7515 (mp0) cc_final: 0.6876 (pm20) REVERT: L 61 ARG cc_start: 0.8693 (ptt-90) cc_final: 0.7815 (ptt180) REVERT: M 52 ASN cc_start: 0.9278 (p0) cc_final: 0.8722 (p0) REVERT: M 53 ASP cc_start: 0.9160 (p0) cc_final: 0.8814 (p0) REVERT: N 10 ASP cc_start: 0.8531 (t0) cc_final: 0.8269 (t70) REVERT: N 53 ASP cc_start: 0.8430 (p0) cc_final: 0.8168 (p0) REVERT: O 24 ILE cc_start: 0.9256 (mm) cc_final: 0.8790 (mt) REVERT: P 33 LEU cc_start: 0.7825 (tp) cc_final: 0.7600 (mt) REVERT: P 46 LEU cc_start: 0.8786 (tt) cc_final: 0.8573 (pt) REVERT: P 71 PHE cc_start: 0.6849 (m-10) cc_final: 0.6259 (m-10) REVERT: Q 81 GLU cc_start: 0.6668 (tm-30) cc_final: 0.6075 (tm-30) REVERT: R 24 ARG cc_start: 0.7464 (mmp80) cc_final: 0.7049 (mmp80) REVERT: R 27 GLU cc_start: 0.9046 (pm20) cc_final: 0.8475 (pm20) REVERT: S 32 TYR cc_start: 0.8444 (m-80) cc_final: 0.8027 (m-80) REVERT: S 46 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8309 (mm-30) REVERT: S 100 PHE cc_start: 0.8615 (p90) cc_final: 0.8242 (p90) REVERT: S 105 GLN cc_start: 0.8605 (pm20) cc_final: 0.8262 (pm20) REVERT: T 39 LYS cc_start: 0.8561 (mppt) cc_final: 0.8318 (mmtm) REVERT: T 81 GLU cc_start: 0.8858 (pm20) cc_final: 0.8550 (pm20) REVERT: T 82 ASP cc_start: 0.8745 (m-30) cc_final: 0.8216 (m-30) REVERT: T 94 TRP cc_start: 0.8064 (t-100) cc_final: 0.7721 (t-100) REVERT: U 10 GLU cc_start: 0.7834 (tt0) cc_final: 0.7530 (tt0) REVERT: U 12 LYS cc_start: 0.8994 (tptt) cc_final: 0.8700 (tptt) REVERT: U 99 GLU cc_start: 0.7945 (mp0) cc_final: 0.7695 (mp0) outliers start: 86 outliers final: 65 residues processed: 625 average time/residue: 0.3395 time to fit residues: 336.9681 Evaluate side-chains 616 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 550 time to evaluate : 2.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain E residue 540 GLN Chi-restraints excluded: chain E residue 603 ILE Chi-restraints excluded: chain E residue 604 CYS Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain I residue 2 GLU Chi-restraints excluded: chain I residue 20 VAL Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain J residue 10 PHE Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain K residue 100 MET Chi-restraints excluded: chain L residue 3 GLN Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 63 ASP Chi-restraints excluded: chain M residue 86 VAL Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 42 SER Chi-restraints excluded: chain N residue 61 LEU Chi-restraints excluded: chain N residue 86 VAL Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain O residue 11 THR Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 86 VAL Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain Q residue 53 ILE Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 53 THR Chi-restraints excluded: chain S residue 100 GLU Chi-restraints excluded: chain T residue 48 ILE Chi-restraints excluded: chain T residue 53 THR Chi-restraints excluded: chain T residue 102 THR Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 74 SER Chi-restraints excluded: chain U residue 100 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 296 optimal weight: 4.9990 chunk 209 optimal weight: 6.9990 chunk 211 optimal weight: 10.0000 chunk 160 optimal weight: 2.9990 chunk 271 optimal weight: 8.9990 chunk 217 optimal weight: 8.9990 chunk 31 optimal weight: 6.9990 chunk 289 optimal weight: 10.0000 chunk 120 optimal weight: 3.9990 chunk 108 optimal weight: 0.6980 chunk 218 optimal weight: 9.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 658 GLN ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 20 GLN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 64 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.133851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.099400 restraints weight = 46644.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.096862 restraints weight = 35887.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.098041 restraints weight = 42806.600| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.069 25113 Z= 0.343 Angle : 0.815 18.885 34170 Z= 0.398 Chirality : 0.049 0.389 3875 Planarity : 0.005 0.075 4320 Dihedral : 7.835 105.774 3712 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.53 % Favored : 92.43 % Rotamer: Outliers : 4.11 % Allowed : 21.07 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.20 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.15), residues: 3079 helix: -0.29 (0.27), residues: 388 sheet: 0.18 (0.17), residues: 979 loop : -1.57 (0.14), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP G 36 HIS 0.010 0.002 HIS B 105 PHE 0.020 0.002 PHE A 53 TYR 