Starting phenix.real_space_refine on Fri Sep 19 07:59:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d90_46655/09_2025/9d90_46655.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d90_46655/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9d90_46655/09_2025/9d90_46655.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d90_46655/09_2025/9d90_46655.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9d90_46655/09_2025/9d90_46655.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d90_46655/09_2025/9d90_46655.map" } resolution = 3.91 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'GLU:plan': 10, 'ASP:plan': 3, 'ARG:plan': 1, 'GLN:plan1': 2} 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: {'GLU:plan': 10, 'ASP:plan': 3, 'ARG:plan': 1, 'GLN:plan1': 2} 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: {'GLU:plan': 10, 'ASP:plan': 3, 'ARG:plan': 1, 'GLN:plan1': 2} 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: 4.85, per 1000 atoms: 0.20 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: 1.88 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.96 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: 4.58 Time building geometry restraints manager: 2.50 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 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: 2.820 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.030 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.070 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.110 ------------------------------------------------------------------------------- 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 : 4.78 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.023 0.001 ARG J 24 TYR 0.036 0.002 TYR J 49 PHE 0.060 0.002 PHE O 67 TRP 0.063 0.003 TRP A 112 HIS 0.009 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00483 (25050) covalent geometry : angle 0.98073 (34026) SS BOND : bond 0.00679 ( 45) SS BOND : angle 2.04732 ( 90) hydrogen bonds : bond 0.14142 ( 809) hydrogen bonds : angle 7.10852 ( 2148) link_ALPHA1-3 : bond 0.00487 ( 3) link_ALPHA1-3 : angle 3.16396 ( 9) 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_NAG-ASN : bond 0.00882 ( 6) link_NAG-ASN : angle 8.66610 ( 18) *********************** 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 : 0.827 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: 0.8713 (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: 0.7456 (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: 0.7729 (t) REVERT: J 79 GLN cc_start: 0.8140 (mm110) cc_final: 0.7838 (mm110) REVERT: J 91 MET cc_start: 0.7852 (ptp) cc_final: 0.7411 (ptp) REVERT: K 47 TRP cc_start: 0.7822 (t60) cc_final: 0.7132 (t60) REVERT: K 81 ASP cc_start: 0.6863 (m-30) cc_final: 0.6040 (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: 0.7853 (mm) REVERT: P 4 MET cc_start: 0.7245 (tpp) cc_final: 0.7034 (tpt) REVERT: P 71 PHE cc_start: 0.6840 (m-10) cc_final: 0.6517 (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: 0.7590 (mm-30) REVERT: T 82 ASP cc_start: 0.8734 (m-30) cc_final: 0.8297 (m-30) REVERT: U 19 LYS cc_start: 0.8945 (tmtt) cc_final: 0.8622 (tmtt) REVERT: U 100 ASN cc_start: 0.7877 (m-40) cc_final: 0.7672 (m-40) outliers start: 3 outliers final: 1 residues processed: 700 average time/residue: 0.1413 time to fit residues: 157.3130 Evaluate side-chains 565 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 564 time to evaluate : 0.932 ------------------------------------------------------------------------------- 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 197 optimal weight: 2.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN ** 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 Q 62 HIS R 37 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.134885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.099494 restraints weight = 47078.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.097379 restraints weight = 36811.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.098287 restraints weight = 45638.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.099130 restraints weight = 28500.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.099720 restraints weight = 24392.422| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.084 25113 Z= 0.372 Angle : 0.863 22.394 34170 Z= 0.427 Chirality : 0.053 0.912 3875 Planarity : 0.006 0.077 4320 Dihedral : 10.345 114.242 3713 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.15 % Favored : 92.82 % Rotamer: Outliers : 2.89 % Allowed : 13.88 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.20 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.59 (0.15), residues: 3079 helix: -1.00 (0.25), residues: 395 sheet: 0.04 (0.18), residues: 922 loop : -1.73 (0.14), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG T 95B TYR 0.021 0.002 TYR R 49 PHE 0.020 0.002 PHE A 53 TRP 0.039 0.003 TRP G 50 HIS 0.009 0.002 HIS B 105 Details of bonding type rmsd covalent geometry : bond 0.00872 (25050) covalent geometry : angle 0.82269 (34026) SS BOND : bond 0.00568 ( 45) SS BOND : angle 2.17340 ( 90) hydrogen bonds : bond 0.05044 ( 809) hydrogen bonds : angle 5.83881 ( 2148) link_ALPHA1-3 : bond 0.00450 ( 3) link_ALPHA1-3 : angle 3.26114 ( 9) link_ALPHA1-6 : bond 0.00254 ( 3) link_ALPHA1-6 : angle 2.81049 ( 9) link_BETA1-4 : bond 0.01257 ( 6) link_BETA1-4 : angle 5.83901 ( 18) link_NAG-ASN : bond 0.00353 ( 6) link_NAG-ASN : angle 8.16479 ( 18) *********************** 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 653 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 577 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 MET cc_start: 0.7955 (mmm) cc_final: 0.7747 (mmm) REVERT: A 434 MET cc_start: 0.8107 (tpt) cc_final: 0.7635 (tpt) REVERT: A 435 TYR cc_start: 0.9065 (m-80) cc_final: 0.8833 (m-10) REVERT: B 74 CYS cc_start: 0.6592 (m) cc_final: 0.6313 (m) REVERT: C 62 GLU cc_start: 0.8077 (tp30) cc_final: 0.7300 (tt0) REVERT: C 83 GLU cc_start: 0.7864 (tm-30) cc_final: 0.7221 (tt0) REVERT: C 475 MET cc_start: 0.8785 (mmm) cc_final: 0.8518 (mmm) REVERT: E 648 GLU cc_start: 0.8340 (tm-30) cc_final: 0.8069 (tm-30) REVERT: F 543 ASN cc_start: 0.8846 (m110) cc_final: 0.8314 (t0) REVERT: F 621 GLU cc_start: 0.8278 (pt0) cc_final: 0.8048 (pt0) REVERT: G 2 GLU cc_start: 0.8561 (pm20) cc_final: 0.8190 (pm20) REVERT: G 100 MET cc_start: 0.8654 (mmm) cc_final: 0.8282 (mmm) REVERT: H 47 LEU cc_start: 0.9345 (mm) cc_final: 0.8905 (mm) REVERT: J 49 TYR cc_start: 0.8500 (p90) cc_final: 0.8245 (p90) REVERT: J 78 LEU cc_start: 0.8695 (mp) cc_final: 0.8358 (mp) REVERT: J 79 GLN cc_start: 0.8082 (mm110) cc_final: 0.7702 (mm110) REVERT: J 82 ASP cc_start: 0.8350 (m-30) cc_final: 0.8116 (m-30) REVERT: K 47 TRP cc_start: 0.8399 (t60) cc_final: 0.8091 (t60) REVERT: K 48 LEU cc_start: 0.8636 (mt) cc_final: 0.8341 (mp) REVERT: L 61 ARG cc_start: 0.8750 (ptp90) cc_final: 0.8218 (ptt180) REVERT: L 62 PHE cc_start: 0.8141 (m-80) cc_final: 0.7804 (m-10) REVERT: M 52 ASN cc_start: 0.9323 (p0) cc_final: 0.8757 (p0) REVERT: M 53 ASP cc_start: 0.9105 (p0) cc_final: 0.8742 (p0) REVERT: N 10 ASP cc_start: 0.8606 (t0) cc_final: 0.8384 (t70) REVERT: N 39 ASN cc_start: 0.8954 (p0) cc_final: 0.8744 (p0) REVERT: N 53 ASP cc_start: 0.8462 (p0) cc_final: 0.8224 (p0) REVERT: N 60 SER cc_start: 0.9237 (p) cc_final: 0.8906 (p) REVERT: P 46 LEU cc_start: 0.8848 (tt) cc_final: 0.8628 (pt) REVERT: P 71 PHE cc_start: 0.6669 (m-10) cc_final: 0.6170 (m-10) REVERT: Q 47 TRP cc_start: 0.7483 (t60) cc_final: 0.6619 (t60) REVERT: Q 81 GLU cc_start: 0.6900 (tm-30) cc_final: 0.6230 (tm-30) REVERT: R 4 MET cc_start: 0.7496 (tpt) cc_final: 0.7278 (tpp) REVERT: R 27 GLU cc_start: 0.9035 (pm20) cc_final: 0.8608 (pm20) REVERT: S 3 GLN cc_start: 0.8375 (pp30) cc_final: 0.8169 (pp30) REVERT: S 32 TYR cc_start: 0.8369 (m-80) cc_final: 0.8149 (m-80) REVERT: S 46 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8296 (mm-30) REVERT: T 39 LYS cc_start: 0.8515 (mppt) cc_final: 0.8065 (mptt) REVERT: T 81 GLU cc_start: 0.8763 (pm20) cc_final: 0.8528 (pm20) REVERT: T 82 ASP cc_start: 0.8800 (m-30) cc_final: 0.8339 (m-30) REVERT: U 100 ASN cc_start: 0.8099 (m-40) cc_final: 0.7829 (m-40) outliers start: 76 outliers final: 60 residues processed: 615 average time/residue: 0.1407 time to fit residues: 137.3165 Evaluate side-chains 596 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 536 time to evaluate : 0.887 ------------------------------------------------------------------------------- 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 255 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 501 CYS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain D residue 615 SER 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 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 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 82 LEU 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 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 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 O residue 95 LEU 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 S residue 110 THR 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 141 optimal weight: 0.9980 chunk 301 optimal weight: 3.9990 chunk 300 optimal weight: 7.9990 chunk 108 optimal weight: 0.0070 chunk 185 optimal weight: 9.9990 chunk 281 optimal weight: 20.0000 chunk 294 optimal weight: 0.8980 chunk 150 optimal weight: 2.9990 chunk 220 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 155 optimal weight: 8.9990 overall best weight: 1.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN L 38 GLN P 38 GLN Q 39 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.138345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.103804 restraints weight = 46398.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.101116 restraints weight = 35897.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.102416 restraints weight = 40346.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.102928 restraints weight = 25111.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.103606 restraints weight = 22269.684| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 25113 Z= 0.144 Angle : 0.683 19.308 34170 Z= 0.330 Chirality : 0.048 0.789 3875 Planarity : 0.005 0.075 4320 Dihedral : 8.780 111.268 3712 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.29 % Favored : 94.67 % Rotamer: Outliers : 2.62 % Allowed : 17.00 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.20 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.22 (0.15), residues: 3079 helix: -0.22 (0.27), residues: 385 sheet: 0.20 (0.18), residues: 940 loop : -1.57 (0.14), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 24 TYR 0.024 0.001 TYR H 49 PHE 0.023 0.001 PHE R 71 TRP 0.032 0.002 TRP G 50 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00332 (25050) covalent geometry : angle 0.64494 (34026) SS BOND : bond 0.00455 ( 45) SS BOND : angle 1.59988 ( 90) hydrogen bonds : bond 0.03803 ( 809) hydrogen bonds : angle 5.41747 ( 2148) link_ALPHA1-3 : bond 0.00372 ( 3) link_ALPHA1-3 : angle 3.19521 ( 9) link_ALPHA1-6 : bond 0.00578 ( 3) link_ALPHA1-6 : angle 2.12979 ( 9) link_BETA1-4 : bond 0.01407 ( 6) link_BETA1-4 : angle 5.14412 ( 18) link_NAG-ASN : bond 0.00568 ( 6) link_NAG-ASN : angle 7.19573 ( 18) *********************** 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 662 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 593 time to evaluate : 0.948 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: A 271 MET cc_start: 0.8046 (mmm) cc_final: 0.7784 (mmm) REVERT: A 434 MET cc_start: 0.8161 (tpt) cc_final: 0.7715 (tpt) REVERT: B 74 CYS cc_start: 0.6498 (m) cc_final: 0.6181 (m) REVERT: B 359 ILE cc_start: 0.8766 (mm) cc_final: 0.8454 (mm) REVERT: C 62 GLU cc_start: 0.7978 (tp30) cc_final: 0.7215 (tt0) REVERT: C 83 GLU cc_start: 0.7830 (tm-30) cc_final: 0.7190 (tt0) REVERT: C 475 MET cc_start: 0.8619 (mmm) cc_final: 0.8395 (mmm) REVERT: E 648 GLU cc_start: 0.8434 (tm-30) cc_final: 0.8089 (tm-30) REVERT: F 543 ASN cc_start: 0.8812 (m110) cc_final: 0.8214 (t0) REVERT: F 621 GLU cc_start: 0.8071 (pt0) cc_final: 0.7508 (tt0) REVERT: G 2 GLU cc_start: 0.8577 (pm20) cc_final: 0.8275 (pm20) REVERT: H 47 LEU cc_start: 0.9304 (mm) cc_final: 0.8903 (mm) REVERT: I 105 GLN cc_start: 0.8754 (pm20) cc_final: 0.8433 (pm20) REVERT: J 49 TYR cc_start: 0.8461 (p90) cc_final: 0.8224 (p90) REVERT: J 78 LEU cc_start: 0.8538 (mp) cc_final: 0.8277 (mp) REVERT: J 79 GLN cc_start: 0.8121 (mm110) cc_final: 0.7475 (mm110) REVERT: J 82 ASP cc_start: 0.8517 (m-30) cc_final: 0.8212 (m-30) REVERT: K 47 TRP cc_start: 0.8392 (t60) cc_final: 0.7973 (t60) REVERT: L 4 LEU cc_start: 0.8192 (mt) cc_final: 0.7933 (mt) REVERT: L 61 ARG cc_start: 0.8781 (ptp90) cc_final: 0.8173 (ptt180) REVERT: L 62 PHE cc_start: 0.8121 (m-80) cc_final: 0.7849 (m-10) REVERT: M 52 ASN cc_start: 0.9311 (p0) cc_final: 0.8695 (p0) REVERT: M 53 ASP cc_start: 0.9093 (p0) cc_final: 0.8719 (p0) REVERT: N 10 ASP cc_start: 0.8602 (t0) cc_final: 0.8362 (t70) REVERT: N 53 ASP cc_start: 0.8406 (p0) cc_final: 0.8128 (p0) REVERT: O 24 ILE cc_start: 0.9225 (mm) cc_final: 0.8761 (mt) REVERT: P 33 LEU cc_start: 0.7894 (tp) cc_final: 0.7657 (mt) REVERT: P 46 LEU cc_start: 0.8821 (tt) cc_final: 0.8614 (pt) REVERT: P 71 PHE cc_start: 0.6869 (m-10) cc_final: 0.6348 (m-10) REVERT: P 104 LEU cc_start: 0.7798 (tp) cc_final: 0.7530 (tp) REVERT: Q 81 GLU cc_start: 0.6820 (tm-30) cc_final: 0.6249 (tm-30) REVERT: R 27 GLU cc_start: 0.9030 (pm20) cc_final: 0.8514 (pm20) REVERT: R 95 ARG cc_start: 0.6743 (mmp80) cc_final: 0.6450 (mmp80) REVERT: S 3 GLN cc_start: 0.8344 (pp30) cc_final: 0.8054 (pp30) REVERT: S 32 TYR cc_start: 0.8423 (m-80) cc_final: 0.8185 (m-80) REVERT: S 100 PHE cc_start: 0.8610 (p90) cc_final: 0.8282 (p90) REVERT: T 39 LYS cc_start: 0.8493 (mppt) cc_final: 0.8026 (mmtm) REVERT: T 81 GLU cc_start: 0.8854 (pm20) cc_final: 0.8555 (pm20) REVERT: T 82 ASP cc_start: 0.8799 (m-30) cc_final: 0.8285 (m-30) REVERT: T 94 TRP cc_start: 0.8177 (t-100) cc_final: 0.7669 (t-100) REVERT: U 10 GLU cc_start: 0.7742 (tt0) cc_final: 0.7227 (tt0) REVERT: U 12 LYS cc_start: 0.9064 (tptt) cc_final: 0.8776 (tptt) outliers start: 69 outliers final: 54 residues processed: 624 average time/residue: 0.1446 time to fit residues: 144.0081 Evaluate side-chains 601 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 547 time to evaluate : 0.903 ------------------------------------------------------------------------------- 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 296 CYS Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 125 LEU 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 D residue 599 SER 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 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 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 107 THR Chi-restraints excluded: chain J residue 10 PHE Chi-restraints excluded: chain J residue 88 CYS 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 53 THR Chi-restraints excluded: chain L residue 78 LEU 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 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 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 46 LEU Chi-restraints excluded: chain R residue 53 THR Chi-restraints excluded: chain S residue 97 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 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 264 optimal weight: 0.2980 chunk 21 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 233 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 271 optimal weight: 8.9990 chunk 244 optimal weight: 10.0000 chunk 202 optimal weight: 10.0000 chunk 256 optimal weight: 10.0000 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 ASN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 100 ASN L 3 GLN L 38 GLN M 20 GLN S 64 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.136599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.101752 restraints weight = 46629.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.098868 restraints weight = 38657.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.100158 restraints weight = 40103.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.101300 restraints weight = 27070.