Starting phenix.real_space_refine on Fri May 23 19:42:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sw3_40796/05_2025/8sw3_40796.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sw3_40796/05_2025/8sw3_40796.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sw3_40796/05_2025/8sw3_40796.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sw3_40796/05_2025/8sw3_40796.map" model { file = "/net/cci-nas-00/data/ceres_data/8sw3_40796/05_2025/8sw3_40796.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sw3_40796/05_2025/8sw3_40796.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.042 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 141 5.16 5 C 15528 2.51 5 N 4239 2.21 5 O 4911 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 24819 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 3469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3469 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 23, 'TRANS': 415} Chain breaks: 3 Chain: "G" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "I" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 803 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "B" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 997 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "H" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 998 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "L" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 789 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "C" Number of atoms: 3469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3469 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 23, 'TRANS': 415} Chain breaks: 3 Chain: "J" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "O" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 803 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "E" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 997 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "M" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 998 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "Q" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 789 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "D" Number of atoms: 3469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3469 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 23, 'TRANS': 415} Chain breaks: 3 Chain: "K" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "P" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 803 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "F" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 997 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "N" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 998 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "R" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 789 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 13.97, per 1000 atoms: 0.56 Number of scatterers: 24819 At special positions: 0 Unit cell: (131.17, 135.206, 161.44, 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 141 16.00 O 4911 8.00 N 4239 7.00 C 15528 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=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.04 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS E 605 " distance=2.02 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.03 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.04 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.04 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.03 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.03 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.03 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS F 605 " distance=2.02 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 92 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA T 3 " - " MAN T 4 " " BMA V 3 " - " MAN V 4 " " BMA X 3 " - " MAN X 4 " BETA1-4 " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " NAG-ASN " NAG A 601 " - " ASN A 160 " " NAG A 602 " - " ASN A 295 " " NAG A 603 " - " ASN A 88 " " NAG A 604 " - " ASN A 133 " " NAG A 605 " - " ASN A 392 " " NAG A 606 " - " ASN A 448 " " NAG A 607 " - " ASN A 234 " " NAG A 608 " - " ASN A 301 " " NAG A 609 " - " ASN A 332 " " NAG A 610 " - " ASN A 339 " " NAG A 611 " - " ASN A 363 " " NAG B 701 " - " ASN B 637 " " NAG B 702 " - " ASN B 611 " " NAG B 703 " - " ASN B 618 " " NAG C 601 " - " ASN C 160 " " NAG C 602 " - " ASN C 295 " " NAG C 603 " - " ASN C 88 " " NAG C 604 " - " ASN C 133 " " NAG C 605 " - " ASN C 392 " " NAG C 606 " - " ASN C 448 " " NAG C 607 " - " ASN C 234 " " NAG C 608 " - " ASN C 301 " " NAG C 609 " - " ASN C 332 " " NAG C 610 " - " ASN C 339 " " NAG C 611 " - " ASN C 363 " " NAG D 601 " - " ASN D 160 " " NAG D 602 " - " ASN D 295 " " NAG D 603 " - " ASN D 88 " " NAG D 604 " - " ASN D 133 " " NAG D 605 " - " ASN D 392 " " NAG D 606 " - " ASN D 448 " " NAG D 607 " - " ASN D 234 " " NAG D 608 " - " ASN D 301 " " NAG D 609 " - " ASN D 332 " " NAG D 610 " - " ASN D 339 " " NAG D 611 " - " ASN D 363 " " NAG E 701 " - " ASN E 637 " " NAG E 702 " - " ASN E 611 " " NAG E 703 " - " ASN E 618 " " NAG F 701 " - " ASN F 637 " " NAG F 702 " - " ASN F 611 " " NAG F 703 " - " ASN F 618 " " NAG S 1 " - " ASN A 156 " " NAG T 1 " - " ASN A 262 " " NAG U 1 " - " ASN C 156 " " NAG V 1 " - " ASN C 262 " " NAG W 1 " - " ASN D 156 " " NAG X 1 " - " ASN D 262 " Time building additional restraints: 5.91 Conformation dependent library (CDL) restraints added in 3.0 seconds 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5682 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 48 sheets defined 18.0% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.01 Creating SS restraints... Processing helix chain 'A' and resid 98 through 117 removed outlier: 3.885A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.822A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 479 through 484 Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 61 through 64 Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.633A pdb=" N GLU I 83 " --> pdb=" O ALA I 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.398A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 535 removed outlier: 3.592A pdb=" N MET B 535 " --> pdb=" O ALA B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.595A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 596 removed outlier: 3.823A pdb=" N GLN B 575 " --> pdb=" O TRP B 571 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 649 removed outlier: 3.765A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER B 649 " --> pdb=" O LEU B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 663 removed outlier: 3.616A pdb=" N LEU B 663 " --> pdb=" O ASP B 659 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 65 No H-bonds generated for 'chain 'H' and resid 63 through 65' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 100B through 100G Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.046A pdb=" N GLU L 83 " --> pdb=" O THR L 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 117 removed outlier: 3.885A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 139 through 151 Processing helix chain 'C' and resid 335 through 354 removed outlier: 3.821A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 479 through 484 Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 61 through 64 Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'O' and resid 79 through 83 removed outlier: 3.633A pdb=" N GLU O 83 " --> pdb=" O ALA O 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 528 removed outlier: 4.398A pdb=" N GLY E 527 " --> pdb=" O GLY E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 531 through 535 removed outlier: 3.592A pdb=" N MET E 535 " --> pdb=" O ALA E 532 " (cutoff:3.500A) Processing helix chain 'E' and resid 536 through 542 removed outlier: 3.595A pdb=" N GLN E 540 " --> pdb=" O THR E 536 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 596 removed outlier: 3.822A pdb=" N GLN E 575 " --> pdb=" O TRP E 571 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU E 576 " --> pdb=" O GLY E 572 " (cutoff:3.500A) Processing helix chain 'E' and resid 619 through 624 Processing helix chain 'E' and resid 627 through 636 Processing helix chain 'E' and resid 638 through 649 removed outlier: 3.765A pdb=" N GLY E 644 " --> pdb=" O GLN E 640 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER E 649 " --> pdb=" O LEU E 645 " (cutoff:3.500A) Processing helix chain 'E' and resid 651 through 663 removed outlier: 3.616A pdb=" N LEU E 663 " --> pdb=" O ASP E 659 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 65 No H-bonds generated for 'chain 'M' and resid 63 through 65' Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'M' and resid 100B through 100G Processing helix chain 'Q' and resid 79 through 83 removed outlier: 4.046A pdb=" N GLU Q 83 " --> pdb=" O THR Q 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 117 removed outlier: 3.884A pdb=" N GLU D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 139 through 151 Processing helix chain 'D' and resid 335 through 354 removed outlier: 3.821A pdb=" N HIS D 352 " --> pdb=" O GLN D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 479 through 484 Processing helix chain 'K' and resid 28 through 32 Processing helix chain 'K' and resid 61 through 64 Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'P' and resid 79 through 83 removed outlier: 3.633A pdb=" N GLU P 83 " --> pdb=" O ALA P 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 528 removed outlier: 