0.026 0.002 TYR J 94 ARG 0.007 0.001 ARG K 38 Details of bonding type rmsd link_NAG-ASN : bond 0.01000 ( 6) link_NAG-ASN : angle 8.38488 ( 18) link_ALPHA1-6 : bond 0.00498 ( 3) link_ALPHA1-6 : angle 2.54758 ( 9) link_BETA1-4 : bond 0.01086 ( 6) link_BETA1-4 : angle 5.26103 ( 18) link_ALPHA1-3 : bond 0.00317 ( 3) link_ALPHA1-3 : angle 3.12813 ( 9) hydrogen bonds : bond 0.04547 ( 809) hydrogen bonds : angle 5.36559 ( 2148) SS BOND : bond 0.00900 ( 45) SS BOND : angle 1.99933 ( 90) covalent geometry : bond 0.00801 (25050) covalent geometry : angle 0.77506 (34026) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 572 time to evaluate : 3.140 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: B 74 CYS cc_start: 0.6530 (m) cc_final: 0.6230 (m) REVERT: C 83 GLU cc_start: 0.7793 (tm-30) cc_final: 0.7527 (tm-30) REVERT: C 475 MET cc_start: 0.8730 (mmm) cc_final: 0.8522 (mmm) REVERT: E 648 GLU cc_start: 0.8493 (tm-30) cc_final: 0.8233 (tm-30) REVERT: E 656 ASN cc_start: 0.7938 (t0) cc_final: 0.7602 (t0) REVERT: E 658 GLN cc_start: 0.8093 (mt0) cc_final: 0.7845 (mt0) REVERT: F 543 ASN cc_start: 0.9013 (m110) cc_final: 0.8363 (t0) REVERT: G 1 GLN cc_start: 0.7092 (tp40) cc_final: 0.6768 (tp40) REVERT: G 2 GLU cc_start: 0.8650 (pm20) cc_final: 0.8334 (pm20) REVERT: G 97 TYR cc_start: 0.9165 (t80) cc_final: 0.8656 (t80) REVERT: H 47 LEU cc_start: 0.9336 (mm) cc_final: 0.8934 (mm) REVERT: I 47 TRP cc_start: 0.8709 (t60) cc_final: 0.8371 (t60) REVERT: J 79 GLN cc_start: 0.8045 (mm110) cc_final: 0.7598 (mm110) REVERT: J 85 THR cc_start: 0.8412 (OUTLIER) cc_final: 0.8204 (p) REVERT: J 86 TYR cc_start: 0.8256 (m-10) cc_final: 0.7998 (m-10) REVERT: K 47 TRP cc_start: 0.8356 (t60) cc_final: 0.8107 (t60) REVERT: M 52 ASN cc_start: 0.9303 (p0) cc_final: 0.8785 (p0) REVERT: M 53 ASP cc_start: 0.9187 (p0) cc_final: 0.8961 (p0) REVERT: M 60 SER cc_start: 0.8945 (t) cc_final: 0.8704 (t) REVERT: N 10 ASP cc_start: 0.8530 (t0) cc_final: 0.8248 (t70) REVERT: N 53 ASP cc_start: 0.8485 (p0) cc_final: 0.8256 (p0) REVERT: N 60 SER cc_start: 0.9246 (p) cc_final: 0.8850 (p) REVERT: P 33 LEU cc_start: 0.8145 (tp) cc_final: 0.7872 (mt) REVERT: P 46 LEU cc_start: 0.8905 (tt) cc_final: 0.8618 (pt) REVERT: P 71 PHE cc_start: 0.6861 (m-10) cc_final: 0.6217 (m-10) REVERT: Q 81 GLU cc_start: 0.6960 (tm-30) cc_final: 0.6334 (tm-30) REVERT: S 32 TYR cc_start: 0.8617 (m-80) cc_final: 0.8369 (m-80) REVERT: S 46 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8447 (mm-30) REVERT: S 63 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7935 (pp) REVERT: S 100 PHE cc_start: 0.8870 (p90) cc_final: 0.8567 (p90) REVERT: T 81 GLU cc_start: 0.8983 (pm20) cc_final: 0.8715 (pm20) REVERT: T 82 ASP cc_start: 0.8738 (m-30) cc_final: 0.8252 (m-30) REVERT: T 94 TRP cc_start: 0.8122 (t-100) cc_final: 0.7915 (t-100) REVERT: U 12 LYS cc_start: 0.9010 (tptt) cc_final: 0.8110 (mmmm) REVERT: U 99 GLU cc_start: 0.7976 (mp0) cc_final: 0.7765 (mp0) REVERT: U 100 PHE cc_start: 0.8134 (p90) cc_final: 0.7902 (p90) outliers start: 108 outliers final: 86 residues processed: 635 average time/residue: 0.3599 time to fit residues: 366.9505 Evaluate side-chains 635 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 547 time to evaluate : 2.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 418 CYS Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain E residue 580 VAL Chi-restraints excluded: chain E residue 603 ILE Chi-restraints excluded: chain E residue 604 CYS Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain I residue 2 GLU Chi-restraints excluded: chain I residue 20 VAL Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain J residue 10 PHE Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain M residue 86 VAL Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 42 SER Chi-restraints excluded: chain N residue 61 LEU Chi-restraints excluded: chain N residue 86 VAL Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain O residue 11 THR Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 86 VAL Chi-restraints excluded: chain O residue 95 LEU Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 53 THR Chi-restraints excluded: chain R residue 89 GLN Chi-restraints excluded: chain S residue 63 LEU Chi-restraints excluded: chain S residue 78 VAL Chi-restraints excluded: chain S residue 100 GLU Chi-restraints excluded: chain T residue 48 ILE Chi-restraints excluded: chain T residue 53 THR Chi-restraints excluded: chain T residue 91 TYR Chi-restraints excluded: chain T residue 102 THR Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 63 LEU Chi-restraints excluded: chain U residue 74 SER Chi-restraints excluded: chain U residue 100 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 87 optimal weight: 2.9990 chunk 256 optimal weight: 9.9990 chunk 241 optimal weight: 9.9990 chunk 67 optimal weight: 1.9990 chunk 222 optimal weight: 0.0270 chunk 85 optimal weight: 0.9990 chunk 166 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 217 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 overall best weight: 1.