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.101809 restraints weight = 24036.291| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2445 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= 0.225 Angle : 0.722 18.460 34170 Z= 0.348 Chirality : 0.047 0.392 3875 Planarity : 0.005 0.071 4320 Dihedral : 8.316 108.012 3712 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.59 % Favored : 93.37 % Rotamer: Outliers : 4.03 % Allowed : 18.52 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.20 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.15), residues: 3079 helix: -0.14 (0.27), residues: 386 sheet: 0.19 (0.17), residues: 961 loop : -1.53 (0.14), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 38 TYR 0.024 0.002 TYR H 49 PHE 0.020 0.002 PHE R 71 TRP 0.039 0.002 TRP G 50 HIS 0.006 0.001 HIS B 105 Details of bonding type rmsd covalent geometry : bond 0.00527 (25050) covalent geometry : angle 0.67968 (34026) SS BOND : bond 0.00444 ( 45) SS BOND : angle 1.80828 ( 90) hydrogen bonds : bond 0.03961 ( 809) hydrogen bonds : angle 5.32288 ( 2148) link_ALPHA1-3 : bond 0.00079 ( 3) link_ALPHA1-3 : angle 3.17774 ( 9) link_ALPHA1-6 : bond 0.00527 ( 3) link_ALPHA1-6 : angle 2.35080 ( 9) link_BETA1-4 : bond 0.01316 ( 6) link_BETA1-4 : angle 5.13177 ( 18) link_NAG-ASN : bond 0.01318 ( 6) link_NAG-ASN : angle 8.09356 ( 18) *********************** 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 673 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 567 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 ASN cc_start: 0.8748 (t0) cc_final: 0.8403 (t0) REVERT: B 359 ILE cc_start: 0.8768 (mm) cc_final: 0.8436 (mm) REVERT: C 62 GLU cc_start: 0.8026 (tp30) cc_final: 0.7271 (tt0) REVERT: C 83 GLU cc_start: 0.7791 (tm-30) cc_final: 0.7567 (tm-30) REVERT: E 648 GLU cc_start: 0.8495 (tm-30) cc_final: 0.7719 (tm-30) REVERT: F 543 ASN cc_start: 0.8890 (m110) cc_final: 0.8278 (t0) REVERT: G 2 GLU cc_start: 0.8625 (pm20) cc_final: 0.8315 (pm20) REVERT: G 50 TRP cc_start: 0.7914 (p-90) cc_final: 0.7712 (p-90) REVERT: G 100 MET cc_start: 0.8595 (mmm) cc_final: 0.7826 (mmt) REVERT: H 46 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8922 (tt) REVERT: H 47 LEU cc_start: 0.9327 (mm) cc_final: 0.8948 (mm) REVERT: I 46 GLU cc_start: 0.7699 (pt0) cc_final: 0.7456 (pt0) REVERT: I 47 TRP cc_start: 0.8581 (t60) cc_final: 0.8246 (t60) REVERT: I 63 PHE cc_start: 0.8883 (m-80) cc_final: 0.8510 (m-80) REVERT: J 49 TYR cc_start: 0.8494 (p90) cc_final: 0.8165 (p90) REVERT: J 78 LEU cc_start: 0.8570 (mp) cc_final: 0.8303 (mp) REVERT: J 79 GLN cc_start: 0.8086 (mm110) cc_final: 0.7397 (mm110) REVERT: J 86 TYR cc_start: 0.8208 (m-10) cc_final: 0.8007 (m-10) REVERT: K 47 TRP cc_start: 0.8290 (t60) cc_final: 0.7903 (t60) REVERT: K 50 TRP cc_start: 0.8275 (p-90) cc_final: 0.7973 (p-90) REVERT: L 32 GLU cc_start: 0.7361 (mp0) cc_final: 0.6839 (pm20) REVERT: L 61 ARG cc_start: 0.8755 (ptp90) cc_final: 0.8534 (ptt-90) REVERT: L 82 ASP cc_start: 0.8212 (m-30) cc_final: 0.7798 (m-30) REVERT: M 52 ASN cc_start: 0.9308 (p0) cc_final: 0.8719 (p0) REVERT: M 53 ASP cc_start: 0.9127 (p0) cc_final: 0.8757 (p0) REVERT: M 60 SER cc_start: 0.8893 (t) cc_final: 0.8670 (t) REVERT: N 10 ASP cc_start: 0.8601 (t0) cc_final: 0.8365 (t70) REVERT: N 53 ASP cc_start: 0.8407 (p0) cc_final: 0.8157 (p0) REVERT: O 24 ILE cc_start: 0.9275 (mm) cc_final: 0.8803 (mt) REVERT: P 33 LEU cc_start: 0.7956 (tp) cc_final: 0.7661 (mt) REVERT: P 46 LEU cc_start: 0.8898 (tt) cc_final: 0.8635 (pt) REVERT: P 71 PHE cc_start: 0.6783 (m-10) cc_final: 0.6211 (m-10) REVERT: P 104 LEU cc_start: 0.7990 (tp) cc_final: 0.7740 (tp) REVERT: Q 81 GLU cc_start: 0.6883 (tm-30) cc_final: 0.6286 (tm-30) REVERT: R 27 GLU cc_start: 0.9043 (pm20) cc_final: 0.8836 (pm20) REVERT: S 3 GLN cc_start: 0.8403 (pp30) cc_final: 0.8091 (pp30) REVERT: S 32 TYR cc_start: 0.8450 (m-80) cc_final: 0.8172 (m-80) REVERT: S 82 ASN cc_start: 0.8663 (t0) cc_final: 0.8375 (t0) REVERT: S 100 PHE cc_start: 0.8670 (p90) cc_final: 0.8339 (p90) REVERT: S 105 GLN cc_start: 0.8648 (pm20) cc_final: 0.8281 (pm20) REVERT: T 81 GLU cc_start: 0.8828 (pm20) cc_final: 0.8604 (pm20) REVERT: T 82 ASP cc_start: 0.8769 (m-30) cc_final: 0.8296 (m-30) REVERT: T 94 TRP cc_start: 0.8063 (t-100) cc_final: 0.7770 (t-100) REVERT: U 10 GLU cc_start: 0.7639 (tt0) cc_final: 0.7143 (tt0) REVERT: U 12 LYS cc_start: 0.8997 (tptt) cc_final: 0.8710 (tptt) REVERT: U 99 GLU cc_start: 0.7988 (mp0) cc_final: 0.7767 (mp0) outliers start: 106 outliers final: 77 residues processed: 623 average time/residue: 0.1421 time to fit residues: 141.2684 Evaluate side-chains 622 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 544 time to evaluate : 0.724 ------------------------------------------------------------------------------- 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 36 VAL 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 446 VAL 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 C residue 373 THR 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 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 17 ASP 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 100 MET 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 72 THR Chi-restraints excluded: chain L residue 78 LEU 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 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 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 53 THR Chi-restraints excluded: chain P residue 72 THR Chi-restraints excluded: chain P residue 97 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 46 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 37 VAL Chi-restraints excluded: chain U residue 63 LEU Chi-restraints excluded: chain U residue 74 SER Chi-restraints excluded: chain U residue 108 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 70 optimal weight: 0.6980 chunk 232 optimal weight: 0.0170 chunk 266 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 chunk 182 optimal weight: 10.0000 chunk 126 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 4 optimal weight: 6.9990 chunk 183 optimal weight: 3.9990 chunk 243 optimal weight: 30.0000 chunk 285 optimal weight: 4.9990 overall best weight: 0.7018 ------------------------------------------------------------------------------- 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** I 6 GLN ** 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 20 GLN T 92 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.139151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.104317 restraints weight = 46198.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.102725 restraints weight = 35007.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.103799 restraints weight = 40066.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.104393 restraints weight = 24588.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.105596 restraints weight = 21993.812| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 25113 Z= 0.118 Angle : 0.663 16.790 34170 Z= 0.316 Chirality : 0.045 0.414 3875 Planarity : 0.004 0.072 4320 Dihedral : 7.743 106.389 3712 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.58 % Favored : 95.39 % Rotamer: Outliers : 2.97 % Allowed : 20.69 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.20 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.15), residues: 3079 helix: 0.17 (0.28), residues: 385 sheet: 0.34 (0.18), residues: 949 loop : -1.40 (0.15), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 38 TYR 0.028 0.001 TYR H 49 PHE 0.017 0.001 PHE R 71 TRP 0.032 0.001 TRP T 35 HIS 0.004 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00270 (25050) covalent geometry : angle 0.62473 (34026) SS BOND : bond 0.00375 ( 45) SS BOND : angle 1.60174 ( 90) hydrogen bonds : bond 0.03193 ( 809) hydrogen bonds : angle 5.08892 ( 2148) link_ALPHA1-3 : bond 0.00497 ( 3) link_ALPHA1-3 : angle 3.40834 ( 9) link_ALPHA1-6 : bond 0.00741 ( 3) link_ALPHA1-6 : angle 2.10541 ( 9) link_BETA1-4 : bond 0.01379 ( 6) link_BETA1-4 : angle 4.65920 ( 18) link_NAG-ASN : bond 0.01168 ( 6) link_NAG-ASN : angle 7.40122 ( 18) *********************** 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 671 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 593 