4.398A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 535 removed outlier: 3.592A pdb=" N MET F 535 " --> pdb=" O ALA F 532 " (cutoff:3.500A) Processing helix chain 'F' and resid 536 through 542 removed outlier: 3.595A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 596 removed outlier: 3.822A pdb=" N GLN F 575 " --> pdb=" O TRP F 571 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU F 576 " --> pdb=" O GLY F 572 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 624 Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 649 removed outlier: 3.766A pdb=" N GLY F 644 " --> pdb=" O GLN F 640 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER F 649 " --> pdb=" O LEU F 645 " (cutoff:3.500A) Processing helix chain 'F' and resid 651 through 663 removed outlier: 3.616A pdb=" N LEU F 663 " --> pdb=" O ASP F 659 " (cutoff:3.500A) Processing helix chain 'N' and resid 63 through 65 No H-bonds generated for 'chain 'N' and resid 63 through 65' Processing helix chain 'N' and resid 83 through 87 Processing helix chain 'N' and resid 100B through 100G Processing helix chain 'R' and resid 79 through 83 removed outlier: 4.046A pdb=" N GLU R 83 " --> pdb=" O THR R 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.607A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.923A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 6.865A pdb=" N CYS A 54 " --> pdb=" O VAL A 75 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.244A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 302 removed outlier: 4.083A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 322 through 323 current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 465 through 470 Processing sheet with id=AA8, first strand: chain 'A' and resid 305 through 312 removed outlier: 6.371A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'G' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 10 through 12 current: chain 'G' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 57 through 59 current: chain 'G' and resid 100H through 103 Processing sheet with id=AB2, first strand: chain 'I' and resid 18 through 24 Processing sheet with id=AB3, first strand: chain 'I' and resid 33 through 38 removed outlier: 6.339A pdb=" N TRP I 35 " --> pdb=" O MET I 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 45 through 48 current: chain 'I' and resid 96 through 98 Processing sheet with id=AB4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB5, first strand: chain 'H' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 11 through 12 current: chain 'H' and resid 45 through 52 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 102 through 103 Processing sheet with id=AB6, first strand: chain 'L' and resid 9 through 12 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 9 through 12 current: chain 'L' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 53 through 54 current: chain 'L' and resid 95B through 98 Processing sheet with id=AB7, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AB8, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.607A pdb=" N VAL E 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N VAL C 38 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N THR E 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N TYR C 40 " --> pdb=" O CYS E 604 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N CYS E 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.924A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 75 through 76 removed outlier: 6.865A pdb=" N CYS C 54 " --> pdb=" O VAL C 75 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AC3, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AC4, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.244A pdb=" N ALA C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N TYR C 435 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 259 through 261 current: chain 'C' and resid 284 through 302 removed outlier: 4.083A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 322 through 323 current: chain 'C' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 381 through 385 current: chain 'C' and resid 465 through 470 Processing sheet with id=AC6, first strand: chain 'C' and resid 305 through 312 removed outlier: 6.371A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AC8, first strand: chain 'J' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 10 through 12 current: chain 'J' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 57 through 59 current: chain 'J' and resid 100H through 103 Processing sheet with id=AC9, first strand: chain 'O' and resid 18 through 24 Processing sheet with id=AD1, first strand: chain 'O' and resid 33 through 38 removed outlier: 6.338A pdb=" N TRP O 35 " --> pdb=" O MET O 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 45 through 48 current: chain 'O' and resid 96 through 98 Processing sheet with id=AD2, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AD3, first strand: chain 'M' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 11 through 12 current: chain 'M' and resid 45 through 52 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 57 through 59 current: chain 'M' and resid 102 through 103 Processing sheet with id=AD4, first strand: chain 'Q' and resid 9 through 12 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 9 through 12 current: chain 'Q' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 53 through 54 current: chain 'Q' and resid 95B through 98 Processing sheet with id=AD5, first strand: chain 'Q' and resid 19 through 24 Processing sheet with id=AD6, first strand: chain 'D' and resid 494 through 499 removed outlier: 5.607A pdb=" N VAL F 608 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N VAL D 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N THR F 606 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N TYR D 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N CYS F 604 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 45 through 47 removed outlier: 3.924A pdb=" N ILE D 225 " --> pdb=" O VAL D 245 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N VAL D 242 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 75 through 76 removed outlier: 6.865A pdb=" N CYS D 54 " --> pdb=" O VAL D 75 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 91 through 94 Processing sheet with id=AE1, first strand: chain 'D' and resid 169 through 177 Processing sheet with id=AE2, first strand: chain 'D' and resid 200 through 203 removed outlier: 6.243A pdb=" N ALA D 200 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N TYR D 435 " --> pdb=" O ALA D 200 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N THR D 202 " --> pdb=" O TYR D 435 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 259 through 261 current: chain 'D' and resid 284 through 302 removed outlier: 4.083A pdb=" N ASN D 301 " --> pdb=" O ILE D 323 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 322 through 323 current: chain 'D' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 381 through 385 current: chain 'D' and resid 465 through 470 Processing sheet with id=AE4, first strand: chain 'D' and resid 305 through 312 removed outlier: 6.371A pdb=" N GLN D 315 " --> pdb=" O ILE D 309 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AE6, first strand: chain 'K' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 10 through 12 current: chain 'K' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 57 through 59 current: chain 'K' and resid 100H through 103 Processing sheet with id=AE7, first strand: chain 'P' and resid 18 through 24 Processing sheet with id=AE8, first strand: chain 'P' and resid 33 through 38 removed outlier: 6.339A pdb=" N TRP P 35 " --> pdb=" O MET P 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 45 through 48 current: chain 'P' and resid 96 through 98 Processing sheet with id=AE9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AF1, first strand: chain 'N' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 11 through 12 current: chain 'N' and resid 45 through 52 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 57 through 59 current: chain 'N' and resid 102 through 103 Processing sheet with id=AF2, first strand: chain 'R' and resid 9 through 12 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 9 through 12 current: chain 'R' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 53 through 54 current: chain 'R' and resid 95B through 98 Processing sheet with id=AF3, first strand: chain 'R' and resid 19 through 24 651 hydrogen bonds defined for protein. 1656 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: 8.38 Time building geometry restraints manager: 6.