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 HIS H 6 GLN ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN M 20 GLN N 20 GLN ** T 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.136226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.101354 restraints weight = 46683.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.099580 restraints weight = 35974.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.100571 restraints weight = 42360.349| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 25113 Z= 0.181 Angle : 0.718 17.355 34170 Z= 0.345 Chirality : 0.046 0.405 3875 Planarity : 0.005 0.070 4320 Dihedral : 7.181 102.271 3712 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.42 % Favored : 94.54 % Rotamer: Outliers : 3.80 % Allowed : 22.56 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.20 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.15), residues: 3079 helix: 0.01 (0.28), residues: 388 sheet: 0.20 (0.17), residues: 997 loop : -1.44 (0.15), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP G 36 HIS 0.006 0.001 HIS L 90 PHE 0.017 0.002 PHE L 87 TYR 0.027 0.002 TYR H 49 ARG 0.014 0.001 ARG K 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00975 ( 6) link_NAG-ASN : angle 7.59565 ( 18) link_ALPHA1-6 : bond 0.00569 ( 3) link_ALPHA1-6 : angle 2.19497 ( 9) link_BETA1-4 : bond 0.01303 ( 6) link_BETA1-4 : angle 4.79647 ( 18) link_ALPHA1-3 : bond 0.00608 ( 3) link_ALPHA1-3 : angle 3.36519 ( 9) hydrogen bonds : bond 0.03656 ( 809) hydrogen bonds : angle 5.11479 ( 2148) SS BOND : bond 0.00484 ( 45) SS BOND : angle 1.84867 ( 90) covalent geometry : bond 0.00425 (25050) covalent geometry : angle 0.67928 (34026) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 577 time to evaluate : 2.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 THR cc_start: 0.8895 (OUTLIER) cc_final: 0.8537 (t) REVERT: B 74 CYS cc_start: 0.6407 (m) cc_final: 0.6138 (m) REVERT: C 83 GLU cc_start: 0.7767 (tm-30) cc_final: 0.7533 (tm-30) REVERT: C 102 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.7921 (mt-10) REVERT: E 648 GLU cc_start: 0.8450 (tm-30) cc_final: 0.8191 (tm-30) REVERT: E 656 ASN cc_start: 0.7872 (t0) cc_final: 0.7633 (t0) REVERT: F 543 ASN cc_start: 0.8918 (m110) cc_final: 0.8402 (t0) REVERT: G 1 GLN cc_start: 0.7238 (tp40) cc_final: 0.6896 (tp40) REVERT: G 2 GLU cc_start: 0.8613 (pm20) cc_final: 0.8093 (pm20) REVERT: G 97 TYR cc_start: 0.9107 (t80) cc_final: 0.8637 (t80) REVERT: G 100 MET cc_start: 0.8537 (mmm) cc_final: 0.7757 (mmt) REVERT: H 24 ARG cc_start: 0.7969 (mmp-170) cc_final: 0.7530 (mmp-170) REVERT: H 47 LEU cc_start: 0.9361 (mm) cc_final: 0.9024 (mm) REVERT: I 47 TRP cc_start: 0.8638 (t60) cc_final: 0.8253 (t60) REVERT: J 81 GLU cc_start: 0.9015 (pm20) cc_final: 0.8763 (pm20) REVERT: J 85 THR cc_start: 0.8494 (OUTLIER) cc_final: 0.8276 (p) REVERT: J 86 TYR cc_start: 0.8100 (m-10) cc_final: 0.7799 (m-10) REVERT: K 38 ARG cc_start: 0.7785 (ttm110) cc_final: 0.7579 (ttm110) REVERT: K 47 TRP cc_start: 0.8300 (t60) cc_final: 0.7944 (t60) REVERT: K 81 ASP cc_start: 0.6906 (m-30) cc_final: 0.6106 (p0) REVERT: L 32 GLU cc_start: 0.7533 (mp0) cc_final: 0.7045 (pm20) REVERT: L 42 LYS cc_start: 0.8171 (mmmm) cc_final: 0.7915 (mtmm) REVERT: M 52 ASN cc_start: 0.9279 (p0) cc_final: 0.8747 (p0) REVERT: M 53 ASP cc_start: 0.9149 (p0) cc_final: 0.8920 (p0) REVERT: M 60 SER cc_start: 0.8919 (t) cc_final: 0.8682 (t) REVERT: N 10 ASP cc_start: 0.8416 (t0) cc_final: 0.8187 (t70) REVERT: N 53 ASP cc_start: 0.8439 (p0) cc_final: 0.8198 (p0) REVERT: O 24 ILE cc_start: 0.9295 (mm) cc_final: 0.8784 (mt) REVERT: P 71 PHE cc_start: 0.6907 (m-80) cc_final: 0.6321 (m-10) REVERT: Q 47 TRP cc_start: 0.7614 (t60) cc_final: 0.6834 (t60) REVERT: Q 81 GLU cc_start: 0.6938 (tm-30) cc_final: 0.6348 (tm-30) REVERT: R 24 ARG cc_start: 0.7389 (mmp80) cc_final: 0.7051 (mmp80) REVERT: S 32 TYR cc_start: 0.8487 (m-80) cc_final: 0.8207 (m-80) REVERT: S 46 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8377 (mm-30) REVERT: S 63 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7848 (pp) REVERT: S 100 PHE cc_start: 0.8769 (p90) cc_final: 0.8427 (p90) REVERT: T 81 GLU cc_start: 0.8839 (pm20) cc_final: 0.8617 (pm20) REVERT: T 82 ASP cc_start: 0.8793 (m-30) cc_final: 0.8335 (m-30) REVERT: U 12 LYS cc_start: 0.8866 (tptt) cc_final: 0.8653 (mttp) outliers start: 100 outliers final: 82 residues processed: 630 average time/residue: 0.3314 time to fit residues: 331.0508 Evaluate side-chains 637 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 551 time to evaluate : 2.