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 ASN cc_start: 0.8697 (t0) cc_final: 0.8419 (t0) REVERT: C 62 GLU cc_start: 0.7953 (tp30) cc_final: 0.7201 (tt0) REVERT: C 83 GLU cc_start: 0.7779 (tm-30) cc_final: 0.7512 (tm-30) REVERT: D 622 ILE cc_start: 0.9111 (mt) cc_final: 0.8846 (mt) REVERT: E 540 GLN cc_start: 0.7769 (mp-120) cc_final: 0.7319 (mt0) REVERT: F 543 ASN cc_start: 0.8782 (m110) cc_final: 0.8269 (t0) REVERT: F 589 ASP cc_start: 0.8433 (t0) cc_final: 0.8226 (t0) REVERT: F 621 GLU cc_start: 0.7856 (pt0) cc_final: 0.7543 (tt0) REVERT: G 1 GLN cc_start: 0.7086 (tp40) cc_final: 0.6712 (tp40) REVERT: G 2 GLU cc_start: 0.8573 (pm20) cc_final: 0.8243 (pm20) REVERT: G 97 TYR cc_start: 0.8969 (t80) cc_final: 0.8588 (t80) REVERT: G 100 MET cc_start: 0.8624 (mmm) cc_final: 0.7815 (mmt) REVERT: H 47 LEU cc_start: 0.9285 (mm) cc_final: 0.8960 (mm) REVERT: I 47 TRP cc_start: 0.8569 (t60) cc_final: 0.8345 (t60) REVERT: J 49 TYR cc_start: 0.8360 (p90) cc_final: 0.8135 (p90) REVERT: J 78 LEU cc_start: 0.8457 (mp) cc_final: 0.8230 (mp) REVERT: J 79 GLN cc_start: 0.8263 (mm110) cc_final: 0.7846 (mm110) REVERT: J 86 TYR cc_start: 0.8144 (m-10) cc_final: 0.7906 (m-10) REVERT: K 38 ARG cc_start: 0.7954 (ttm110) cc_final: 0.7560 (ttm110) REVERT: K 47 TRP cc_start: 0.8306 (t60) cc_final: 0.7935 (t60) REVERT: L 61 ARG cc_start: 0.8842 (ptp90) cc_final: 0.8636 (ptt-90) REVERT: L 82 ASP cc_start: 0.8225 (m-30) cc_final: 0.7854 (m-30) REVERT: M 52 ASN cc_start: 0.9227 (p0) cc_final: 0.8637 (p0) REVERT: M 53 ASP cc_start: 0.9109 (p0) cc_final: 0.8758 (p0) REVERT: M 87 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7892 (mm-30) REVERT: N 53 ASP cc_start: 0.8333 (p0) cc_final: 0.8064 (p0) REVERT: O 21 LYS cc_start: 0.7007 (tptt) cc_final: 0.6384 (tppt) REVERT: O 24 ILE cc_start: 0.9245 (mm) cc_final: 0.8797 (mt) REVERT: P 33 LEU cc_start: 0.7743 (tp) cc_final: 0.7521 (mt) REVERT: P 71 PHE cc_start: 0.6849 (m-10) cc_final: 0.6251 (m-10) REVERT: P 104 LEU cc_start: 0.8012 (tp) cc_final: 0.7778 (tp) REVERT: Q 81 GLU cc_start: 0.6699 (tm-30) cc_final: 0.6121 (tm-30) REVERT: R 24 ARG cc_start: 0.7368 (mmp80) cc_final: 0.7028 (mmp80) REVERT: R 27 GLU cc_start: 0.9055 (pm20) cc_final: 0.8482 (pm20) REVERT: S 3 GLN cc_start: 0.8363 (pp30) cc_final: 0.8114 (pp30) REVERT: S 100 PHE cc_start: 0.8620 (p90) cc_final: 0.8275 (p90) REVERT: S 105 GLN cc_start: 0.8625 (pm20) cc_final: 0.8285 (pm20) REVERT: T 24 ARG cc_start: 0.8299 (mmm160) cc_final: 0.8020 (mmm-85) REVERT: T 81 GLU cc_start: 0.8903 (pm20) cc_final: 0.8666 (pm20) REVERT: T 82 ASP cc_start: 0.8770 (m-30) cc_final: 0.8282 (m-30) REVERT: T 94 TRP cc_start: 0.8025 (t-100) cc_final: 0.7711 (t-100) REVERT: U 12 LYS cc_start: 0.8879 (tptt) cc_final: 0.8468 (tptt) REVERT: U 89 VAL cc_start: 0.7729 (OUTLIER) cc_final: 0.7322 (m) outliers start: 78 outliers final: 58 residues processed: 630 average time/residue: 0.1430 time to fit residues: 144.1224 Evaluate side-chains 610 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 551 time to evaluate : 1.016 ------------------------------------------------------------------------------- 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 296 CYS 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 D residue 615 SER 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 573 ILE 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 I residue 77 THR Chi-restraints excluded: chain J residue 10 PHE Chi-restraints excluded: chain J residue 47 LEU 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 78 LEU Chi-restraints excluded: chain M residue 36 ILE 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 17 THR 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 R residue 33 LEU Chi-restraints excluded: chain R residue 53 THR 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 37 VAL Chi-restraints excluded: chain U residue 74 SER Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 100 LEU Chi-restraints excluded: chain U residue 108 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 141 optimal weight: 7.9990 chunk 189 optimal weight: 8.9990 chunk 151 optimal weight: 4.9990 chunk 176 optimal weight: 1.9990 chunk 134 optimal weight: 5.9990 chunk 177 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 256 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 282 optimal weight: 30.0000 chunk 146 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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** 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** ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 92 ASN ** T 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.133343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.098601 restraints weight = 46758.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.096176 restraints weight = 39442.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.097582 restraints weight = 43403.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.098117 restraints weight = 27803.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.099680 restraints weight = 25084.467| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 25113 Z= 0.329 Angle : 0.805 18.274 34170 Z= 0.393 Chirality : 0.050 0.399 3875 Planarity : 0.005 0.076 4320 Dihedral : 7.790 105.430 3712 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.79 % Favored : 92.17 % Rotamer: Outliers : 4.53 % Allowed : 21.19 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.20 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.15), residues: 3079 helix: -0.30 (0.27), residues: 388 sheet: 0.20 (0.17), residues: 974 loop : -1.55 (0.15), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 82B TYR 0.029 0.002 TYR C 486 PHE 0.020 0.002 PHE A 53 TRP 0.041 0.002 TRP G 50 HIS 0.009 0.002 HIS B 105 Details of bonding type rmsd covalent geometry : bond 0.00767 (25050) covalent geometry : angle 0.76512 (34026) SS BOND : bond 0.00714 ( 45) SS BOND : angle 2.02035 ( 90) hydrogen bonds : bond 0.04544 ( 809) hydrogen bonds : angle 5.38869 ( 2148) link_ALPHA1-3 : bond 0.00368 ( 3) link_ALPHA1-3 : angle 3.09910 ( 9) link_ALPHA1-6 : bond 0.00521 ( 3) link_ALPHA1-6 : angle 2.55328 ( 9) link_BETA1-4 : bond 0.01131 ( 6) link_BETA1-4 : angle 5.22619 ( 18) link_NAG-ASN : bond 0.00959 ( 6) link_NAG-ASN : angle 8.25709 ( 18) *********************** 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 687 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 568 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 LYS cc_start: 0.7908 (mmmm) cc_final: 0.7696 (mmmm) REVERT: C 83 GLU cc_start: 0.7725 (tm-30) cc_final: 0.7438 (tm-30) REVERT: E 656 ASN cc_start: 0.7942 (t0) cc_final: 0.7671 (t0) REVERT: F 543 ASN cc_start: 0.8959 (m110) cc_final: 0.8325 (t0) REVERT: G 1 GLN cc_start: 0.7251 (tp40) cc_final: 0.6862 (tp40) REVERT: G 2 GLU cc_start: 0.8618 (pm20) cc_final: 0.8063 (pm20) REVERT: G 97 TYR cc_start: 0.9195 (t80) cc_final: 0.8749 (t80) REVERT: G 100 MET cc_start: 0.8871 (mmm) cc_final: 0.8414 (mmm) REVERT: H 46 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.8791 (tt) REVERT: H 47 LEU cc_start: 0.9346 (mm) cc_final: 0.8870 (mm) REVERT: H 61 ARG cc_start: 0.8400 (ptp-170) cc_final: 0.8172 (ptp-170) REVERT: I 47 TRP cc_start: 0.8658 (t60) cc_final: 0.8410 (t60) REVERT: J 78 LEU cc_start: 0.8712 (mp) cc_final: 0.8456 (mp) REVERT: J 79 GLN cc_start: 0.8111 (mm110) cc_final: 0.7495 (mm110) REVERT: J 85 THR cc_start: 0.8576 (OUTLIER) cc_final: 0.8309 (p) REVERT: J 86 TYR cc_start: 0.8238 (m-10) cc_final: 0.7955 (m-10) REVERT: K 38 ARG cc_start: 0.8167 (ttm110) cc_final: 0.7568 (ttm110) REVERT: K 47 TRP cc_start: 0.8340 (t60) cc_final: 0.8069 (t60) REVERT: K 66 ARG cc_start: 0.7323 (mmm-85) cc_final: 0.6917 (mmm-85) REVERT: L 32 GLU cc_start: 0.7623 (mp0) cc_final: 0.7068 (pm20) REVERT: M 52 ASN cc_start: 0.9267 (p0) cc_final: 0.8738 (p0) REVERT: M 53 ASP cc_start: 0.9140 (p0) cc_final: 0.8906 (p0) REVERT: N 10 ASP cc_start: 0.8448 (t0) cc_final: 0.8162 (t70) REVERT: N 53 ASP cc_start: 0.8391 (p0) cc_final: 0.8152 (p0) REVERT: N 60 SER cc_start: 0.9257 (p) cc_final: 0.8872 (p) REVERT: O 21 LYS cc_start: 0.7416 (tptt) cc_final: 0.6732 (tppt) REVERT: O 64 GLN