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4751 1.33 - 1.45: 7420 1.45 - 1.58: 12972 1.58 - 1.71: 0 1.71 - 1.84: 192 Bond restraints: 25335 Sorted by residual: bond pdb=" N ILE B 595 " pdb=" CA ILE B 595 " ideal model delta sigma weight residual 1.461 1.497 -0.036 1.19e-02 7.06e+03 9.18e+00 bond pdb=" N ILE F 595 " pdb=" CA ILE F 595 " ideal model delta sigma weight residual 1.461 1.496 -0.036 1.19e-02 7.06e+03 9.08e+00 bond pdb=" N ILE E 595 " pdb=" CA ILE E 595 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.19e-02 7.06e+03 8.85e+00 bond pdb=" C TRP B 596 " pdb=" O TRP B 596 " ideal model delta sigma weight residual 1.234 1.200 0.034 1.33e-02 5.65e+03 6.67e+00 bond pdb=" C TRP F 596 " pdb=" O TRP F 596 " ideal model delta sigma weight residual 1.234 1.200 0.034 1.33e-02 5.65e+03 6.65e+00 ... (remaining 25330 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 31779 1.87 - 3.74: 2248 3.74 - 5.61: 308 5.61 - 7.47: 51 7.47 - 9.34: 12 Bond angle restraints: 34398 Sorted by residual: angle pdb=" N TRP B 596 " pdb=" CA TRP B 596 " pdb=" C TRP B 596 " ideal model delta sigma weight residual 110.55 101.21 9.34 1.35e+00 5.49e-01 4.79e+01 angle pdb=" N TRP E 596 " pdb=" CA TRP E 596 " pdb=" C TRP E 596 " ideal model delta sigma weight residual 110.55 101.21 9.34 1.35e+00 5.49e-01 4.78e+01 angle pdb=" N TRP F 596 " pdb=" CA TRP F 596 " pdb=" C TRP F 596 " ideal model delta sigma weight residual 110.55 101.22 9.33 1.35e+00 5.49e-01 4.78e+01 angle pdb=" CA TRP E 596 " pdb=" C TRP E 596 " pdb=" N GLY E 597 " ideal model delta sigma weight residual 115.27 123.02 -7.75 1.30e+00 5.92e-01 3.55e+01 angle pdb=" CA TRP F 596 " pdb=" C TRP F 596 " pdb=" N GLY F 597 " ideal model delta sigma weight residual 115.27 123.00 -7.73 1.30e+00 5.92e-01 3.53e+01 ... (remaining 34393 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.51: 15294 21.51 - 43.03: 355 43.03 - 64.54: 131 64.54 - 86.05: 39 86.05 - 107.56: 18 Dihedral angle restraints: 15837 sinusoidal: 6984 harmonic: 8853 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " pdb=" CB CYS H 92 " ideal model delta sinusoidal sigma weight residual 93.00 52.22 40.78 1 1.00e+01 1.00e-02 2.33e+01 dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 92 " pdb=" CB CYS N 92 " ideal model delta sinusoidal sigma weight residual 93.00 52.23 40.77 1 1.00e+01 1.00e-02 2.33e+01 dihedral pdb=" CB CYS M 22 " pdb=" SG CYS M 22 " pdb=" SG CYS M 92 " pdb=" CB CYS M 92 " ideal model delta sinusoidal sigma weight residual 93.00 52.25 40.75 1 1.00e+01 1.00e-02 2.33e+01 ... (remaining 15834 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 3447 0.091 - 0.181: 528 0.181 - 0.272: 21 0.272 - 0.363: 15 0.363 - 0.453: 3 Chirality restraints: 4014 Sorted by residual: chirality pdb=" C1 NAG D 607 " pdb=" ND2 ASN D 234 " pdb=" C2 NAG D 607 " pdb=" O5 NAG D 607 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.14e+00 chirality pdb=" C1 NAG C 607 " pdb=" ND2 ASN C 234 " pdb=" C2 NAG C 607 " pdb=" O5 NAG C 607 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.13e+00 chirality pdb=" C1 NAG A 607 " pdb=" ND2 ASN A 234 " pdb=" C2 NAG A 607 " pdb=" O5 NAG A 607 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.08e+00 ... (remaining 4011 not shown) Planarity restraints: 4377 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 604 " 0.329 2.00e-02 2.50e+03 2.84e-01 1.01e+03 pdb=" C7 NAG C 604 " -0.076 2.00e-02 2.50e+03 pdb=" C8 NAG C 604 " 0.046 2.00e-02 2.50e+03 pdb=" N2 NAG C 604 " -0.499 2.00e-02 2.50e+03 pdb=" O7 NAG C 604 " 0.199 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 604 " 0.329 2.00e-02 2.50e+03 2.84e-01 1.01e+03 pdb=" C7 NAG D 604 " -0.076 2.00e-02 2.50e+03 pdb=" C8 NAG D 604 " 0.047 2.00e-02 2.50e+03 pdb=" N2 NAG D 604 " -0.498 2.00e-02 2.50e+03 pdb=" O7 NAG D 604 " 0.199 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 604 " -0.329 2.00e-02 2.50e+03 2.84e-01 1.01e+03 pdb=" C7 NAG A 604 " 0.076 2.00e-02 2.50e+03 pdb=" C8 NAG A 604 " -0.046 2.00e-02 2.50e+03 pdb=" N2 NAG A 604 " 0.498 2.00e-02 2.50e+03 pdb=" O7 NAG A 604 " -0.199 2.00e-02 2.50e+03 ... (remaining 4374 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 1593 2.72 - 3.27: 23096 3.27 - 3.81: 41189 3.81 - 4.36: 54729 4.36 - 4.90: 89565 Nonbonded interactions: 210172 Sorted by model distance: nonbonded pdb=" NZ LYS D 46 " pdb=" OD2 ASP F 632 " model vdw 2.180 3.120 nonbonded pdb=" NZ LYS A 46 " pdb=" OD2 ASP B 632 " model vdw 2.181 3.120 nonbonded pdb=" NZ LYS C 46 " pdb=" OD2 ASP E 632 " model vdw 2.181 3.120 nonbonded pdb=" NZ LYS A 97 " pdb=" CE LYS A 275 " model vdw 2.274 3.520 nonbonded pdb=" O ILE E 595 " pdb=" ND2 ASN E 651 " model vdw 2.285 3.120 ... (remaining 210167 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: 0.17 Found NCS groups: ncs_group { reference = chain 'I' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'H' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'T' selection = chain 'V' selection = chain 'X' } ncs_group { reference = chain 'L' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = chain 'G' selection = chain 'K' selection = chain 'J' } ncs_group { reference = chain 'S' selection = chain 'U' selection = chain 'W' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.920 Check model and map are aligned: 0.170 Set scattering table: 0.250 Process input model: 52.230 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 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 : 0.006 0.072 25440 Z= 0.299 Angle : 1.081 11.191 34668 Z= 0.626 Chirality : 0.065 0.453 4014 Planarity : 0.015 0.284 4329 Dihedral : 11.680 107.563 10020 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.19 % Allowed : 1.05 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.15), residues: 3039 helix: -0.50 (0.26), residues: 417 sheet: 1.18 (0.18), residues: 831 loop : 0.46 (0.14), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP N 47 HIS 0.019 0.003 HIS M 50 PHE 0.027 0.003 PHE C 53 TYR 0.018 0.003 TYR D 318 ARG 0.018 0.001 ARG A 360 Details of bonding type rmsd link_NAG-ASN : bond 0.00574 ( 48) link_NAG-ASN : angle 3.10454 ( 144) link_BETA1-4 : bond 0.00414 ( 9) link_BETA1-4 : angle 1.41537 ( 27) link_ALPHA1-3 : bond 0.00370 ( 3) link_ALPHA1-3 : angle 1.44083 ( 9) hydrogen bonds : bond 0.13677 ( 651) hydrogen bonds : angle 7.14903 ( 1656) SS BOND : bond 0.00593 ( 45) SS BOND : angle 2.55238 ( 90) covalent geometry : bond 0.00640 (25335) covalent geometry : angle 1.05768 (34398) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 597 time to evaluate : 2.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ARG cc_start: 0.7249 (mtp85) cc_final: 0.6627 (ttp80) REVERT: A 168 LYS cc_start: 0.7687 (tttt) cc_final: 0.7454 (ttpt) REVERT: A 178 LYS cc_start: 0.7712 (tttt) cc_final: 0.6906 (ttpp) REVERT: A 215 ILE cc_start: 0.8116 (mt) cc_final: 0.7710 (mm) REVERT: A 232 LYS cc_start: 0.7927 (mttp) cc_final: 0.7223 (mmtp) REVERT: A 267 GLU cc_start: 0.6979 (mp0) cc_final: 0.6701 (mp0) REVERT: A 283 ASN cc_start: 0.8332 (m-40) cc_final: 0.8114 (m-40) REVERT: A 347 LYS cc_start: 0.7376 (mttt) cc_final: 0.6975 (pttp) REVERT: A 355 ASN cc_start: 0.6570 (m-40) cc_final: 0.6084 (t0) REVERT: A 440 GLN cc_start: 0.7552 (mt0) cc_final: 0.7333 (tt0) REVERT: A 478 ASN cc_start: 0.7191 (m-40) cc_final: 0.6895 (t0) REVERT: A 490 LYS cc_start: 0.8488 (ttpp) cc_final: 0.7397 (tptp) REVERT: G 70 SER cc_start: 0.8137 (t) cc_final: 0.7935 (p) REVERT: I 45 LYS cc_start: 0.7659 (tttt) cc_final: 0.7187 (ttmm) REVERT: I 47 MET cc_start: 0.8242 (mmm) cc_final: 0.8020 (mmt) REVERT: B 530 MET cc_start: 0.9095 (mtp) cc_final: 0.8704 (mtp) REVERT: B 542 ARG cc_start: 0.7048 (mmm-85) cc_final: 0.6445 (mtm110) REVERT: B 590 GLN cc_start: 0.8066 (mm-40) cc_final: 0.7840 (mm-40) REVERT: B 657 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7246 (mm-30) REVERT: H 56 SER cc_start: 0.8106 (t) cc_final: 0.7732 (p) REVERT: H 100 ARG cc_start: 0.7820 (mtm180) cc_final: 0.6767 (mmm160) REVERT: L 27 SER cc_start: 0.8124 (m) cc_final: 0.7579 (p) REVERT: L 97 VAL cc_start: 0.8052 (t) cc_final: 0.7834 (m) REVERT: C 46 LYS cc_start: 0.8494 (mmtm) cc_final: 0.8270 (mptt) REVERT: C 97 LYS cc_start: 0.8251 (mmtm) cc_final: 0.7974 (mttp) REVERT: C 117 LYS cc_start: 0.7339 (mttt) cc_final: 0.6744 (mmtm) REVERT: C 166 ARG cc_start: 0.7268 (mtp85) cc_final: 0.6597 (ttp80) REVERT: C 178 LYS cc_start: 0.7832 (tttt) cc_final: 0.7142 (ttpp) REVERT: C 211 GLU cc_start: 0.6693 (tt0) cc_final: 0.6209 (tp30) REVERT: C 232 LYS cc_start: 0.7993 (mttp) cc_final: 0.7399 (mmtp) REVERT: C 267 GLU cc_start: 0.6976 (mp0) cc_final: 0.6712 (mp0) REVERT: C 325 ASP cc_start: 0.7296 (m-30) cc_final: 0.7082 (p0) REVERT: C 347 LYS cc_start: 0.7129 (mttt) cc_final: 0.6831 (pttp) REVERT: C 355 ASN cc_start: 0.6668 (m-40) cc_final: 0.6396 (t0) REVERT: C 381 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7590 (mm-30) REVERT: C 444 ARG cc_start: 0.7622 (mtt90) cc_final: 0.7342 (mmm160) REVERT: C 478 ASN cc_start: 0.7320 (m-40) cc_final: 0.6943 (t0) REVERT: C 490 LYS cc_start: 0.8366 (ttpp) cc_final: 0.7284 (tptp) REVERT: J 67 PHE cc_start: 0.7987 (m-10) cc_final: 0.7774 (m-10) REVERT: J 70 SER cc_start: 0.8278 (t) cc_final: 0.7909 (p) REVERT: J 81 GLN cc_start: 0.8309 (tp40) cc_final: 0.7979 (tp40) REVERT: J 90 TYR cc_start: 0.8197 (m-80) cc_final: 0.7763 (m-80) REVERT: J 91 TYR cc_start: 0.8094 (m-80) cc_final: 0.7835 (m-80) REVERT: O 54 ARG cc_start: 0.8301 (mtm-85) cc_final: 0.8004 (mtm-85) REVERT: E 542 ARG cc_start: 0.6985 (mmm-85) cc_final: 0.6208 (mtm-85) REVERT: E 657 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7214 (mm-30) REVERT: M 25 SER cc_start: 0.7767 (t) cc_final: 0.7065 (m) REVERT: M 27 ASN cc_start: 0.8612 (t0) cc_final: 0.8361 (t0) REVERT: M 56 SER cc_start: 0.8069 (t) cc_final: 0.7614 (p) REVERT: M 100 ARG cc_start: 0.7865 (mtm180) cc_final: 0.6946 (mmm160) REVERT: M 101 ASP cc_start: 0.6651 (m-30) cc_final: 0.6200 (m-30) REVERT: D 97 LYS cc_start: 0.8196 (mmtm) cc_final: 0.7912 (mttp) REVERT: D 112 TRP cc_start: 0.7330 (t-100) cc_final: 0.7122 (t-100) REVERT: D 117 LYS cc_start: 0.7515 (mttt) cc_final: 0.6994 (mmtm) REVERT: D 136 ASN cc_start: 0.6287 (m-40) cc_final: 0.5974 (m-40) REVERT: D 166 ARG cc_start: 0.7310 (mtp85) cc_final: 0.6500 (ttp80) REVERT: D 232 LYS cc_start: 0.7700 (mttp) cc_final: 0.7168 (mmtm) REVERT: D 267 GLU cc_start: 0.6969 (mp0) cc_final: 0.6648 (mp0) REVERT: D 315 GLN cc_start: 0.7901 (mm-40) cc_final: 0.7600 (mt0) REVERT: D 347 LYS cc_start: 0.7211 (mttt) cc_final: 0.6965 (pttp) REVERT: D 355 ASN cc_start: 0.6695 (m-40) cc_final: 0.6304 (t0) REVERT: D 381 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7422 (tp30) REVERT: D 444 ARG cc_start: 0.7713 (mtt90) cc_final: 0.7481 (mmm160) REVERT: D 490 LYS cc_start: 0.8366 (ttpp) cc_final: 0.7373 (tptp) REVERT: K 70 SER cc_start: 0.8116 (t) cc_final: 0.7795 (p) REVERT: P 97 ILE cc_start: 0.8008 (mt) cc_final: 0.7710 (mm) REVERT: F 542 ARG cc_start: 0.6966 (mmm-85) cc_final: 0.6502 (mtm110) REVERT: F 653 GLN cc_start: 0.8275 (mt0) cc_final: 0.7841 (mt0) REVERT: F 657 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7491 (mt-10) REVERT: N 5 GLN cc_start: 0.7223 (tp40) cc_final: 0.7010 (tp40) REVERT: N 25 SER cc_start: 0.7612 (t) cc_final: 0.6994 (m) REVERT: N 27 ASN cc_start: 0.8467 (t0) cc_final: 0.8246 (t0) REVERT: N 56 SER cc_start: 0.7770 (t) cc_final: 0.7335 (p) REVERT: N 100 ARG cc_start: 0.7696 (mtm180) cc_final: 0.6873 (mmm160) outliers start: 5 outliers final: 2 residues processed: 602 average time/residue: 1.2573 time to fit residues: 877.7963 Evaluate side-chains 440 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 438 time to evaluate : 2.