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 418 CYS Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain E residue 603 ILE Chi-restraints excluded: chain E residue 604 CYS Chi-restraints excluded: chain E residue 627 THR Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain I residue 2 GLU Chi-restraints excluded: chain I residue 20 VAL Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain J residue 10 PHE Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain M residue 86 VAL Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 42 SER Chi-restraints excluded: chain N residue 45 THR Chi-restraints excluded: chain N residue 61 LEU Chi-restraints excluded: chain N residue 76 ILE Chi-restraints excluded: chain N residue 86 VAL Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain O residue 86 VAL Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 53 THR Chi-restraints excluded: chain S residue 63 LEU Chi-restraints excluded: chain S residue 78 VAL Chi-restraints excluded: chain S residue 100 GLU Chi-restraints excluded: chain T residue 48 ILE Chi-restraints excluded: chain T residue 53 THR Chi-restraints excluded: chain T residue 91 TYR Chi-restraints excluded: chain T residue 102 THR Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 63 LEU Chi-restraints excluded: chain U residue 74 SER Chi-restraints excluded: chain U residue 100 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 109 optimal weight: 4.9990 chunk 47 optimal weight: 0.3980 chunk 141 optimal weight: 9.9990 chunk 225 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 chunk 231 optimal weight: 5.9990 chunk 201 optimal weight: 10.0000 chunk 174 optimal weight: 10.0000 chunk 282 optimal weight: 30.0000 chunk 44 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 658 GLN F 656 ASN H 6 GLN ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.133558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.098992 restraints weight = 46464.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.095864 restraints weight = 33917.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.096918 restraints weight = 44411.073| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 25113 Z= 0.288 Angle : 0.795 17.655 34170 Z= 0.385 Chirality : 0.049 0.399 3875 Planarity : 0.005 0.071 4320 Dihedral : 7.224 99.376 3712 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.57 % Favored : 92.40 % Rotamer: Outliers : 4.53 % Allowed : 22.29 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.20 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.15), residues: 3079 helix: -0.21 (0.27), residues: 388 sheet: 0.11 (0.17), residues: 1006 loop : -1.54 (0.15), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP G 36 HIS 0.006 0.001 HIS C 105 PHE 0.017 0.002 PHE L 87 TYR 0.024 0.002 TYR T 96 ARG 0.014 0.001 ARG T 95B Details of bonding type rmsd link_NAG-ASN : bond 0.00913 ( 6) link_NAG-ASN : angle 7.97206 ( 18) link_ALPHA1-6 : bond 0.00542 ( 3) link_ALPHA1-6 : angle 2.48520 ( 9) link_BETA1-4 : bond 0.01187 ( 6) link_BETA1-4 : angle 5.10121 ( 18) link_ALPHA1-3 : bond 0.00117 ( 3) link_ALPHA1-3 : angle 2.83681 ( 9) hydrogen bonds : bond 0.04222 ( 809) hydrogen bonds : angle 5.24446 ( 2148) SS BOND : bond 0.00546 ( 45) SS BOND : angle 1.93955 ( 90) covalent geometry : bond 0.00673 (25050) covalent geometry : angle 0.75719 (34026) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 562 time to evaluate : 2.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 THR cc_start: 0.8947 (OUTLIER) cc_final: 0.8656 (t) REVERT: B 74 CYS cc_start: 0.6513 (m) cc_final: 0.6219 (m) REVERT: C 83 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7564 (tm-30) REVERT: C 102 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.7999 (mp0) REVERT: E 648 GLU cc_start: 0.8462 (tm-30) cc_final: 0.8190 (tm-30) REVERT: E 656 ASN cc_start: 0.8008 (t0) cc_final: 0.7708 (t0) REVERT: F 543 ASN cc_start: 0.8922 (m110) cc_final: 0.8429 (t0) REVERT: F 656 ASN cc_start: 0.8240 (OUTLIER) cc_final: 0.7988 (t160) REVERT: F 657 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7981 (tm-30) REVERT: G 1 GLN cc_start: 0.7285 (tp40) cc_final: 0.6996 (tp40) REVERT: G 2 GLU cc_start: 0.8629 (pm20) cc_final: 0.8256 (pm20) REVERT: G 97 TYR cc_start: 0.9208 (t80) cc_final: 0.8672 (t80) REVERT: G 100 MET cc_start: 0.8786 (mmm) cc_final: 0.7950 (mmt) REVERT: H 24 ARG cc_start: 0.7990 (mmp-170) cc_final: 0.7596 (mmp-170) REVERT: H 46 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.9032 (tt) REVERT: H 47 LEU cc_start: 0.9385 (mm) cc_final: 0.9015 (mm) REVERT: I 47 TRP cc_start: 0.8674 (t60) cc_final: 0.8318 (t60) REVERT: J 85 THR cc_start: 0.8519 (OUTLIER) cc_final: 0.8316 (p) REVERT: J 86 TYR cc_start: 0.8128 (m-10) cc_final: 0.7846 (m-10) REVERT: K 47 TRP cc_start: 0.8402 (t60) cc_final: 0.8154 (t60) REVERT: L 32 GLU cc_start: 0.7690 (mp0) cc_final: 0.7207 (pm20) REVERT: M 52 ASN cc_start: 0.9309 (p0) cc_final: 0.8830 (p0) REVERT: N 10 ASP cc_start: 0.8500 (t0) cc_final: 0.8239 (t0) REVERT: N 53 ASP cc_start: 0.8486 (p0) cc_final: 0.8283 (p0) REVERT: N 60 SER cc_start: 0.9215 (p) cc_final: 0.8897 (p) REVERT: O 24 ILE cc_start: 0.9294 (mm) cc_final: 0.8855 (mt) REVERT: P 46 LEU cc_start: 0.8940 (tt) cc_final: 0.8636 (pt) REVERT: P 71 PHE cc_start: 0.6895 (m-80) cc_final: 0.6384 (m-10) REVERT: Q 47 TRP cc_start: 0.7815 (t60) cc_final: 0.7133 (t60) REVERT: Q 81 GLU cc_start: 0.6971 (tm-30) cc_final: 0.6338 (tm-30) REVERT: R 24 ARG cc_start: 0.7403 (mmp80) cc_final: 0.6935 (mmp80) REVERT: R 92 ASN cc_start: 0.9201 (t0) cc_final: 0.8917 (t0) REVERT: R 95 ARG cc_start: 0.6853 (mmp80) cc_final: 0.6578 (mmp80) REVERT: S 32 TYR cc_start: 0.8603 (m-80) cc_final: 0.8312 (m-80) REVERT: S 46 GLU cc_start: 0.8766 (mm-30) cc_final: 0.8472 (mm-30) REVERT: S 63 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7882 (pp) REVERT: S 81 GLU cc_start: 0.7263 (tm-30) cc_final: 0.6521 (tm-30) REVERT: S 100 PHE cc_start: 0.8900 (p90) cc_final: 0.8563 (p90) REVERT: T 81 GLU cc_start: 0.8889 (pm20) cc_final: 0.8667 (pm20) REVERT: T 82 ASP cc_start: 0.8723 (m-30) cc_final: 0.8219 (m-30) REVERT: U 12 LYS cc_start: 0.8885 (tptt) cc_final: 0.8461 (mttp) outliers start: 119 outliers final: 100 residues processed: 625 average time/residue: 0.3471 time to fit residues: 345.9642 Evaluate side-chains 654 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 548 time to evaluate : 2.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 418 CYS Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain E residue 603 ILE Chi-restraints excluded: chain E residue 604 CYS Chi-restraints excluded: chain E residue 627 THR Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain E residue 645 LEU Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 656 ASN Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain I residue 2 GLU Chi-restraints excluded: chain I residue 20 VAL Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain J residue 10 PHE Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain M residue 74 LEU Chi-restraints excluded: chain M residue 86 VAL Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 15 THR Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 42 SER Chi-restraints excluded: chain N residue 45 THR Chi-restraints excluded: chain N residue 61 LEU Chi-restraints excluded: chain N residue 86 VAL Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 86 VAL Chi-restraints excluded: chain O residue 95 LEU Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain Q residue 30 ILE Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 53 THR Chi-restraints excluded: chain S residue 63 LEU Chi-restraints excluded: chain S residue 78 VAL Chi-restraints excluded: chain S residue 100 GLU Chi-restraints excluded: chain T residue 48 ILE Chi-restraints excluded: chain T residue 53 THR Chi-restraints excluded: chain T residue 102 THR Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 63 LEU Chi-restraints excluded: chain U residue 74 SER Chi-restraints excluded: chain U residue 100 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 78 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 109 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 162 optimal weight: 5.9990 chunk 249 optimal weight: 10.0000 chunk 76 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 237 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 6 optimal weight: 0.1980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 HIS E 658 GLN H 6 GLN ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN L 38 GLN M 64 GLN ** T 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.137627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.102462 restraints weight = 46659.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.100300 restraints weight = 35112.