cc_start: 0.8687 (tp40) cc_final: 0.8482 (tp40) REVERT: P 46 LEU cc_start: 0.8961 (tt) cc_final: 0.8589 (pt) REVERT: P 47 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7850 (pp) REVERT: P 71 PHE cc_start: 0.6813 (m-10) cc_final: 0.6202 (m-10) REVERT: P 104 LEU cc_start: 0.8136 (tp) cc_final: 0.7903 (tp) REVERT: Q 81 GLU cc_start: 0.7041 (tm-30) cc_final: 0.6425 (tm-30) REVERT: R 95 ARG cc_start: 0.6821 (mmp80) cc_final: 0.6613 (mmp80) REVERT: S 3 GLN cc_start: 0.8480 (pp30) cc_final: 0.8143 (pp30) REVERT: S 63 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7891 (pp) REVERT: S 81 GLU cc_start: 0.7346 (tm-30) cc_final: 0.6581 (tm-30) REVERT: S 100 PHE cc_start: 0.8856 (p90) cc_final: 0.8489 (p90) REVERT: S 105 GLN cc_start: 0.8624 (pm20) cc_final: 0.8273 (pm20) REVERT: T 42 GLN cc_start: 0.8190 (mp10) cc_final: 0.7878 (mp10) REVERT: T 81 GLU cc_start: 0.8891 (pm20) cc_final: 0.8649 (pm20) REVERT: T 82 ASP cc_start: 0.8729 (m-30) cc_final: 0.8266 (m-30) REVERT: U 89 VAL cc_start: 0.7732 (OUTLIER) cc_final: 0.7344 (m) REVERT: U 100 PHE cc_start: 0.8052 (p90) cc_final: 0.7794 (p90) outliers start: 119 outliers final: 93 residues processed: 635 average time/residue: 0.1427 time to fit residues: 144.6918 Evaluate side-chains 641 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 543 time to evaluate : 0.916 ------------------------------------------------------------------------------- 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 491 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 236 THR 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 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 C residue 373 THR 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 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 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 I residue 100 MET Chi-restraints excluded: chain J residue 10 PHE Chi-restraints excluded: chain J residue 17 ASP 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 5 VAL 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 34 ILE 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 73 ASN Chi-restraints excluded: chain N residue 76 ILE 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 P residue 72 THR 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 T residue 11 LEU 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 37 VAL Chi-restraints excluded: chain U residue 63 LEU Chi-restraints excluded: chain U residue 74 SER Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 100 LEU Chi-restraints excluded: chain U residue 108 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 208 optimal weight: 20.0000 chunk 230 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 290 optimal weight: 3.9990 chunk 189 optimal weight: 7.9990 chunk 8 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 191 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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** C 72 HIS E 658 GLN H 6 GLN ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN M 20 GLN N 20 GLN T 93 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.138001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.103134 restraints weight = 46390.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.101132 restraints weight = 34235.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.102181 restraints weight = 40861.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.102929 restraints weight = 26101.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.103618 restraints weight = 22855.408| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 25113 Z= 0.131 Angle : 0.691 16.308 34170 Z= 0.332 Chirality : 0.046 0.428 3875 Planarity : 0.004 0.070 4320 Dihedral : 7.052 101.969 3712 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.77 % Favored : 95.19 % Rotamer: Outliers : 3.84 % Allowed : 22.52 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.15), residues: 3079 helix: 0.11 (0.28), residues: 387 sheet: 0.26 (0.17), residues: 992 loop : -1.43 (0.15), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG T 95B TYR 0.031 0.002 TYR H 49 PHE 0.015 0.001 PHE L 87 TRP 0.039 0.002 TRP G 50 HIS 0.005 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00305 (25050) covalent geometry : angle 0.65642 (34026) SS BOND : bond 0.00432 ( 45) SS BOND : angle 1.61047 ( 90) hydrogen bonds : bond 0.03329 ( 809) hydrogen bonds : angle 5.04947 ( 2148) link_ALPHA1-3 : bond 0.00683 ( 3) link_ALPHA1-3 : angle 3.47711 ( 9) link_ALPHA1-6 : bond 0.00676 ( 3) link_ALPHA1-6 : angle 2.05708 ( 9) link_BETA1-4 : bond 0.01389 ( 6) link_BETA1-4 : angle 4.62555 ( 18) link_NAG-ASN : bond 0.00978 ( 6) link_NAG-ASN : angle 7.11199 ( 18) *********************** 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 679 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 578 time to evaluate : 0.887 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: 0.8837 (OUTLIER) cc_final: 0.8502 (t) REVERT: C 83 GLU cc_start: 0.7785 (tm-30) cc_final: 0.7560 (tm-30) REVERT: C 102 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.7883 (mt-10) REVERT: C 375 SER cc_start: 0.8807 (OUTLIER) cc_final: 0.8450 (p) REVERT: E 540 GLN cc_start: 0.7716 (OUTLIER) cc_final: 0.7311 (mt0) REVERT: E 648 GLU cc_start: 0.8311 (tm-30) cc_final: 0.8086 (tm-30) REVERT: E 656 ASN cc_start: 0.7852 (t0) cc_final: 0.7633 (t0) REVERT: F 543 ASN cc_start: 0.8811 (m110) cc_final: 0.8265 (t0) REVERT: F 589 ASP cc_start: 0.8572 (t0) cc_final: 0.8277 (t0) REVERT: F 593 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8805 (tt) REVERT: G 1 GLN cc_start: 0.7241 (tp40) cc_final: 0.6881 (tp40) REVERT: G 2 GLU cc_start: 0.8562 (pm20) cc_final: 0.8068 (pm20) REVERT: G 97 TYR cc_start: 0.9088 (t80) cc_final: 0.8618 (t80) REVERT: H 24 ARG cc_start: 0.7957 (mmp-170) cc_final: 0.7583 (mmp-170) REVERT: H 47 LEU cc_start: 0.9320 (mm) cc_final: 0.8983 (mm) REVERT: J 49 TYR cc_start: 0.8504 (p90) cc_final: 0.8200 (p90) REVERT: J 78 LEU cc_start: 0.8593 (mp) cc_final: 0.8297 (mp) REVERT: J 79 GLN cc_start: 0.8129 (mm110) cc_final: 0.7862 (mm110) REVERT: J 86 TYR cc_start: 0.8107 (m-10) cc_final: 0.7792 (m-10) REVERT: K 38 ARG cc_start: 0.8035 (ttm110) cc_final: 0.7635 (ttm110) REVERT: K 47 TRP cc_start: 0.8302 (t60) cc_final: 0.7918 (t60) REVERT: K 66 ARG cc_start: 0.7190 (mmm-85) cc_final: 0.6733 (mmm-85) REVERT: K 81 ASP cc_start: 0.6809 (m-30) cc_final: 0.5913 (p0) REVERT: L 32 GLU cc_start: 0.7552 (mp0) cc_final: 0.7157 (pm20) REVERT: L 42 LYS cc_start: 0.8109 (mmmm) cc_final: 0.7853 (mtmm) REVERT: L 61 ARG cc_start: 0.8908 (ptp90) cc_final: 0.8665 (ptt-90) REVERT: M 52 ASN cc_start: 0.9243 (p0) cc_final: 0.8668 (p0) REVERT: M 53 ASP cc_start: 0.9108 (p0) cc_final: 0.8806 (p0) REVERT: M 87 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7898 (mm-30) REVERT: N 10 ASP cc_start: 0.8446 (t0) cc_final: 0.8200 (t70) REVERT: N 53 ASP cc_start: 0.8375 (p0) cc_final: 0.8115 (p0) REVERT: O 24 ILE cc_start: 0.9287 (mm) cc_final: 0.8769 (mt) REVERT: P 71 PHE cc_start: 0.6767 (m-80) cc_final: 0.6258 (m-10) REVERT: P 104 LEU cc_start: 0.8234 (tp) cc_final: 0.8029 (tp) REVERT: Q 47 TRP cc_start: 0.7483 (t60) cc_final: 0.6900 (t60) REVERT: Q 81 GLU cc_start: 0.6800 (tm-30) cc_final: 0.6219 (tm-30) REVERT: R 24 ARG cc_start: 0.7289 (mmp80) cc_final: 0.7001 (mmp80) REVERT: R 27 GLU cc_start: 0.9074 (pm20) cc_final: 0.8538 (pm20) REVERT: R 95 ARG cc_start: 0.6851 (mmp80) cc_final: 0.6358 (mmp80) REVERT: S 3 GLN cc_start: 0.8376 (pp30) cc_final: 0.8094 (pp30) REVERT: S 100 PHE cc_start: 0.8775 (p90) cc_final: 0.8394 (p90) REVERT: T 11 LEU cc_start: 0.6708 (OUTLIER) cc_final: 0.5994 (mp) REVERT: T 42 GLN cc_start: 0.8140 (mp10) cc_final: 0.7813 (mp10) REVERT: T 81 GLU cc_start: 0.8898 (pm20) cc_final: 0.8658 (pm20) REVERT: T 82 ASP cc_start: 0.8797 (m-30) cc_final: 0.8351 (m-30) REVERT: U 10 GLU cc_start: 0.7257 (tp30) cc_final: 0.6227 (tp30) REVERT: U 12 LYS cc_start: 0.8741 (mmtm) cc_final: 0.8186 (mmtp) REVERT: U 89 VAL cc_start: 0.7721 (OUTLIER) cc_final: 0.7312 (m) outliers start: 101 outliers final: 68 residues processed: 630 average time/residue: 0.1453 time to fit residues: 145.5713 Evaluate side-chains 625 