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 275 LYS Chi-restraints excluded: chain D residue 283 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 250 optimal weight: 0.9980 chunk 225 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 76 optimal weight: 0.4980 chunk 151 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 chunk 232 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 chunk 141 optimal weight: 0.9980 chunk 173 optimal weight: 0.8980 chunk 269 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 ASN A 352 HIS A 377 ASN A 422 GLN G 76 ASN I 31 ASN I 53 GLN B 591 GLN C 85 HIS C 103 GLN C 197 ASN C 352 HIS J 76 ASN O 53 GLN E 591 GLN M 77 GLN D 85 HIS D 197 ASN D 352 HIS D 377 ASN K 76 ASN P 31 ASN P 38 GLN P 53 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.167341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.132159 restraints weight = 24446.955| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.80 r_work: 0.3188 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 25440 Z= 0.154 Angle : 0.603 7.744 34668 Z= 0.313 Chirality : 0.045 0.172 4014 Planarity : 0.004 0.038 4329 Dihedral : 7.305 72.331 4572 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.25 % Favored : 98.65 % Rotamer: Outliers : 2.07 % Allowed : 7.15 % Favored : 90.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.15), residues: 3039 helix: 0.22 (0.28), residues: 396 sheet: 0.86 (0.16), residues: 915 loop : 0.42 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 479 HIS 0.007 0.001 HIS H 50 PHE 0.017 0.002 PHE A 53 TYR 0.015 0.001 TYR O 96 ARG 0.006 0.001 ARG D 419 Details of bonding type rmsd link_NAG-ASN : bond 0.00532 ( 48) link_NAG-ASN : angle 2.57114 ( 144) link_BETA1-4 : bond 0.00427 ( 9) link_BETA1-4 : angle 1.68512 ( 27) link_ALPHA1-3 : bond 0.00842 ( 3) link_ALPHA1-3 : angle 2.43417 ( 9) hydrogen bonds : bond 0.04479 ( 651) hydrogen bonds : angle 5.50135 ( 1656) SS BOND : bond 0.00707 ( 45) SS BOND : angle 1.15963 ( 90) covalent geometry : bond 0.00355 (25335) covalent geometry : angle 0.57561 (34398) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 430 time to evaluate : 2.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LYS cc_start: 0.7759 (mttt) cc_final: 0.7328 (mmtm) REVERT: A 136 ASN cc_start: 0.6204 (m-40) cc_final: 0.6001 (m110) REVERT: A 166 ARG cc_start: 0.7441 (mtp85) cc_final: 0.6862 (ttp80) REVERT: A 178 LYS cc_start: 0.7946 (tttt) cc_final: 0.7292 (ttpp) REVERT: A 232 LYS cc_start: 0.8374 (mttp) cc_final: 0.7761 (mmpt) REVERT: A 267 GLU cc_start: 0.7350 (mp0) cc_final: 0.7037 (mp0) REVERT: A 278 ARG cc_start: 0.8168 (mmt-90) cc_final: 0.7922 (mmt90) REVERT: A 347 LYS cc_start: 0.7888 (mttt) cc_final: 0.7478 (pttp) REVERT: A 490 LYS cc_start: 0.8745 (ttpp) cc_final: 0.7821 (tptt) REVERT: A 504 ARG cc_start: 0.6766 (tpp-160) cc_final: 0.6324 (mpp-170) REVERT: G 11 LEU cc_start: 0.7224 (OUTLIER) cc_final: 0.6945 (tt) REVERT: G 20 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7796 (mt) REVERT: I 47 MET cc_start: 0.8365 (mmm) cc_final: 0.8061 (mmt) REVERT: B 530 MET cc_start: 0.9202 (mtp) cc_final: 0.8967 (mtp) REVERT: B 542 ARG cc_start: 0.7547 (mmm-85) cc_final: 0.7154 (mtm110) REVERT: B 657 GLU cc_start: 0.8306 (mt-10) cc_final: 0.8030 (mm-30) REVERT: H 56 SER cc_start: 0.8292 (t) cc_final: 0.8089 (p) REVERT: H 100 ARG cc_start: 0.8365 (mtm180) cc_final: 0.7359 (mmm160) REVERT: C 97 LYS cc_start: 0.8470 (mmtm) cc_final: 0.8228 (mptt) REVERT: C 117 LYS cc_start: 0.7548 (mttt) cc_final: 0.7202 (mmtm) REVERT: C 136 ASN cc_start: 0.6676 (m-40) cc_final: 0.6316 (m-40) REVERT: C 166 ARG cc_start: 0.7392 (mtp85) cc_final: 0.6841 (ttp80) REVERT: C 178 LYS cc_start: 0.8114 (tttt) cc_final: 0.7526 (ttpp) REVERT: C 211 GLU cc_start: 0.7253 (tt0) cc_final: 0.6798 (tp30) REVERT: C 232 LYS cc_start: 0.8415 (mttp) cc_final: 0.7879 (mmtm) REVERT: C 267 GLU cc_start: 0.7472 (mp0) cc_final: 0.7092 (mp0) REVERT: C 325 ASP cc_start: 0.7474 (m-30) cc_final: 0.7205 (p0) REVERT: C 347 LYS cc_start: 0.7716 (mttt) cc_final: 0.7332 (pttp) REVERT: C 356 ASN cc_start: 0.8020 (OUTLIER) cc_final: 0.7533 (t0) REVERT: C 444 ARG cc_start: 0.7977 (mtt90) cc_final: 0.7668 (mmm160) REVERT: C 475 MET cc_start: 0.6825 (mpt) cc_final: 0.6367 (mpp) REVERT: C 490 LYS cc_start: 0.8683 (ttpp) cc_final: 0.7864 (tptp) REVERT: J 11 LEU cc_start: 0.7388 (OUTLIER) cc_final: 0.7029 (tt) REVERT: J 70 SER cc_start: 0.8460 (t) cc_final: 0.8210 (p) REVERT: J 81 GLN cc_start: 0.8505 (tp40) cc_final: 0.8209 (tp40) REVERT: J 90 TYR cc_start: 0.8425 (m-80) cc_final: 0.8065 (m-80) REVERT: J 91 TYR cc_start: 0.8430 (m-80) cc_final: 0.8178 (m-80) REVERT: O 54 ARG cc_start: 0.8526 (mtm-85) cc_final: 0.8210 (mtm110) REVERT: E 542 ARG cc_start: 0.7559 (mmm-85) cc_final: 0.6889 (mtm-85) REVERT: E 657 GLU cc_start: 0.8390 (mt-10) cc_final: 0.7942 (mm-30) REVERT: M 25 SER cc_start: 0.7888 (t) cc_final: 0.7311 (m) REVERT: M 56 SER cc_start: 0.8255 (t) cc_final: 0.8022 (p) REVERT: M 70 SER cc_start: 0.7985 (p) cc_final: 0.7668 (t) REVERT: M 100 ARG cc_start: 0.8445 (mtm180) cc_final: 0.7477 (mmm160) REVERT: Q 93 ASP cc_start: 0.8486 (m-30) cc_final: 0.8211 (m-30) REVERT: D 97 LYS cc_start: 0.8586 (mmtm) cc_final: 0.8268 (mttp) REVERT: D 106 THR cc_start: 0.8611 (m) cc_final: 0.8372 (m) REVERT: D 117 LYS cc_start: 0.7633 (mttt) cc_final: 0.7306 (mmtm) REVERT: D 136 ASN cc_start: 0.6684 (m-40) cc_final: 0.6331 (m-40) REVERT: D 166 ARG cc_start: 0.7527 (mtp85) cc_final: 0.6806 (ttp80) REVERT: D 232 LYS cc_start: 0.8239 (mttp) cc_final: 0.7632 (mmtm) REVERT: D 267 GLU cc_start: 0.7366 (mp0) cc_final: 0.7072 (mp0) REVERT: D 347 LYS cc_start: 0.7768 (mttt) cc_final: 0.7535 (pttp) REVERT: D 355 ASN cc_start: 0.6928 (m-40) cc_final: 0.6720 (t0) REVERT: D 444 ARG cc_start: 0.8077 (mtt90) cc_final: 0.7811 (mmm160) REVERT: D 475 MET cc_start: 0.7262 (mpt) cc_final: 0.6977 (mpp) REVERT: D 490 LYS cc_start: 0.8758 (ttpp) cc_final: 0.7894 (tptp) REVERT: P 97 ILE cc_start: 0.8142 (mt) cc_final: 0.7899 (mm) REVERT: F 542 ARG cc_start: 0.7593 (mmm-85) cc_final: 0.7159 (mtm110) REVERT: F 636 SER cc_start: 0.8465 (m) cc_final: 0.8088 (p) REVERT: F 653 GLN cc_start: 0.8548 (mt0) cc_final: 0.8319 (mt0) REVERT: F 657 GLU cc_start: 0.8358 (mt-10) cc_final: 0.8154 (mt-10) REVERT: N 25 SER cc_start: 0.7809 (t) cc_final: 0.7309 (m) REVERT: N 56 SER cc_start: 0.8144 (t) cc_final: 0.7914 (p) REVERT: N 100 ARG cc_start: 0.8264 (mtm180) cc_final: 0.7363 (mmm160) outliers start: 55 outliers final: 16 residues processed: 461 average time/residue: 1.2219 time to fit residues: 657.9803 Evaluate side-chains 396 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 376 time to evaluate : 2.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain C residue 356 ASN Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain O residue 27 ILE Chi-restraints excluded: chain E residue 660 LEU Chi-restraints excluded: chain Q residue 27 SER Chi-restraints excluded: chain Q residue 70 SER Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 275 LYS Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 478 ASN Chi-restraints excluded: chain P residue 27 SER Chi-restraints excluded: chain R residue 27 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 263 optimal weight: 2.9990 chunk 290 optimal weight: 4.9990 chunk 224 optimal weight: 1.9990 chunk 288 optimal weight: 0.1980 chunk 265 optimal weight: 1.9990 chunk 261 optimal weight: 7.9990 chunk 292 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 270 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 ASN G 100BGLN I 31 ASN I 53 GLN H 27 ASN L 31 ASN L 53 GLN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 ASN O 31 ASN M 27 ASN M 77 GLN Q 31 ASN D 103 GLN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 377 ASN P 31 ASN P 53 GLN N 5 GLN N 27 ASN R 31 ASN R 53 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.162047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.127105 restraints weight = 24382.580| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.73 r_work: 0.3105 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 25440 Z= 0.166 Angle : 0.579 7.262 34668 Z= 0.298 Chirality : 0.045 0.170 4014 Planarity : 0.004 0.037 4329 Dihedral : 6.231 58.395 4570 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.96 % Allowed : 8.99 