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.101434 restraints weight = 40454.434| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 25113 Z= 0.133 Angle : 0.722 16.958 34170 Z= 0.345 Chirality : 0.046 0.436 3875 Planarity : 0.005 0.073 4320 Dihedral : 6.929 96.313 3712 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.26 % Favored : 94.71 % Rotamer: Outliers : 3.12 % Allowed : 24.08 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.20 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.15), residues: 3079 helix: 0.16 (0.28), residues: 387 sheet: 0.22 (0.17), residues: 952 loop : -1.39 (0.15), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP G 50 HIS 0.005 0.001 HIS B 374 PHE 0.016 0.001 PHE C 53 TYR 0.029 0.002 TYR H 49 ARG 0.017 0.001 ARG K 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00976 ( 6) link_NAG-ASN : angle 7.05226 ( 18) link_ALPHA1-6 : bond 0.00693 ( 3) link_ALPHA1-6 : angle 2.14609 ( 9) link_BETA1-4 : bond 0.01382 ( 6) link_BETA1-4 : angle 4.58285 ( 18) link_ALPHA1-3 : bond 0.00455 ( 3) link_ALPHA1-3 : angle 3.04882 ( 9) hydrogen bonds : bond 0.03340 ( 809) hydrogen bonds : angle 5.00259 ( 2148) SS BOND : bond 0.00419 ( 45) SS BOND : angle 1.68809 ( 90) covalent geometry : bond 0.00309 (25050) covalent geometry : angle 0.68915 (34026) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 588 time to evaluate : 2.980 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: B 63 THR cc_start: 0.8880 (OUTLIER) cc_final: 0.8558 (t) REVERT: B 74 CYS cc_start: 0.6338 (m) cc_final: 0.6079 (m) REVERT: C 83 GLU cc_start: 0.7672 (tm-30) cc_final: 0.7453 (tm-30) REVERT: C 102 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.7918 (mp0) REVERT: C 375 SER cc_start: 0.8829 (OUTLIER) cc_final: 0.8507 (p) REVERT: E 540 GLN cc_start: 0.7689 (OUTLIER) cc_final: 0.7233 (mt0) REVERT: E 648 GLU cc_start: 0.8428 (tm-30) cc_final: 0.8168 (tm-30) REVERT: E 656 ASN cc_start: 0.7935 (t0) cc_final: 0.7693 (t0) REVERT: F 543 ASN cc_start: 0.8857 (m110) cc_final: 0.8345 (t0) REVERT: F 589 ASP cc_start: 0.8578 (t0) cc_final: 0.8341 (t0) REVERT: G 1 GLN cc_start: 0.7240 (tp40) cc_final: 0.6977 (tp40) REVERT: G 2 GLU cc_start: 0.8526 (pm20) cc_final: 0.8201 (pm20) REVERT: G 97 TYR cc_start: 0.9083 (t80) cc_final: 0.8556 (t80) REVERT: G 100 MET cc_start: 0.8664 (mmm) cc_final: 0.7906 (mmt) REVERT: H 24 ARG cc_start: 0.7863 (mmp-170) cc_final: 0.7500 (mmp-170) REVERT: H 47 LEU cc_start: 0.9325 (mm) cc_final: 0.9041 (mm) REVERT: H 61 ARG cc_start: 0.8392 (ptp-170) cc_final: 0.8064 (mtm180) REVERT: H 62 PHE cc_start: 0.8498 (m-80) cc_final: 0.8252 (m-80) REVERT: H 79 GLN cc_start: 0.8413 (mp10) cc_final: 0.7735 (mp10) REVERT: I 47 TRP cc_start: 0.8606 (t60) cc_final: 0.8244 (t60) REVERT: J 49 TYR cc_start: 0.8551 (p90) cc_final: 0.8297 (p90) REVERT: J 85 THR cc_start: 0.8442 (OUTLIER) cc_final: 0.8235 (p) REVERT: J 86 TYR cc_start: 0.8008 (m-10) cc_final: 0.7739 (m-10) REVERT: K 38 ARG cc_start: 0.7744 (ttm110) cc_final: 0.7443 (ttm110) REVERT: K 47 TRP cc_start: 0.8328 (t60) cc_final: 0.7967 (t60) REVERT: L 32 GLU cc_start: 0.7485 (mp0) cc_final: 0.7173 (pm20) REVERT: M 52 ASN cc_start: 0.9166 (p0) cc_final: 0.8717 (p0) REVERT: M 87 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7894 (mm-30) REVERT: N 10 ASP cc_start: 0.8487 (t0) cc_final: 0.8254 (t0) REVERT: N 53 ASP cc_start: 0.8434 (p0) cc_final: 0.8188 (p0) REVERT: O 24 ILE cc_start: 0.9271 (mm) cc_final: 0.8742 (mt) REVERT: P 71 PHE cc_start: 0.6817 (m-80) cc_final: 0.6293 (m-10) REVERT: Q 47 TRP cc_start: 0.7524 (t60) cc_final: 0.7133 (t60) REVERT: Q 81 GLU cc_start: 0.6816 (tm-30) cc_final: 0.6246 (tm-30) REVERT: R 24 ARG cc_start: 0.7304 (mmp80) cc_final: 0.6981 (mmp80) REVERT: R 95 ARG cc_start: 0.6946 (mmp80) cc_final: 0.6664 (mmp80) REVERT: S 32 TYR cc_start: 0.8552 (m-80) cc_final: 0.8197 (m-80) REVERT: S 46 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8355 (mm-30) REVERT: S 63 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7776 (pp) REVERT: S 79 TYR cc_start: 0.8389 (m-10) cc_final: 0.8134 (m-10) REVERT: S 100 PHE cc_start: 0.8759 (p90) cc_final: 0.8416 (p90) REVERT: T 81 GLU cc_start: 0.8855 (pm20) cc_final: 0.8650 (pm20) REVERT: T 82 ASP cc_start: 0.8752 (m-30) cc_final: 0.8321 (m-30) REVERT: U 12 LYS cc_start: 0.8736 (tptt) cc_final: 0.8399 (mttp) outliers start: 82 outliers final: 64 residues processed: 629 average time/residue: 0.3422 time to fit residues: 342.6899 Evaluate side-chains 635 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 565 time to evaluate : 3.