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 550 time to evaluate : 0.646 ------------------------------------------------------------------------------- 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 201 ILE Chi-restraints excluded: chain A residue 242 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 75 VAL 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 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 62 LYS 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 4 LEU 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 47 LEU 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 M residue 34 ILE Chi-restraints excluded: chain N residue 3 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 76 ILE 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 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 78 VAL Chi-restraints excluded: chain T residue 11 LEU 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 37 VAL Chi-restraints excluded: chain U residue 63 LEU Chi-restraints excluded: chain U residue 74 SER Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 100 LEU Chi-restraints excluded: chain U residue 108 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 110 optimal weight: 0.0980 chunk 298 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 178 optimal weight: 2.9990 chunk 93 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 244 optimal weight: 9.9990 chunk 191 optimal weight: 5.9990 chunk 114 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 625 ASN E 658 GLN F 656 ASN H 6 GLN ** H 89 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 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 64 GLN T 93 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.135585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.101119 restraints weight = 46615.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.098537 restraints weight = 36948.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.099945 restraints weight = 42573.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.100341 restraints weight = 26530.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.101164 restraints weight = 23580.982| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 25113 Z= 0.226 Angle : 0.741 16.547 34170 Z= 0.359 Chirality : 0.047 0.401 3875 Planarity : 0.005 0.075 4320 Dihedral : 7.036 99.755 3712 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.50 % Favored : 93.47 % Rotamer: Outliers : 3.84 % Allowed : 23.32 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.20 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.15), residues: 3079 helix: -0.08 (0.28), residues: 388 sheet: 0.17 (0.17), residues: 948 loop : -1.40 (0.15), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 617 TYR 0.022 0.002 TYR H 49 PHE 0.017 0.002 PHE R 71 TRP 0.040 0.002 TRP G 50 HIS 0.005 0.001 HIS G 35 Details of bonding type rmsd covalent geometry : bond 0.00533 (25050) covalent geometry : angle 0.70541 (34026) SS BOND : bond 0.00477 ( 45) SS BOND : angle 1.84960 ( 90) hydrogen bonds : bond 0.03838 ( 809) hydrogen bonds : angle 5.09540 ( 2148) link_ALPHA1-3 : bond 0.00175 ( 3) link_ALPHA1-3 : angle 2.81246 ( 9) link_ALPHA1-6 : bond 0.00583 ( 3) link_ALPHA1-6 : angle 2.43126 ( 9) link_BETA1-4 : bond 0.01214 ( 6) link_BETA1-4 : angle 4.86809 ( 18) link_NAG-ASN : bond 0.00920 ( 6) link_NAG-ASN : angle 7.41027 ( 18) *********************** 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 669 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 568 time to evaluate : 0.839 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: 0.8933 (OUTLIER) cc_final: 0.8640 (t) REVERT: C 83 GLU cc_start: 0.7723 (tm-30) cc_final: 0.7470 (tm-30) REVERT: E 648 GLU cc_start: 0.8400 (tm-30) cc_final: 0.7910 (tp30) REVERT: E 656 ASN cc_start: 0.7915 (t0) cc_final: 0.7677 (t0) REVERT: F 543 ASN cc_start: 0.8872 (m110) cc_final: 0.8352 (t0) REVERT: F 593 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8907 (tt) REVERT: F 656 ASN cc_start: 0.8223 (OUTLIER) cc_final: 0.7952 (t160) REVERT: G 1 GLN cc_start: 0.7254 (tp40) cc_final: 0.6986 (tp40) REVERT: G 2 GLU cc_start: 0.8570 (pm20) cc_final: 0.8245 (pm20) REVERT: G 97 TYR cc_start: 0.9151 (t80) cc_final: 0.8644 (t80) REVERT: G 100 MET cc_start: 0.8349 (mmm) cc_final: 0.7768 (mmt) REVERT: H 24 ARG cc_start: 0.7923 (mmp-170) cc_final: 0.7575 (mmp-170) REVERT: H 46 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8935 (tt) REVERT: H 47 LEU cc_start: 0.9352 (mm) cc_final: 0.9008 (mm) REVERT: H 61 ARG cc_start: 0.7931 (ptp-170) cc_final: 0.7629 (mtm180) REVERT: J 78 LEU cc_start: 0.8669 (mp) cc_final: 0.8389 (mp) REVERT: J 79 GLN cc_start: 0.8029 (mm110) cc_final: 0.7776 (mm110) REVERT: J 85 THR cc_start: 0.8431 (OUTLIER) cc_final: 0.8114 (p) REVERT: J 86 TYR cc_start: 0.8160 (m-10) cc_final: 0.7845 (m-10) REVERT: K 38 ARG cc_start: 0.8160 (ttm110) cc_final: 0.7698 (ttm110) REVERT: K 47 TRP cc_start: 0.8389 (t60) cc_final: 0.8074 (t60) REVERT: L 32 GLU cc_start: 0.7540 (mp0) cc_final: 0.7166 (pm20) REVERT: M 52 ASN cc_start: 0.9262 (p0) cc_final: 0.8711 (p0) REVERT: M 53 ASP cc_start: 0.9139 (p0) cc_final: 0.8881 (p0) REVERT: M 87 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7946 (mm-30) REVERT: N 10 ASP cc_start: 0.8402 (t0) cc_final: 0.8158 (t0) REVERT: N 53 ASP cc_start: 0.8385 (p0) cc_final: 0.8138 (p0) REVERT: N 60 SER cc_start: 0.9242 (p) cc_final: 0.8909 (p) REVERT: O 24 ILE cc_start: 0.9286 (mm) cc_final: 0.8803 (mt) REVERT: P 71 PHE cc_start: 0.6806 (m-80) cc_final: 0.6315 (m-10) REVERT: P 104 LEU cc_start: 0.8227 (tp) cc_final: 0.8023 (tp) REVERT: Q 47 TRP cc_start: 0.7604 (t60) cc_final: 0.7010 (t60) REVERT: Q 81 GLU cc_start: 0.6881 (tm-30) cc_final: 0.6278 (tm-30) REVERT: R 24 ARG cc_start: 0.7244 (mmp80) cc_final: 0.6849 (mmp80) REVERT: S 3 GLN cc_start: 0.8401 (pp30) cc_final: 0.8105 (pp30) REVERT: S 100 GLU cc_start: 0.9040 (mm-30) cc_final: 0.8817 (mp0) REVERT: T 42 GLN cc_start: 0.8155 (mp10) cc_final: 0.7804 (mp10) REVERT: T 81 GLU cc_start: 0.8891 (pm20) cc_final: 0.8669 (pm20) REVERT: T 82 ASP cc_start: 0.8739 (m-30) cc_final: 0.8287 (m-30) REVERT: U 10 GLU cc_start: 0.7336 (tp30) cc_final: 0.6326 (tp30) REVERT: U 12 LYS cc_start: 0.8797 (mmtm) cc_final: 0.8223 (mmtp) REVERT: U 89 VAL cc_start: 0.7717 (OUTLIER) cc_final: 0.7311 (m) outliers start: 101 outliers final: 78 residues processed: 625 average time/residue: 0.1391 time to fit residues: 139.1963 Evaluate side-chains 636 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 552 time to evaluate : 0.654 ------------------------------------------------------------------------------- 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 491 ILE 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 109 ILE Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 294 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 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 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 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 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 4 LEU 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 45 LEU Chi-restraints excluded: chain I residue 51 ILE 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 46 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain M residue 34 ILE 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 39 ASN Chi-restraints excluded: chain N residue 42 SER 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 88 ASP 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 53 THR 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 48 ILE 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 37 VAL Chi-restraints excluded: chain U residue 63 LEU Chi-restraints excluded: chain U residue 74 SER Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 100 LEU Chi-restraints excluded: chain U residue 108 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 187 optimal weight: 3.9990 chunk 193 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 243 optimal weight: 20.0000 chunk 130 optimal weight: 0.2980 chunk 74 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 126 optimal weight: 0.2980 chunk 175 optimal weight: 9.9990 chunk 47 optimal weight: 8.9990 chunk 296 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN ** 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** P 89 GLN Q 100HASN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 93 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.136552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.102078 restraints weight = 46461.