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.15), residues: 3039 helix: 0.34 (0.28), residues: 393 sheet: 0.56 (0.16), residues: 945 loop : 0.35 (0.15), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 47 HIS 0.008 0.001 HIS H 50 PHE 0.019 0.002 PHE H 78 TYR 0.019 0.002 TYR C 191 ARG 0.006 0.001 ARG D 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00374 ( 48) link_NAG-ASN : angle 2.19953 ( 144) link_BETA1-4 : bond 0.00454 ( 9) link_BETA1-4 : angle 1.40737 ( 27) link_ALPHA1-3 : bond 0.01020 ( 3) link_ALPHA1-3 : angle 1.48335 ( 9) hydrogen bonds : bond 0.04160 ( 651) hydrogen bonds : angle 5.17226 ( 1656) SS BOND : bond 0.00413 ( 45) SS BOND : angle 1.15239 ( 90) covalent geometry : bond 0.00388 (25335) covalent geometry : angle 0.55886 (34398) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 383 time to evaluate : 2.464 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 117 LYS cc_start: 0.7706 (mttt) cc_final: 0.7278 (mmtm) REVERT: A 166 ARG cc_start: 0.7487 (mtp85) cc_final: 0.6920 (ttp80) REVERT: A 178 LYS cc_start: 0.8068 (tttt) cc_final: 0.7492 (ttpp) REVERT: A 232 LYS cc_start: 0.8481 (mttp) cc_final: 0.7821 (mmpt) REVERT: A 267 GLU cc_start: 0.7362 (mp0) cc_final: 0.7075 (mp0) REVERT: A 278 ARG cc_start: 0.8221 (mmt-90) cc_final: 0.8014 (mmp80) REVERT: A 347 LYS cc_start: 0.7928 (mttt) cc_final: 0.7682 (ttpp) REVERT: A 474 ASP cc_start: 0.7112 (p0) cc_final: 0.6789 (p0) REVERT: A 476 ARG cc_start: 0.7318 (mtm-85) cc_final: 0.6819 (mtm180) REVERT: A 490 LYS cc_start: 0.8724 (ttpp) cc_final: 0.7796 (tptt) REVERT: G 11 LEU cc_start: 0.7321 (OUTLIER) cc_final: 0.7024 (tt) REVERT: G 20 LEU cc_start: 0.8031 (mp) cc_final: 0.7824 (mt) REVERT: B 530 MET cc_start: 0.9215 (mtp) cc_final: 0.8911 (mtp) REVERT: B 542 ARG cc_start: 0.7753 (mmm-85) cc_final: 0.7319 (mtm110) REVERT: H 56 SER cc_start: 0.8425 (t) cc_final: 0.8211 (p) REVERT: C 95 MET cc_start: 0.9159 (ptm) cc_final: 0.8883 (ptm) REVERT: C 117 LYS cc_start: 0.7583 (mttt) cc_final: 0.7215 (mmtm) REVERT: C 136 ASN cc_start: 0.6839 (m-40) cc_final: 0.6627 (m110) REVERT: C 166 ARG cc_start: 0.7496 (mtp85) cc_final: 0.6945 (ttp80) REVERT: C 178 LYS cc_start: 0.8172 (tttt) cc_final: 0.7594 (ttpp) REVERT: C 211 GLU cc_start: 0.7252 (tt0) cc_final: 0.6831 (tp30) REVERT: C 232 LYS cc_start: 0.8472 (mttp) cc_final: 0.7927 (mmtm) REVERT: C 267 GLU cc_start: 0.7575 (mp0) cc_final: 0.7172 (mp0) REVERT: C 325 ASP cc_start: 0.7570 (m-30) cc_final: 0.7352 (p0) REVERT: C 347 LYS cc_start: 0.7761 (mttt) cc_final: 0.7424 (pttm) REVERT: C 444 ARG cc_start: 0.8060 (mtt90) cc_final: 0.7686 (mmm160) REVERT: C 475 MET cc_start: 0.6907 (mpt) cc_final: 0.6675 (mpp) REVERT: C 490 LYS cc_start: 0.8664 (ttpp) cc_final: 0.7774 (tptp) REVERT: J 11 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.7108 (tt) REVERT: J 70 SER cc_start: 0.8517 (t) cc_final: 0.8229 (p) REVERT: J 81 GLN cc_start: 0.8388 (tp40) cc_final: 0.8008 (tp40) REVERT: J 91 TYR cc_start: 0.8538 (m-80) cc_final: 0.8297 (m-80) REVERT: O 54 ARG cc_start: 0.8581 (mtm-85) cc_final: 0.8330 (mtm110) REVERT: E 542 ARG cc_start: 0.7873 (mmm-85) cc_final: 0.7447 (mtm110) REVERT: M 25 SER cc_start: 0.8092 (t) cc_final: 0.7543 (m) REVERT: M 56 SER cc_start: 0.8420 (t) cc_final: 0.8147 (p) REVERT: M 100 ARG cc_start: 0.8531 (mtm180) cc_final: 0.7569 (mmm160) REVERT: D 97 LYS cc_start: 0.8688 (mmtm) cc_final: 0.8397 (mttp) REVERT: D 106 THR cc_start: 0.8570 (m) cc_final: 0.8291 (m) REVERT: D 117 LYS cc_start: 0.7613 (mttt) cc_final: 0.7290 (mmtm) REVERT: D 136 ASN cc_start: 0.6784 (m-40) cc_final: 0.6521 (m110) REVERT: D 166 ARG cc_start: 0.7558 (mtp85) cc_final: 0.6875 (ttp80) REVERT: D 232 LYS cc_start: 0.8404 (mttp) cc_final: 0.7779 (mmtm) REVERT: D 267 GLU cc_start: 0.7408 (mp0) cc_final: 0.7076 (mp0) REVERT: D 444 ARG cc_start: 0.8078 (mtt90) cc_final: 0.7704 (mmm160) REVERT: D 490 LYS cc_start: 0.8750 (ttpp) cc_final: 0.7870 (tptp) REVERT: P 97 ILE cc_start: 0.8135 (mt) cc_final: 0.7930 (mm) REVERT: F 542 ARG cc_start: 0.7890 (mmm-85) cc_final: 0.7449 (mtm110) REVERT: F 636 SER cc_start: 0.8418 (m) cc_final: 0.8192 (p) REVERT: F 640 GLN cc_start: 0.8829 (mm-40) cc_final: 0.8522 (tp40) REVERT: F 657 GLU cc_start: 0.8415 (mt-10) cc_final: 0.8148 (mt-10) REVERT: N 56 SER cc_start: 0.8275 (t) cc_final: 0.8009 (p) REVERT: N 100 ARG cc_start: 0.8434 (mtm180) cc_final: 0.7477 (mmm160) outliers start: 52 outliers final: 30 residues processed: 416 average time/residue: 1.2654 time to fit residues: 609.3981 Evaluate side-chains 391 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 359 time to evaluate : 2.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain O residue 12 SER Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 660 LEU Chi-restraints excluded: chain M residue 19 SER Chi-restraints excluded: chain M residue 101 ASP Chi-restraints excluded: chain Q residue 27 SER Chi-restraints excluded: chain Q residue 70 SER Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 275 LYS Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 478 ASN Chi-restraints excluded: chain P residue 27 SER Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain R residue 27 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 13 optimal weight: 1.9990 chunk 240 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 291 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 236 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 223 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 GLN G 76 ASN G 100BGLN I 31 ASN I 53 GLN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 53 GLN E 652 GLN M 27 ASN M 77 GLN D 98 ASN D 246 GLN D 280 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 31 ASN P 53 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.160218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.124944 restraints weight = 24604.968| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.78 r_work: 0.3073 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 25440 Z= 0.181 Angle : 0.578 8.942 34668 Z= 0.295 Chirality : 0.045 0.151 4014 Planarity : 0.004 0.039 4329 Dihedral : 5.668 58.885 4570 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.33 % Allowed : 9.89 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.15), residues: 3039 helix: 0.36 (0.28), residues: 393 sheet: 0.37 (0.15), residues: 933 loop : 0.21 (0.15), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 47 HIS 0.007 0.001 HIS H 50 PHE 0.018 0.002 PHE H 78 TYR 0.020 0.002 TYR O 49 ARG 0.006 0.001 ARG D 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00319 ( 48) link_NAG-ASN : angle 2.23781 ( 144) link_BETA1-4 : bond 0.00402 ( 9) link_BETA1-4 : angle 1.45525 ( 27) link_ALPHA1-3 : bond 0.01056 ( 3) link_ALPHA1-3 : angle 1.70490 ( 9) hydrogen bonds : bond 0.04181 ( 651) hydrogen bonds : angle 5.11155 ( 1656) SS BOND : bond 0.00401 ( 45) SS BOND : angle 0.99608 ( 90) covalent geometry : bond 0.00430 (25335) covalent geometry : angle 0.55745 (34398) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 368 time to evaluate : 2.597 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 117 LYS cc_start: 0.7725 (mttt) cc_final: 0.7269 (mmtm) REVERT: A 166 ARG cc_start: 0.7472 (mtp85) cc_final: 0.6899 (ttp80) REVERT: A 178 LYS cc_start: 0.8154 (tttt) cc_final: 0.7592 (ttpp) REVERT: A 232 LYS cc_start: 0.8496 (mttp) cc_final: 0.7797 (mmpt) REVERT: A 267 GLU cc_start: 0.7375 (mp0) cc_final: 0.7061 (mp0) REVERT: A 278 ARG cc_start: 0.8230 (mmt-90) cc_final: 0.8013 (mmp80) REVERT: A 347 LYS cc_start: 0.7989 (mttt) cc_final: 0.7700 (ttpp) REVERT: A 474 ASP cc_start: 0.7154 (OUTLIER) cc_final: 0.6669 (p0) REVERT: A 490 LYS cc_start: 0.8718 (ttpp) cc_final: 0.7788 (tptt) REVERT: G 11 LEU cc_start: 0.7332 (OUTLIER) cc_final: 0.7026 (tt) REVERT: B 530 MET cc_start: 0.9215 (mtp) cc_final: 0.8941 (mtp) REVERT: B 542 ARG cc_start: 0.7863 (mmm-85) cc_final: 0.7491 (mtm110) REVERT: H 56 SER cc_start: 0.8502 (t) cc_final: 0.8227 (p) REVERT: C 95 MET cc_start: 0.9153 (ptm) cc_final: 0.8869 (ptm) REVERT: C 117 LYS cc_start: 0.7596 (mttt) cc_final: 0.7268 (mmtm) REVERT: C 166 ARG cc_start: 0.7463 (mtp85) cc_final: 0.6959 (ttp80) REVERT: C 171 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8380 (tmmt) REVERT: C 178 LYS cc_start: 0.8281 (tttt) cc_final: 0.7619 (tttm) REVERT: C 211 GLU cc_start: 0.7220 (tt0) cc_final: 0.6896 (tp30) REVERT: C 232 LYS cc_start: 0.8476 (mttp) cc_final: 0.7919 (mmtm) REVERT: C 267 GLU cc_start: 0.7608 (mp0) cc_final: 0.7177 (mp0) REVERT: C 325 ASP cc_start: 0.7697 (m-30) cc_final: 0.7428 (p0) REVERT: C 347 LYS cc_start: 0.7848 (mttt) cc_final: 0.7589 (ttpp) REVERT: C 444 ARG cc_start: 0.8126 (mtt90) cc_final: 0.7699 (mmm160) REVERT: C 474 ASP cc_start: 0.7215 (OUTLIER) cc_final: 0.7009 (p0) REVERT: C 490 LYS cc_start: 0.8771 (ttpp) cc_final: 0.7844 (tptp) REVERT: J 11 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.7090 (tt) REVERT: J 70 SER cc_start: 0.8612 (t) cc_final: 0.8396 (p) REVERT: J 81 GLN cc_start: 0.8322 (tp40) cc_final: 0.7932 (tp40) REVERT: J 91 TYR cc_start: 0.8675 (m-80) cc_final: 0.8415 (m-80) REVERT: O 54 ARG cc_start: 0.8540 (mtm-85) cc_final: 0.8320 (mtm110) REVERT: E 542 ARG cc_start: 0.8033 (mmm-85) cc_final: 0.7623 (mtm110) REVERT: E 657 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8417 (mt-10) REVERT: M 27 ASN cc_start: 0.8817 (OUTLIER) cc_final: 0.8610 (t0) REVERT: M 56 SER cc_start: 0.8465 (t) cc_final: 0.8157 (p) REVERT: M 100 ARG cc_start: 0.8492 (mtm180) cc_final: 0.7456 (mmm160) REVERT: D 97 LYS cc_start: 0.8639 (mmtm) cc_final: 0.8303 (mptt) REVERT: D 117 LYS cc_start: 0.7545 (mttt) cc_final: 0.7215 (mmtm) REVERT: D 166 ARG cc_start: 0.7564 (mtp85) cc_final: 0.6880 (ttp80) REVERT: D 232 LYS cc_start: 0.8447 (mttp) cc_final: 0.7818 (mmtm) REVERT: D 267 GLU cc_start: 0.7330 (mp0) cc_final: 0.7024 (mp0) REVERT: D 444 ARG cc_start: 0.8107 (mtt90) cc_final: 0.7827 (mmm-85) REVERT: D 490 LYS cc_start: 0.8724 (ttpp) cc_final: 0.7959 (tptp) REVERT: P 97 ILE cc_start: 0.8204 (mt) cc_final: 0.7988 (mm) REVERT: F 542 ARG cc_start: 0.7991 (mmm-85) cc_final: 0.7549 (mtm110) REVERT: F 640 GLN cc_start: 0.8971 (mm-40) cc_final: 0.8657 (tp40) REVERT: N 100 ARG cc_start: 0.8474 (mtm180) cc_final: 0.7487 (mmm160) outliers start: 62 outliers final: 37 residues processed: 407 average time/residue: 1.3267 time to fit residues: 623.4639 Evaluate side-chains 390 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 347 time to evaluate : 2.