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain E residue 540 GLN Chi-restraints excluded: chain E residue 603 ILE Chi-restraints excluded: chain E residue 604 CYS Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain I residue 2 GLU Chi-restraints excluded: chain I residue 20 VAL Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain J residue 10 PHE Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain L residue 3 GLN Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 86 VAL Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 42 SER Chi-restraints excluded: chain N residue 61 LEU Chi-restraints excluded: chain N residue 86 VAL Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain O residue 86 VAL Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain Q residue 100 TYR Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 53 THR Chi-restraints excluded: chain S residue 63 LEU Chi-restraints excluded: chain S residue 78 VAL Chi-restraints excluded: chain S residue 100 GLU Chi-restraints excluded: chain T residue 48 ILE Chi-restraints excluded: chain T residue 53 THR Chi-restraints excluded: chain T residue 102 THR Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 74 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 189 optimal weight: 10.0000 chunk 272 optimal weight: 0.9980 chunk 252 optimal weight: 0.8980 chunk 154 optimal weight: 9.9990 chunk 131 optimal weight: 0.5980 chunk 101 optimal weight: 0.0970 chunk 5 optimal weight: 4.9990 chunk 199 optimal weight: 0.7980 chunk 279 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 658 GLN H 6 GLN ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN L 38 GLN N 20 GLN P 89 GLN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.138631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.103381 restraints weight = 46620.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.101563 restraints weight = 34095.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.102553 restraints weight = 39226.283| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25113 Z= 0.128 Angle : 0.716 18.757 34170 Z= 0.342 Chirality : 0.046 0.412 3875 Planarity : 0.004 0.071 4320 Dihedral : 6.662 93.079 3712 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.91 % Favored : 94.06 % Rotamer: Outliers : 2.66 % Allowed : 24.95 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.20 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.15), residues: 3079 helix: 0.23 (0.28), residues: 387 sheet: 0.27 (0.18), residues: 954 loop : -1.36 (0.15), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP G 50 HIS 0.005 0.001 HIS B 374 PHE 0.018 0.001 PHE J 62 TYR 0.029 0.002 TYR H 49 ARG 0.016 0.000 ARG K 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00982 ( 6) link_NAG-ASN : angle 6.67691 ( 18) link_ALPHA1-6 : bond 0.00721 ( 3) link_ALPHA1-6 : angle 2.25578 ( 9) link_BETA1-4 : bond 0.01542 ( 6) link_BETA1-4 : angle 4.50970 ( 18) link_ALPHA1-3 : bond 0.00447 ( 3) link_ALPHA1-3 : angle 2.82717 ( 9) hydrogen bonds : bond 0.03186 ( 809) hydrogen bonds : angle 4.89754 ( 2148) SS BOND : bond 0.00389 ( 45) SS BOND : angle 1.56934 ( 90) covalent geometry : bond 0.00299 (25050) covalent geometry : angle 0.68594 (34026) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 579 time to evaluate : 2.938 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: B 63 THR cc_start: 0.8894 (OUTLIER) cc_final: 0.8567 (t) REVERT: B 74 CYS cc_start: 0.6473 (m) cc_final: 0.6190 (m) REVERT: C 83 GLU cc_start: 0.7737 (tm-30) cc_final: 0.7519 (tm-30) REVERT: C 375 SER cc_start: 0.8817 (OUTLIER) cc_final: 0.8454 (p) REVERT: E 540 GLN cc_start: 0.7594 (OUTLIER) cc_final: 0.7154 (mt0) REVERT: E 648 GLU cc_start: 0.8410 (tm-30) cc_final: 0.8158 (tm-30) REVERT: E 656 ASN cc_start: 0.7906 (t0) cc_final: 0.7644 (t0) REVERT: F 543 ASN cc_start: 0.8861 (m110) cc_final: 0.8396 (t0) REVERT: F 589 ASP cc_start: 0.8432 (t0) cc_final: 0.8225 (t0) REVERT: G 1 GLN cc_start: 0.7274 (tp40) cc_final: 0.7015 (tp40) REVERT: G 2 GLU cc_start: 0.8486 (pm20) cc_final: 0.8172 (pm20) REVERT: G 100 MET cc_start: 0.8665 (mmm) cc_final: 0.7959 (mmt) REVERT: H 24 ARG cc_start: 0.7813 (mmp-170) cc_final: 0.7440 (mmp-170) REVERT: H 47 LEU cc_start: 0.9287 (mm) cc_final: 0.9014 (mm) REVERT: H 61 ARG cc_start: 0.8342 (ptp-170) cc_final: 0.8044 (mtm180) REVERT: H 62 PHE cc_start: 0.8477 (m-80) cc_final: 0.8206 (m-80) REVERT: H 79 GLN cc_start: 0.8398 (mp10) cc_final: 0.7720 (mp10) REVERT: I 47 TRP cc_start: 0.8587 (t60) cc_final: 0.8332 (t60) REVERT: J 49 TYR cc_start: 0.8500 (p90) cc_final: 0.8216 (p90) REVERT: J 85 THR cc_start: 0.8415 (OUTLIER) cc_final: 0.8181 (p) REVERT: J 86 TYR cc_start: 0.7975 (m-10) cc_final: 0.7704 (m-10) REVERT: K 47 TRP cc_start: 0.8367 (t60) cc_final: 0.7967 (t60) REVERT: K 81 ASP cc_start: 0.6830 (m-30) cc_final: 0.6079 (p0) REVERT: L 32 GLU cc_start: 0.7517 (mp0) cc_final: 0.7187 (pm20) REVERT: M 52 ASN cc_start: 0.9116 (p0) cc_final: 0.8714 (p0) REVERT: M 87 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7924 (mm-30) REVERT: N 10 ASP cc_start: 0.8499 (t0) cc_final: 0.8273 (t0) REVERT: N 53 ASP cc_start: 0.8386 (p0) cc_final: 0.8136 (p0) REVERT: O 24 ILE cc_start: 0.9238 (mm) cc_final: 0.8878 (mt) REVERT: P 71 PHE cc_start: 0.6841 (m-80) cc_final: 0.6308 (m-80) REVERT: Q 47 TRP cc_start: 0.7563 (t60) cc_final: 0.7315 (t60) REVERT: Q 81 GLU cc_start: 0.6811 (tm-30) cc_final: 0.6200 (tm-30) REVERT: R 24 ARG cc_start: 0.7222 (mmp80) cc_final: 0.6924 (mmp80) REVERT: R 95 ARG cc_start: 0.6943 (mmp80) cc_final: 0.6686 (mmp80) REVERT: S 32 TYR cc_start: 0.8547 (m-80) cc_final: 0.8271 (m-80) REVERT: S 46 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8316 (mm-30) REVERT: S 63 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7750 (pp) REVERT: S 100 PHE cc_start: 0.8727 (p90) cc_final: 0.8354 (p90) REVERT: T 82 ASP cc_start: 0.8711 (m-30) cc_final: 0.8291 (m-30) REVERT: U 12 LYS cc_start: 0.8671 (tptt) cc_final: 0.8342 (mttp) outliers start: 70 outliers final: 61 residues processed: 616 average time/residue: 0.3348 time to fit residues: 328.7879 Evaluate side-chains 627 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 561 time to evaluate : 3.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain E residue 540 GLN Chi-restraints excluded: chain E residue 603 ILE Chi-restraints excluded: chain E residue 604 CYS Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain I residue 2 GLU Chi-restraints excluded: chain I residue 20 VAL Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain J residue 10 PHE Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 86 VAL Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 42 SER Chi-restraints excluded: chain N residue 61 LEU Chi-restraints excluded: chain N residue 86 VAL Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain O residue 86 VAL Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain Q residue 100 TYR Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain S residue 63 LEU Chi-restraints excluded: chain S residue 78 VAL Chi-restraints excluded: chain T residue 48 ILE Chi-restraints excluded: chain T residue 53 THR Chi-restraints excluded: chain T residue 102 THR Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 74 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 160 optimal weight: 6.9990 chunk 142 optimal weight: 0.9980 chunk 168 optimal weight: 3.9990 chunk 285 optimal weight: 0.0980 chunk 175 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 chunk 195 optimal weight: 9.9990 chunk 57 optimal weight: 3.9990 chunk 128 optimal weight: 6.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 355 ASN ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 70 HIS ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN N 20 GLN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.136150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.101623 restraints weight = 46504.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.100082 restraints weight = 36501.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.101117 restraints weight = 41550.232| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 25113 Z= 0.197 Angle : 0.748 18.838 34170 Z= 0.359 Chirality : 0.047 0.399 3875 Planarity : 0.005 0.074 4320 Dihedral : 6.681 90.143 3712 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.33 % Favored : 93.63 % Rotamer: Outliers : 3.12 % Allowed : 24.88 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.20 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.15), residues: 3079 helix: 0.10 (0.28), residues: 388 sheet: 0.19 (0.17), residues: 1003 loop : -1.36 (0.15), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP G 36 HIS 0.005 0.001 HIS L 90 PHE 0.017 0.001 PHE R 71 TYR 0.031 0.002 TYR T 36 ARG 0.009 0.001 ARG K 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00886 ( 6) link_NAG-ASN : angle 7.00567 ( 18) link_ALPHA1-6 : bond 0.00653 ( 3) link_ALPHA1-6 : angle 2.44827 ( 9) link_BETA1-4 : bond 0.01284 ( 6) link_BETA1-4 : angle 4.60965 ( 18) link_ALPHA1-3 : bond 0.00274 ( 3) link_ALPHA1-3 : angle 2.71950 ( 9) hydrogen bonds : bond 0.03604 ( 809) hydrogen bonds : angle 4.96572 ( 2148) SS BOND : bond 0.00448 ( 45) SS BOND : angle 1.78239 ( 90) covalent geometry : bond 0.00464 (25050) covalent geometry : angle 0.71587 (34026) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8717.39 seconds wall clock time: 151 minutes 57.19 seconds (9117.19 seconds total)