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.099036 restraints weight = 33590.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.099861 restraints weight = 44049.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.101051 restraints weight = 28104.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.102390 restraints weight = 23451.235| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 25113 Z= 0.179 Angle : 0.731 15.656 34170 Z= 0.351 Chirality : 0.047 0.419 3875 Planarity : 0.005 0.074 4320 Dihedral : 6.920 96.909 3712 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.65 % Favored : 94.32 % Rotamer: Outliers : 3.46 % Allowed : 24.08 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.20 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.15), residues: 3079 helix: -0.01 (0.28), residues: 388 sheet: 0.21 (0.18), residues: 931 loop : -1.37 (0.15), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 82B TYR 0.027 0.002 TYR H 49 PHE 0.026 0.002 PHE S 100J TRP 0.065 0.002 TRP G 36 HIS 0.007 0.001 HIS L 90 Details of bonding type rmsd covalent geometry : bond 0.00423 (25050) covalent geometry : angle 0.69711 (34026) SS BOND : bond 0.00439 ( 45) SS BOND : angle 1.76614 ( 90) hydrogen bonds : bond 0.03570 ( 809) hydrogen bonds : angle 5.02815 ( 2148) link_ALPHA1-3 : bond 0.00299 ( 3) link_ALPHA1-3 : angle 2.90121 ( 9) link_ALPHA1-6 : bond 0.00626 ( 3) link_ALPHA1-6 : angle 2.27154 ( 9) link_BETA1-4 : bond 0.01302 ( 6) link_BETA1-4 : angle 4.69289 ( 18) link_NAG-ASN : bond 0.00916 ( 6) link_NAG-ASN : angle 7.12316 ( 18) *********************** 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 653 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 562 time to evaluate : 0.999 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: 0.8921 (OUTLIER) cc_final: 0.8590 (t) REVERT: C 83 GLU cc_start: 0.7672 (tm-30) cc_final: 0.7409 (tm-30) REVERT: C 102 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.7893 (mp0) REVERT: E 540 GLN cc_start: 0.7689 (mp-120) cc_final: 0.7148 (mt0) REVERT: E 648 GLU cc_start: 0.8361 (tm-30) cc_final: 0.7865 (tp30) REVERT: E 656 ASN cc_start: 0.7920 (t0) cc_final: 0.7681 (t0) REVERT: F 543 ASN cc_start: 0.8845 (m110) cc_final: 0.8409 (t0) REVERT: F 593 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8868 (tt) REVERT: G 1 GLN cc_start: 0.7326 (tp40) cc_final: 0.7074 (tp40) REVERT: G 2 GLU cc_start: 0.8506 (pm20) cc_final: 0.8202 (pm20) REVERT: G 97 TYR cc_start: 0.9170 (t80) cc_final: 0.8653 (t80) REVERT: G 100 MET cc_start: 0.8227 (mmm) cc_final: 0.7827 (mmt) REVERT: H 24 ARG cc_start: 0.7904 (mmp-170) cc_final: 0.7479 (mmp-170) REVERT: H 46 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8899 (tt) REVERT: H 47 LEU cc_start: 0.9361 (mm) cc_final: 0.9025 (mm) REVERT: H 61 ARG cc_start: 0.7973 (ptp-170) cc_final: 0.7555 (mtm180) REVERT: H 79 GLN cc_start: 0.8334 (mp10) cc_final: 0.7768 (mp10) REVERT: J 78 LEU cc_start: 0.8606 (mp) cc_final: 0.8324 (mp) REVERT: J 79 GLN cc_start: 0.8066 (mm110) cc_final: 0.7824 (mm110) REVERT: J 85 THR cc_start: 0.8408 (OUTLIER) cc_final: 0.8079 (p) REVERT: J 86 TYR cc_start: 0.8139 (m-10) cc_final: 0.7833 (m-10) REVERT: K 47 TRP cc_start: 0.8399 (t60) cc_final: 0.8062 (t60) REVERT: L 32 GLU cc_start: 0.7540 (mp0) cc_final: 0.7178 (pm20) REVERT: M 52 ASN cc_start: 0.9257 (p0) cc_final: 0.8724 (p0) REVERT: M 53 ASP cc_start: 0.9127 (p0) cc_final: 0.8917 (p0) REVERT: M 87 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7922 (mm-30) REVERT: N 10 ASP cc_start: 0.8428 (t0) cc_final: 0.8189 (t0) REVERT: N 53 ASP cc_start: 0.8367 (p0) cc_final: 0.8124 (p0) REVERT: O 24 ILE cc_start: 0.9288 (mm) cc_final: 0.8820 (mt) REVERT: P 71 PHE cc_start: 0.6842 (m-80) cc_final: 0.6348 (m-10) REVERT: P 104 LEU cc_start: 0.8220 (tp) cc_final: 0.7983 (tp) REVERT: Q 47 TRP cc_start: 0.7580 (t60) cc_final: 0.7063 (t60) REVERT: Q 81 GLU cc_start: 0.6823 (tm-30) cc_final: 0.6209 (tm-30) REVERT: R 24 ARG cc_start: 0.7302 (mmp80) cc_final: 0.6975 (mmp80) REVERT: S 3 GLN cc_start: 0.8377 (pp30) cc_final: 0.8077 (pp30) REVERT: S 100 GLU cc_start: 0.9028 (mm-30) cc_final: 0.8808 (mp0) REVERT: T 24 ARG cc_start: 0.8176 (mmm160) cc_final: 0.7796 (mmm-85) REVERT: T 42 GLN cc_start: 0.8165 (mp10) cc_final: 0.7802 (mp10) REVERT: T 81 GLU cc_start: 0.8904 (pm20) cc_final: 0.8672 (pm20) REVERT: T 82 ASP cc_start: 0.8739 (m-30) cc_final: 0.8272 (m-30) REVERT: T 95 ARG cc_start: 0.8350 (mmm160) cc_final: 0.7946 (mmp-170) REVERT: U 10 GLU cc_start: 0.7424 (tp30) cc_final: 0.6702 (tp30) REVERT: U 12 LYS cc_start: 0.8857 (mmtm) cc_final: 0.8366 (mmtp) REVERT: U 89 VAL cc_start: 0.7679 (OUTLIER) cc_final: 0.7256 (m) outliers start: 91 outliers final: 78 residues processed: 612 average time/residue: 0.1430 time to fit residues: 140.6873 Evaluate side-chains 635 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 551 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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 A residue 373 THR Chi-restraints excluded: chain A residue 491 ILE 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 125 LEU Chi-restraints excluded: chain B residue 294 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 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 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 4 LEU 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 45 LEU Chi-restraints excluded: chain I residue 51 ILE 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 82 LEU Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain L residue 11 LEU 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 34 ILE Chi-restraints excluded: chain M residue 36 ILE 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 39 ASN Chi-restraints excluded: chain N residue 42 SER 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 95 LEU 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 53 THR 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 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 37 VAL Chi-restraints excluded: chain U residue 63 LEU Chi-restraints excluded: chain U residue 74 SER Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 100 LEU Chi-restraints excluded: chain U residue 108 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 18 optimal weight: 0.0470 chunk 193 optimal weight: 9.9990 chunk 291 optimal weight: 4.9990 chunk 147 optimal weight: 8.9990 chunk 0 optimal weight: 3.9990 chunk 292 optimal weight: 20.0000 chunk 97 optimal weight: 2.9990 chunk 240 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 120 optimal weight: 0.0030 chunk 117 optimal weight: 0.0970 overall best weight: 0.8290 ------------------------------------------------------------------------------- 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** ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 20 GLN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 93 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.138131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.103220 restraints weight = 46255.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.101182 restraints weight = 33434.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.102484 restraints weight = 38338.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.102744 restraints weight = 25333.