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 100 GLN Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain C residue 171 LYS Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain E residue 660 LEU Chi-restraints excluded: chain M residue 19 SER Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 27 ASN Chi-restraints excluded: chain M residue 101 ASP Chi-restraints excluded: chain Q residue 27 SER Chi-restraints excluded: chain Q residue 70 SER Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 275 LYS Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 478 ASN Chi-restraints excluded: chain P residue 27 SER Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain R residue 27 SER Chi-restraints excluded: chain R residue 70 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 232 optimal weight: 0.9990 chunk 220 optimal weight: 3.9990 chunk 125 optimal weight: 0.2980 chunk 63 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 284 optimal weight: 0.9980 chunk 156 optimal weight: 2.9990 chunk 269 optimal weight: 0.9980 chunk 222 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 GLN G 76 ASN G 100BGLN I 31 ASN I 53 GLN C 440 GLN O 53 GLN E 652 GLN M 27 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 81 GLN P 31 ASN P 53 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.160467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.125537 restraints weight = 24524.974| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.75 r_work: 0.3086 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25440 Z= 0.149 Angle : 0.545 8.499 34668 Z= 0.278 Chirality : 0.044 0.157 4014 Planarity : 0.004 0.039 4329 Dihedral : 5.416 59.770 4570 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.18 % Allowed : 10.99 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.15), residues: 3039 helix: 0.44 (0.28), residues: 393 sheet: 0.29 (0.15), residues: 933 loop : 0.20 (0.15), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 112 HIS 0.007 0.001 HIS H 50 PHE 0.017 0.002 PHE H 78 TYR 0.017 0.001 TYR C 191 ARG 0.004 0.000 ARG D 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00336 ( 48) link_NAG-ASN : angle 2.30717 ( 144) link_BETA1-4 : bond 0.00407 ( 9) link_BETA1-4 : angle 1.35868 ( 27) link_ALPHA1-3 : bond 0.01034 ( 3) link_ALPHA1-3 : angle 1.48346 ( 9) hydrogen bonds : bond 0.03965 ( 651) hydrogen bonds : angle 5.03599 ( 1656) SS BOND : bond 0.00430 ( 45) SS BOND : angle 0.96332 ( 90) covalent geometry : bond 0.00350 (25335) covalent geometry : angle 0.52217 (34398) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 359 time to evaluate : 2.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LYS cc_start: 0.7657 (mttt) cc_final: 0.7430 (mmtm) REVERT: A 166 ARG cc_start: 0.7448 (mtp85) cc_final: 0.6871 (ttp80) REVERT: A 178 LYS cc_start: 0.8114 (tttt) cc_final: 0.7565 (ttpp) REVERT: A 232 LYS cc_start: 0.8529 (mttp) cc_final: 0.7894 (mmpt) REVERT: A 267 GLU cc_start: 0.7358 (mp0) cc_final: 0.7047 (mp0) REVERT: A 278 ARG cc_start: 0.8223 (mmt-90) cc_final: 0.8020 (mmp80) REVERT: A 347 LYS cc_start: 0.7976 (mttt) cc_final: 0.7697 (ttpp) REVERT: A 476 ARG cc_start: 0.7336 (mtm-85) cc_final: 0.6752 (mtm180) REVERT: A 490 LYS cc_start: 0.8697 (ttpp) cc_final: 0.7758 (tptt) REVERT: A 504 ARG cc_start: 0.6794 (tpp-160) cc_final: 0.6583 (mmt-90) REVERT: G 11 LEU cc_start: 0.7329 (OUTLIER) cc_final: 0.7028 (tt) REVERT: B 530 MET cc_start: 0.9223 (mtp) cc_final: 0.8922 (mtp) REVERT: B 542 ARG cc_start: 0.7837 (mmm-85) cc_final: 0.7464 (mtm110) REVERT: H 5 GLN cc_start: 0.7637 (tp40) cc_final: 0.7412 (tp-100) REVERT: H 56 SER cc_start: 0.8459 (t) cc_final: 0.8178 (p) REVERT: C 95 MET cc_start: 0.9144 (ptm) cc_final: 0.8850 (ptm) REVERT: C 117 LYS cc_start: 0.7571 (mttt) cc_final: 0.7254 (mmtm) REVERT: C 166 ARG cc_start: 0.7409 (mtp85) cc_final: 0.6913 (ttp80) REVERT: C 171 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8418 (tmmt) REVERT: C 178 LYS cc_start: 0.8231 (tttt) cc_final: 0.7599 (tttm) REVERT: C 211 GLU cc_start: 0.7323 (tt0) cc_final: 0.6848 (tp30) REVERT: C 232 LYS cc_start: 0.8449 (mttp) cc_final: 0.7973 (mmpt) REVERT: C 267 GLU cc_start: 0.7616 (mp0) cc_final: 0.7234 (mp0) REVERT: C 325 ASP cc_start: 0.7628 (m-30) cc_final: 0.7386 (p0) REVERT: C 327 ARG cc_start: 0.7725 (mtm180) cc_final: 0.7500 (mtm-85) REVERT: C 347 LYS cc_start: 0.7857 (mttt) cc_final: 0.7632 (ttpp) REVERT: C 444 ARG cc_start: 0.8091 (mtt90) cc_final: 0.7687 (mmm160) REVERT: C 490 LYS cc_start: 0.8810 (ttpp) cc_final: 0.7810 (tptp) REVERT: J 11 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.7109 (tt) REVERT: J 70 SER cc_start: 0.8552 (t) cc_final: 0.8251 (p) REVERT: J 81 GLN cc_start: 0.8321 (tp40) cc_final: 0.7910 (tp40) REVERT: J 91 TYR cc_start: 0.8643 (m-80) cc_final: 0.8363 (m-80) REVERT: E 542 ARG cc_start: 0.8028 (mmm-85) cc_final: 0.7614 (mtm110) REVERT: M 56 SER cc_start: 0.8458 (t) cc_final: 0.8157 (p) REVERT: M 100 ARG cc_start: 0.8516 (mtm180) cc_final: 0.7463 (mmm160) REVERT: D 97 LYS cc_start: 0.8687 (mmtm) cc_final: 0.8337 (mttp) REVERT: D 117 LYS cc_start: 0.7600 (mttt) cc_final: 0.7276 (mmtm) REVERT: D 166 ARG cc_start: 0.7520 (mtp85) cc_final: 0.6877 (ttp80) REVERT: D 171 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.7565 (tmmt) REVERT: D 232 LYS cc_start: 0.8416 (mttp) cc_final: 0.7809 (mmtm) REVERT: D 267 GLU cc_start: 0.7342 (mp0) cc_final: 0.7017 (mp0) REVERT: D 444 ARG cc_start: 0.8081 (mtt90) cc_final: 0.7822 (mmm-85) REVERT: D 490 LYS cc_start: 0.8720 (ttpp) cc_final: 0.7933 (tptp) REVERT: F 542 ARG cc_start: 0.7990 (mmm-85) cc_final: 0.7558 (mtm110) REVERT: F 640 GLN cc_start: 0.8912 (mm-40) cc_final: 0.8539 (tp40) REVERT: N 100 ARG cc_start: 0.8472 (mtm180) cc_final: 0.7456 (mmm160) outliers start: 58 outliers final: 29 residues processed: 398 average time/residue: 1.3538 time to fit residues: 620.9420 Evaluate side-chains 382 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 349 time to evaluate : 2.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 100 GLN Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 171 LYS Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 464 THR Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain E residue 660 LEU Chi-restraints excluded: chain M residue 19 SER Chi-restraints excluded: chain M residue 27 ASN Chi-restraints excluded: chain M residue 101 ASP Chi-restraints excluded: chain Q residue 27 SER Chi-restraints excluded: chain Q residue 70 SER Chi-restraints excluded: chain D residue 171 LYS Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 275 LYS Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 478 ASN Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain P residue 27 SER Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain R residue 27 SER Chi-restraints excluded: chain R residue 70 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 241 optimal weight: 9.9990 chunk 143 optimal weight: 7.9990 chunk 291 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 191 optimal weight: 0.7980 chunk 108 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 167 optimal weight: 0.5980 chunk 135 optimal weight: 0.6980 chunk 168 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 103 GLN ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 GLN G 76 ASN I 31 ASN I 53 GLN C 98 ASN ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 53 GLN E 652 GLN M 27 ASN M 77 GLN D 283 ASN K 81 GLN P 31 ASN P 53 GLN N 27 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.160660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.125800 restraints weight = 24582.557| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.76 r_work: 0.3103 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25440 Z= 0.138 Angle : 0.533 8.214 34668 Z= 0.272 Chirality : 0.043 0.184 4014 Planarity : 0.004 0.040 4329 Dihedral : 5.259 59.352 4570 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.11 % Allowed : 11.29 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.15), residues: 3039 helix: 0.53 (0.28), residues: 393 sheet: 0.24 (0.15), residues: 933 loop : 0.20 (0.15), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 112 HIS 0.006 0.001 HIS H 50 PHE 0.017 0.002 PHE H 78 TYR 0.017 0.001 TYR C 191 ARG 0.004 0.000 ARG E 585 Details of bonding type rmsd link_NAG-ASN : bond 0.00417 ( 48) link_NAG-ASN : angle 2.35606 ( 144) link_BETA1-4 : bond 0.00416 ( 9) link_BETA1-4 : angle 1.34144 ( 27) link_ALPHA1-3 : bond 0.01045 ( 3) link_ALPHA1-3 : angle 1.46364 ( 9) hydrogen bonds : bond 0.03846 ( 651) hydrogen bonds : angle 4.97090 ( 1656) SS BOND : bond 0.00400 ( 45) SS BOND : angle 0.91639 ( 90) covalent geometry : bond 0.00321 (25335) covalent geometry : angle 0.50909 (34398) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 355 time to evaluate : 2.