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.103467 restraints weight = 22469.795| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25113 Z= 0.130 Angle : 0.709 15.845 34170 Z= 0.338 Chirality : 0.046 0.418 3875 Planarity : 0.005 0.073 4320 Dihedral : 6.661 93.326 3712 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.85 % Favored : 94.12 % Rotamer: Outliers : 3.39 % Allowed : 24.27 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.20 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.15), residues: 3079 helix: 0.18 (0.28), residues: 387 sheet: 0.23 (0.18), residues: 926 loop : -1.31 (0.15), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG K 38 TYR 0.029 0.002 TYR H 49 PHE 0.016 0.001 PHE H 83 TRP 0.071 0.002 TRP G 36 HIS 0.006 0.001 HIS L 90 Details of bonding type rmsd covalent geometry : bond 0.00311 (25050) covalent geometry : angle 0.67910 (34026) SS BOND : bond 0.00402 ( 45) SS BOND : angle 1.59278 ( 90) hydrogen bonds : bond 0.03213 ( 809) hydrogen bonds : angle 4.92412 ( 2148) link_ALPHA1-3 : bond 0.00432 ( 3) link_ALPHA1-3 : angle 2.84685 ( 9) link_ALPHA1-6 : bond 0.00695 ( 3) link_ALPHA1-6 : angle 2.22623 ( 9) link_BETA1-4 : bond 0.01369 ( 6) link_BETA1-4 : angle 4.46338 ( 18) link_NAG-ASN : bond 0.00935 ( 6) link_NAG-ASN : angle 6.59581 ( 18) ********************** 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 670 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 581 time to evaluate : 0.904 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: 0.8897 (OUTLIER) cc_final: 0.8546 (t) REVERT: C 83 GLU cc_start: 0.7649 (tm-30) cc_final: 0.7402 (tm-30) REVERT: C 102 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.7872 (mp0) REVERT: C 375 SER cc_start: 0.8828 (OUTLIER) cc_final: 0.8444 (p) REVERT: E 540 GLN cc_start: 0.7547 (OUTLIER) cc_final: 0.7032 (mt0) REVERT: E 648 GLU cc_start: 0.8363 (tm-30) cc_final: 0.7847 (tp30) REVERT: E 656 ASN cc_start: 0.7900 (t0) cc_final: 0.7633 (t0) REVERT: F 543 ASN cc_start: 0.8800 (m110) cc_final: 0.8275 (t0) REVERT: F 589 ASP cc_start: 0.8477 (t0) cc_final: 0.8194 (t0) REVERT: F 593 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8867 (tt) REVERT: G 1 GLN cc_start: 0.7259 (tp40) cc_final: 0.7012 (tp40) REVERT: G 2 GLU cc_start: 0.8452 (pm20) cc_final: 0.8165 (pm20) REVERT: G 100 MET cc_start: 0.8193 (mmm) cc_final: 0.7814 (mmt) REVERT: H 24 ARG cc_start: 0.7859 (mmp-170) cc_final: 0.7442 (mmp-170) REVERT: H 47 LEU cc_start: 0.9296 (mm) cc_final: 0.9004 (mm) REVERT: H 61 ARG cc_start: 0.7948 (ptp-170) cc_final: 0.7692 (mtm180) REVERT: H 62 PHE cc_start: 0.8463 (m-80) cc_final: 0.8212 (m-80) REVERT: H 87 PHE cc_start: 0.8748 (m-80) cc_final: 0.8436 (m-10) REVERT: I 90 TYR cc_start: 0.6832 (m-10) cc_final: 0.6590 (m-10) REVERT: J 49 TYR cc_start: 0.8519 (p90) cc_final: 0.8258 (p90) REVERT: J 78 LEU cc_start: 0.8547 (mp) cc_final: 0.8274 (mp) REVERT: J 79 GLN cc_start: 0.8124 (mm110) cc_final: 0.7899 (mm110) REVERT: J 85 THR cc_start: 0.8255 (OUTLIER) cc_final: 0.7950 (p) REVERT: J 86 TYR cc_start: 0.8105 (m-10) cc_final: 0.7792 (m-10) REVERT: K 47 TRP cc_start: 0.8417 (t60) cc_final: 0.8054 (t60) REVERT: K 81 ASP cc_start: 0.6892 (m-30) cc_final: 0.6034 (p0) REVERT: L 32 GLU cc_start: 0.7483 (mp0) cc_final: 0.7164 (pm20) REVERT: M 52 ASN cc_start: 0.9234 (p0) cc_final: 0.8714 (p0) REVERT: M 53 ASP cc_start: 0.9108 (p0) cc_final: 0.8902 (p0) REVERT: M 87 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7948 (mm-30) REVERT: N 10 ASP cc_start: 0.8449 (t0) cc_final: 0.8237 (t0) REVERT: N 53 ASP cc_start: 0.8346 (p0) cc_final: 0.8106 (p0) REVERT: O 24 ILE cc_start: 0.9268 (mm) cc_final: 0.8876 (mt) REVERT: P 71 PHE cc_start: 0.6815 (m-80) cc_final: 0.6324 (m-10) REVERT: P 104 LEU cc_start: 0.8205 (tp) cc_final: 0.7973 (tp) REVERT: Q 81 GLU cc_start: 0.6789 (tm-30) cc_final: 0.6191 (tm-30) REVERT: R 24 ARG cc_start: 0.7134 (mmp80) cc_final: 0.6870 (mmp80) REVERT: S 3 GLN cc_start: 0.8307 (pp30) cc_final: 0.8039 (pp30) REVERT: S 79 TYR cc_start: 0.8335 (m-10) cc_final: 0.8128 (m-10) REVERT: S 100 GLU cc_start: 0.9028 (mm-30) cc_final: 0.8821 (mp0) REVERT: T 24 ARG cc_start: 0.8058 (mmm160) cc_final: 0.7756 (mmm-85) REVERT: T 42 GLN cc_start: 0.8192 (mp10) cc_final: 0.7839 (mp10) REVERT: T 81 GLU cc_start: 0.8902 (pm20) cc_final: 0.8683 (pm20) REVERT: T 82 ASP cc_start: 0.8707 (m-30) cc_final: 0.8276 (m-30) REVERT: U 12 LYS cc_start: 0.8843 (mmtm) cc_final: 0.8135 (mmmm) REVERT: U 89 VAL cc_start: 0.7716 (OUTLIER) cc_final: 0.7298 (m) outliers start: 89 outliers final: 75 residues processed: 629 average time/residue: 0.1372 time to fit residues: 138.1280 Evaluate side-chains 638 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 556 time to evaluate : 0.984 ------------------------------------------------------------------------------- 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 A residue 373 THR Chi-restraints excluded: chain A residue 491 ILE 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 125 LEU Chi-restraints excluded: chain B residue 294 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 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 513 VAL 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 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 77 THR Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain H residue 4 LEU 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 45 LEU Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain J residue 10 PHE Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 37 GLN 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 11 LEU 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 86 VAL Chi-restraints excluded: chain N residue 3 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 N residue 95 LEU 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 R residue 33 LEU Chi-restraints excluded: chain R residue 46 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 37 VAL Chi-restraints excluded: chain U residue 74 SER Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 100 LEU Chi-restraints excluded: chain U residue 108 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 83 optimal weight: 1.9990 chunk 276 optimal weight: 7.9990 chunk 301 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 186 optimal weight: 0.0010 chunk 284 optimal weight: 1.9990 chunk 132 optimal weight: 0.0980 chunk 180 optimal weight: 8.9990 chunk 183 optimal weight: 5.9990 chunk 167 optimal weight: 1.9990 chunk 82 optimal weight: 9.9990 overall best weight: 1.2192 ------------------------------------------------------------------------------- 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 70 HIS ** 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** N 20 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.137748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.102612 restraints weight = 46372.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.100922 restraints weight = 34276.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.101979 restraints weight = 40115.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.102633 restraints weight = 26001.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.103790 restraints weight = 23155.936| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3161 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= 0.150 Angle : 0.728 16.731 34170 Z= 0.347 Chirality : 0.046 0.402 3875 Planarity : 0.005 0.080 4320 Dihedral : 6.571 89.833 3712 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.78 % Favored : 94.19 % Rotamer: Outliers : 3.46 % Allowed : 24.27 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.20 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.15), residues: 3079 helix: 0.16 (0.28), residues: 387 sheet: 0.31 (0.18), residues: 941 loop : -1.36 (0.15), residues: 1751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG K 38 TYR 0.026 0.002 TYR H 49 PHE 0.016 0.001 PHE R 71 TRP 0.056 0.002 TRP G 36 HIS 0.005 0.001 HIS L 90 Details of bonding type rmsd covalent geometry : bond 0.00359 (25050) covalent geometry : angle 0.69823 (34026) SS BOND : bond 0.00436 ( 45) SS BOND : angle 1.68283 ( 90) hydrogen bonds : bond 0.03302 ( 809) hydrogen bonds : angle 4.92493 ( 2148) link_ALPHA1-3 : bond 0.00370 ( 3) link_ALPHA1-3 : angle 2.73030 ( 9) link_ALPHA1-6 : bond 0.00636 ( 3) link_ALPHA1-6 : angle 2.33750 ( 9) link_BETA1-4 : bond 0.01281 ( 6) link_BETA1-4 : angle 4.46316 ( 18) link_NAG-ASN : bond 0.00869 ( 6) link_NAG-ASN : angle 6.61306 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3834.82 seconds wall clock time: 67 minutes 14.36 seconds (4034.36 seconds total)