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LYS cc_start: 0.7643 (mttt) cc_final: 0.7421 (mmtm) REVERT: A 166 ARG cc_start: 0.7457 (mtp85) cc_final: 0.6904 (ttp80) REVERT: A 178 LYS cc_start: 0.8104 (tttt) cc_final: 0.7562 (ttpp) REVERT: A 232 LYS cc_start: 0.8540 (mttp) cc_final: 0.7899 (mmpt) REVERT: A 267 GLU cc_start: 0.7345 (mp0) cc_final: 0.7063 (mp0) REVERT: A 278 ARG cc_start: 0.8194 (mmt-90) cc_final: 0.7984 (mmp80) REVERT: A 347 LYS cc_start: 0.7940 (mttt) cc_final: 0.7676 (ttpp) REVERT: A 490 LYS cc_start: 0.8702 (ttpp) cc_final: 0.7763 (tptt) REVERT: A 504 ARG cc_start: 0.6836 (tpp-160) cc_final: 0.6610 (mmt-90) REVERT: G 11 LEU cc_start: 0.7318 (OUTLIER) cc_final: 0.7016 (tt) REVERT: B 530 MET cc_start: 0.9220 (mtp) cc_final: 0.8877 (mtp) REVERT: B 542 ARG cc_start: 0.7781 (mmm-85) cc_final: 0.7455 (mtm110) REVERT: H 5 GLN cc_start: 0.7588 (tp40) cc_final: 0.7337 (tp40) REVERT: H 56 SER cc_start: 0.8429 (t) cc_final: 0.8141 (p) REVERT: C 95 MET cc_start: 0.9137 (ptm) cc_final: 0.8819 (ptm) REVERT: C 117 LYS cc_start: 0.7542 (mttt) cc_final: 0.7328 (mmtm) REVERT: C 166 ARG cc_start: 0.7384 (mtp85) cc_final: 0.6934 (ttp80) REVERT: C 171 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8398 (tmmt) REVERT: C 178 LYS cc_start: 0.8226 (tttt) cc_final: 0.7598 (tttm) REVERT: C 211 GLU cc_start: 0.7311 (tt0) cc_final: 0.6854 (tp30) REVERT: C 232 LYS cc_start: 0.8455 (mttp) cc_final: 0.7968 (mmpt) REVERT: C 267 GLU cc_start: 0.7604 (mp0) cc_final: 0.7225 (mp0) REVERT: C 275 LYS cc_start: 0.8517 (ttmt) cc_final: 0.8100 (tttm) REVERT: C 321 ASP cc_start: 0.7546 (t0) cc_final: 0.7284 (t0) REVERT: C 325 ASP cc_start: 0.7692 (m-30) cc_final: 0.7492 (p0) REVERT: C 327 ARG cc_start: 0.7824 (mtm180) cc_final: 0.7594 (mtm-85) REVERT: C 347 LYS cc_start: 0.7855 (mttt) cc_final: 0.7631 (ttpp) REVERT: C 356 ASN cc_start: 0.7924 (OUTLIER) cc_final: 0.7593 (t0) REVERT: C 444 ARG cc_start: 0.8049 (mtt90) cc_final: 0.7651 (mmm160) REVERT: C 490 LYS cc_start: 0.8815 (ttpp) cc_final: 0.7806 (tptp) REVERT: J 11 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7121 (tt) REVERT: J 70 SER cc_start: 0.8548 (t) cc_final: 0.8236 (p) REVERT: J 81 GLN cc_start: 0.8289 (tp40) cc_final: 0.7939 (tp40) REVERT: J 91 TYR cc_start: 0.8649 (m-80) cc_final: 0.8365 (m-80) REVERT: E 542 ARG cc_start: 0.8027 (mmm-85) cc_final: 0.7611 (mtm110) REVERT: M 56 SER cc_start: 0.8444 (t) cc_final: 0.8147 (p) REVERT: M 100 ARG cc_start: 0.8562 (mtm180) cc_final: 0.7504 (mmm160) REVERT: D 97 LYS cc_start: 0.8676 (mmtm) cc_final: 0.8366 (mptt) REVERT: D 117 LYS cc_start: 0.7592 (mttt) cc_final: 0.7269 (mmtm) REVERT: D 166 ARG cc_start: 0.7505 (mtp85) cc_final: 0.6879 (ttp80) REVERT: D 171 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.7520 (tmmt) REVERT: D 232 LYS cc_start: 0.8416 (mttp) cc_final: 0.7792 (mmtm) REVERT: D 267 GLU cc_start: 0.7354 (mp0) cc_final: 0.7013 (mp0) REVERT: D 328 GLN cc_start: 0.8217 (tt0) cc_final: 0.7919 (tt0) REVERT: D 444 ARG cc_start: 0.8081 (mtt90) cc_final: 0.7825 (mmm-85) REVERT: D 490 LYS cc_start: 0.8716 (ttpp) cc_final: 0.7928 (tptp) REVERT: F 542 ARG cc_start: 0.8014 (mmm-85) cc_final: 0.7573 (mtm110) REVERT: F 640 GLN cc_start: 0.8889 (mm-40) cc_final: 0.8487 (tp40) REVERT: N 100 ARG cc_start: 0.8454 (mtm180) cc_final: 0.7462 (mmm160) outliers start: 56 outliers final: 33 residues processed: 391 average time/residue: 1.3872 time to fit residues: 629.3183 Evaluate side-chains 382 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 344 time to evaluate : 2.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 171 LYS Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 356 ASN Chi-restraints excluded: chain C residue 464 THR Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain O residue 97 ILE Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain E residue 660 LEU Chi-restraints excluded: chain M residue 19 SER Chi-restraints excluded: chain M residue 101 ASP Chi-restraints excluded: chain Q residue 27 SER Chi-restraints excluded: chain Q residue 70 SER Chi-restraints excluded: chain D residue 171 LYS Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 275 LYS Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 478 ASN Chi-restraints excluded: chain P residue 27 SER Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain R residue 27 SER Chi-restraints excluded: chain R residue 70 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 45 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 95 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 chunk 159 optimal weight: 0.9990 chunk 284 optimal weight: 6.9990 chunk 251 optimal weight: 0.7980 chunk 207 optimal weight: 0.8980 chunk 296 optimal weight: 3.9990 chunk 185 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 HIS A 440 GLN G 76 ASN G 100BGLN I 31 ASN I 53 GLN B 652 GLN ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 HIS O 53 GLN M 77 GLN D 283 ASN D 374 HIS K 81 GLN P 31 ASN P 53 GLN N 27 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.156270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.121386 restraints weight = 24647.754| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.72 r_work: 0.3042 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 25440 Z= 0.266 Angle : 0.665 11.500 34668 Z= 0.334 Chirality : 0.048 0.168 4014 Planarity : 0.004 0.040 4329 Dihedral : 5.633 57.317 4570 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.11 % Allowed : 11.59 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.15), residues: 3039 helix: -0.05 (0.26), residues: 423 sheet: 0.07 (0.15), residues: 948 loop : 0.12 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 112 HIS 0.005 0.002 HIS A 105 PHE 0.018 0.002 PHE C 53 TYR 0.020 0.002 TYR C 191 ARG 0.005 0.001 ARG K 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00496 ( 48) link_NAG-ASN : angle 2.79730 ( 144) link_BETA1-4 : bond 0.00337 ( 9) link_BETA1-4 : angle 1.54049 ( 27) link_ALPHA1-3 : bond 0.00948 ( 3) link_ALPHA1-3 : angle 1.41279 ( 9) hydrogen bonds : bond 0.04667 ( 651) hydrogen bonds : angle 5.22022 ( 1656) SS BOND : bond 0.00560 ( 45) SS BOND : angle 1.29035 ( 90) covalent geometry : bond 0.00643 (25335) covalent geometry : angle 0.63708 (34398) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 351 time to evaluate : 2.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LYS cc_start: 0.7667 (mttt) cc_final: 0.7442 (mmtm) REVERT: A 151 ARG cc_start: 0.7503 (ttm-80) cc_final: 0.6819 (ttm170) REVERT: A 166 ARG cc_start: 0.7499 (mtp85) cc_final: 0.6919 (ttp80) REVERT: A 178 LYS cc_start: 0.8159 (tttt) cc_final: 0.7705 (mmmt) REVERT: A 232 LYS cc_start: 0.8511 (mttp) cc_final: 0.7813 (mmpt) REVERT: A 267 GLU cc_start: 0.7345 (mp0) cc_final: 0.7043 (mp0) REVERT: A 278 ARG cc_start: 0.8156 (mmt-90) cc_final: 0.7894 (mmp80) REVERT: A 347 LYS cc_start: 0.8027 (mttt) cc_final: 0.7700 (ttpp) REVERT: A 490 LYS cc_start: 0.8750 (ttpp) cc_final: 0.7759 (tptt) REVERT: A 504 ARG cc_start: 0.7081 (tpp-160) cc_final: 0.6751 (mmt-90) REVERT: G 11 LEU cc_start: 0.7391 (OUTLIER) cc_final: 0.7081 (tt) REVERT: B 530 MET cc_start: 0.9218 (mtp) cc_final: 0.8980 (mtp) REVERT: B 542 ARG cc_start: 0.7881 (mmm-85) cc_final: 0.7553 (mtm110) REVERT: C 95 MET cc_start: 0.9123 (ptm) cc_final: 0.8874 (ptm) REVERT: C 117 LYS cc_start: 0.7521 (mttt) cc_final: 0.7284 (mmtm) REVERT: C 166 ARG cc_start: 0.7603 (mtp85) cc_final: 0.7066 (ttp80) REVERT: C 171 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8341 (tmmt) REVERT: C 178 LYS cc_start: 0.8271 (tttt) cc_final: 0.7764 (mmmt) REVERT: C 211 GLU cc_start: 0.7309 (tt0) cc_final: 0.6861 (tp30) REVERT: C 232 LYS cc_start: 0.8476 (mttp) cc_final: 0.7885 (mmtm) REVERT: C 267 GLU cc_start: 0.7582 (mp0) cc_final: 0.7213 (mp0) REVERT: C 275 LYS cc_start: 0.8516 (ttmt) cc_final: 0.8121 (tttm) REVERT: C 321 ASP cc_start: 0.7654 (t0) cc_final: 0.7361 (t0) REVERT: C 325 ASP cc_start: 0.7774 (m-30) cc_final: 0.7570 (p0) REVERT: C 327 ARG cc_start: 0.7894 (mtm180) cc_final: 0.7637 (mtm-85) REVERT: C 339 ASN cc_start: 0.8183 (t0) cc_final: 0.7353 (m-40) REVERT: C 347 LYS cc_start: 0.7917 (mttt) cc_final: 0.7566 (ttpp) REVERT: C 444 ARG cc_start: 0.8122 (mtt90) cc_final: 0.7700 (mmm160) REVERT: C 490 LYS cc_start: 0.8869 (ttpp) cc_final: 0.7869 (tptp) REVERT: C 504 ARG cc_start: 0.7667 (ttt180) cc_final: 0.7371 (tpp-160) REVERT: J 11 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7133 (tt) REVERT: J 81 GLN cc_start: 0.8310 (tp40) cc_final: 0.7954 (tp40) REVERT: J 91 TYR cc_start: 0.8682 (m-80) cc_final: 0.8404 (m-80) REVERT: O 54 ARG cc_start: 0.8456 (mtm110) cc_final: 0.8248 (ttp-110) REVERT: E 542 ARG cc_start: 0.8108 (mmm-85) cc_final: 0.7679 (mtm110) REVERT: D 97 LYS cc_start: 0.8672 (mmtm) cc_final: 0.8378 (mptt) REVERT: D 117 LYS cc_start: 0.7670 (mttt) cc_final: 0.7349 (mmtm) REVERT: D 166 ARG cc_start: 0.7573 (mtp85) cc_final: 0.6899 (ttp80) REVERT: D 232 LYS cc_start: 0.8410 (mttp) cc_final: 0.7782 (mmtm) REVERT: D 267 GLU cc_start: 0.7387 (mp0) cc_final: 0.7015 (mp0) REVERT: D 328 GLN cc_start: 0.8153 (tt0) cc_final: 0.7906 (tt0) REVERT: D 356 ASN cc_start: 0.8021 (t0) cc_final: 0.7603 (m-40) REVERT: D 444 ARG cc_start: 0.8141 (mtt90) cc_final: 0.7831 (ttt-90) REVERT: D 474 ASP cc_start: 0.6905 (p0) cc_final: 0.6699 (p0) REVERT: D 490 LYS cc_start: 0.8729 (ttpp) cc_final: 0.7915 (tptp) REVERT: D 502 LYS cc_start: 0.8738 (tttm) cc_final: 0.8390 (tttt) REVERT: F 542 ARG cc_start: 0.8087 (mmm-85) cc_final: 0.7581 (mtm110) REVERT: N 100 ARG cc_start: 0.8498 (mtm180) cc_final: 0.7517 (mmm160) outliers start: 56 outliers final: 33 residues processed: 388 average time/residue: 1.3868 time to fit residues: 618.7839 Evaluate side-chains 370 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 334 time to evaluate : 2.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 100 GLN Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 171 LYS Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain E residue 660 LEU Chi-restraints excluded: chain M residue 19 SER Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 101 ASP Chi-restraints excluded: chain Q residue 27 SER Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 275 LYS Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 478 ASN Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain P residue 27 SER Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain R residue 27 SER Chi-restraints excluded: chain R residue 70 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 226 optimal weight: 0.9980 chunk 129 optimal weight: 0.5980 chunk 96 optimal weight: 10.0000 chunk 257 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 173 optimal weight: 0.6980 chunk 184 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 162 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 273 optimal weight: 0.0970 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 GLN G 100BGLN I 31 ASN I 53 GLN ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 31 ASN O 53 GLN M 27 ASN M 77 GLN D 283 ASN P 31 ASN P 53 GLN N 27 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.159142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.124428 restraints weight = 24602.101| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.74 r_work: 0.3216 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 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 : 0.003 0.046 25440 Z= 0.135 Angle : 0.557 10.443 34668 Z= 0.282 Chirality : 0.044 0.274 4014 Planarity : 0.004 0.041 4329 Dihedral : 5.345 55.652 4570 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.73 % Allowed : 12.72 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.15), residues: 3039 helix: 0.03 (0.26), residues: 429 sheet: 0.01 (0.15), residues: 948 loop : 0.15 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 112 HIS 0.006 0.001 HIS D 105 PHE 0.015 0.001 PHE C 53 TYR 0.017 0.001 TYR C 191 ARG 0.005 0.000 ARG M 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00268 ( 48) link_NAG-ASN : angle 2.67501 ( 144) link_BETA1-4 : bond 0.00384 ( 9) link_BETA1-4 : angle 1.33529 ( 27) link_ALPHA1-3 : bond 0.00940 ( 3) link_ALPHA1-3 : angle 1.32456 ( 9) hydrogen bonds : bond 0.03975 ( 651) hydrogen bonds : angle 5.07838 ( 1656) SS BOND : bond 0.00410 ( 45) SS BOND : angle 1.22029 ( 90) covalent geometry : bond 0.00313 (25335) covalent geometry : angle 0.52681 (34398) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 349 time to evaluate : 2.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.7411 (ttm-80) cc_final: 0.6740 (ttm170) REVERT: A 166 ARG cc_start: 0.7501 (mtp85) cc_final: 0.6939 (ttp80) REVERT: A 178 LYS cc_start: 0.8202 (tttt) cc_final: 0.7702 (mmmt) REVERT: A 208 VAL cc_start: 0.7583 (t) cc_final: 0.7279 (m) REVERT: A 232 LYS cc_start: 0.8597 (mttp) cc_final: 0.7953 (mmpt) REVERT: A 267 GLU cc_start: 0.7361 (mp0) cc_final: 0.7074 (mp0) REVERT: A 278 ARG cc_start: 0.8190 (mmt-90) cc_final: 0.7964 (mmp80) REVERT: A 339 ASN cc_start: 0.8319 (t0) cc_final: 0.7470 (m110) REVERT: A 347 LYS cc_start: 0.8037 (mttt) cc_final: 0.7821 (ttpp) REVERT: A 490 LYS cc_start: 0.8729 (ttpp) cc_final: 0.7805 (tptt) REVERT: A 504 ARG cc_start: 0.7019 (tpp-160) cc_final: 0.6741 (mmt-90) REVERT: G 11 LEU cc_start: 0.7334 (OUTLIER) cc_final: 0.7026 (tt) REVERT: B 530 MET cc_start: 0.9224 (mtp) cc_final: 0.8898 (mtp) REVERT: B 542 ARG cc_start: 0.7915 (mmm-85) cc_final: 0.7592 (mtm110) REVERT: C 95 MET cc_start: 0.9146 (ptm) cc_final: 0.8823 (ptm) REVERT: C 117 LYS cc_start: 0.7622 (mttt) cc_final: 0.7414 (mmtm) REVERT: C 166 ARG cc_start: 0.7469 (mtp85) cc_final: 0.7054 (ttp80) REVERT: C 171 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8365 (tmmt) REVERT: C 178 LYS cc_start: 0.8240 (tttt) cc_final: 0.7701 (mmmt) REVERT: C 211 GLU cc_start: 0.7445 (tt0) cc_final: 0.6963 (tp30) REVERT: C 232 LYS cc_start: 0.8561 (mttp) cc_final: 0.8029 (mmtm) REVERT: C 267 GLU cc_start: 0.7602 (mp0) cc_final: 0.7249 (mp0) REVERT: C 275 LYS cc_start: 0.8539 (ttmt) cc_final: 0.8168 (tttm) REVERT: C 321 ASP cc_start: 0.7534 (t0) cc_final: 0.7288 (t0) REVERT: C 327 ARG cc_start: 0.7903 (mtm180) cc_final: 0.7668 (mtm-85) REVERT: C 339 ASN cc_start: 0.8175 (t0) cc_final: 0.7353 (m-40) REVERT: C 444 ARG cc_start: 0.8096 (mtt90) cc_final: 0.7895 (tpt90) REVERT: C 490 LYS cc_start: 0.8832 (ttpp) cc_final: 0.7898 (tptp) REVERT: J 11 LEU cc_start: 0.7528 (OUTLIER) cc_final: 0.7065 (tt) REVERT: J 81 GLN cc_start: 0.8276 (tp40) cc_final: 0.7856 (tp40) REVERT: J 91 TYR cc_start: 0.8697 (m-80) cc_final: 0.8396 (m-80) REVERT: O 54 ARG cc_start: 0.8471 (mtm110) cc_final: 0.8261 (ttp-110) REVERT: E 538 THR cc_start: 0.9292 (m) cc_final: 0.8881 (p) REVERT: E 542 ARG cc_start: 0.8121 (mmm-85) cc_final: 0.7744 (mtm110) REVERT: E 574 LYS cc_start: 0.8050 (mttt) cc_final: 0.7609 (mtmp) REVERT: E 617 ARG cc_start: 0.8388 (mtp85) cc_final: 0.7861 (mtt180) REVERT: M 27 ASN cc_start: 0.8821 (OUTLIER) cc_final: 0.8621 (t0) REVERT: D 97 LYS cc_start: 0.8721 (mmtm) cc_final: 0.8452 (mptt) REVERT: D 106 THR cc_start: 0.8609 (m) cc_final: 0.8352 (m) REVERT: D 117 LYS cc_start: 0.7676 (mttt) cc_final: 0.7422 (mmtm) REVERT: D 166 ARG cc_start: 0.7432 (mtp85) cc_final: 0.6867 (ttp80) REVERT: D 232 LYS cc_start: 0.8469 (mttp) cc_final: 0.7906 (mmtm) REVERT: D 267 GLU cc_start: 0.7385 (mp0) cc_final: 0.7060 (mp0) REVERT: D 328 GLN cc_start: 0.8257 (tt0) cc_final: 0.7940 (tt0) REVERT: D 356 ASN cc_start: 0.8027 (t0) cc_final: 0.7605 (m-40) REVERT: D 444 ARG cc_start: 0.8134 (mtt90) cc_final: 0.7788 (mmm160) REVERT: D 490 LYS cc_start: 0.8712 (ttpp) cc_final: 0.7944 (tptp) REVERT: F 542 ARG cc_start: 0.8116 (mmm-85) cc_final: 0.7635 (mtm110) REVERT: N 100 ARG cc_start: 0.8487 (mtm180) cc_final: 0.7563 (mmm160) outliers start: 46 outliers final: 30 residues processed: 382 average time/residue: 1.3403 time to fit residues: 589.3571 Evaluate side-chains 373 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 339 time to evaluate : 2.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 100 GLN Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain C residue 171 LYS Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain E residue 660 LEU Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 19 SER Chi-restraints excluded: chain M residue 27 ASN Chi-restraints excluded: chain M residue 101 ASP Chi-restraints excluded: chain Q residue 27 SER Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 275 LYS Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain P residue 27 ASP Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain R residue 27 SER Chi-restraints excluded: chain R residue 70 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 52 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 152 optimal weight: 0.5980 chunk 257 optimal weight: 4.9990 chunk 296 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 226 optimal weight: 1.9990 chunk 198 optimal weight: 0.5980 chunk 245 optimal weight: 2.9990 chunk 209 optimal weight: 0.7980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 GLN G 100BGLN I 31 ASN I 53 GLN L 53 GLN C 98 ASN C 103 GLN ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 53 GLN M 27 ASN M 77 GLN D 283 ASN D 440 GLN P 31 ASN P 53 GLN N 27 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.157814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.122689 restraints weight = 24669.119| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.75 r_work: 0.3190 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 25440 Z= 0.176 Angle : 0.614 24.857 34668 Z= 0.305 Chirality : 0.045 0.351 4014 Planarity : 0.004 0.057 4329 Dihedral : 5.525 53.796 4570 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.73 % Allowed : 13.09 % Favored : 85.18 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.15), residues: 3039 helix: -0.02 (0.26), residues: 429 sheet: -0.03 (0.15), residues: 948 loop : 0.14 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 112 HIS 0.006 0.001 HIS A 105 PHE 0.016 0.002 PHE C 53 TYR 0.021 0.001 TYR O 49 ARG 0.007 0.000 ARG P 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00367 ( 48) link_NAG-ASN : angle 3.37194 ( 144) link_BETA1-4 : bond 0.00365 ( 9) link_BETA1-4 : angle 1.37943 ( 27) link_ALPHA1-3 : bond 0.00900 ( 3) link_ALPHA1-3 : angle 1.31975 ( 9) hydrogen bonds : bond 0.04139 ( 651) hydrogen bonds : angle 5.08350 ( 1656) SS BOND : bond 0.00472 ( 45) SS BOND : angle 1.37334 ( 90) covalent geometry : bond 0.00418 (25335) covalent geometry : angle 0.57062 (34398) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 343 time to evaluate : 2.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.7440 (ttm-80) cc_final: 0.6755 (ttm170) REVERT: A 166 ARG cc_start: 0.7605 (mtp85) cc_final: 0.7027 (ttp80) REVERT: A 178 LYS cc_start: 0.8285 (tttt) cc_final: 0.7794 (mmmt) REVERT: A 208 VAL cc_start: 0.7625 (t) cc_final: 0.7254 (m) REVERT: A 232 LYS cc_start: 0.8638 (mttp) cc_final: 0.8000 (mmpt) REVERT: A 267 GLU cc_start: 0.7391 (mp0) cc_final: 0.7111 (mp0) REVERT: A 278 ARG cc_start: 0.8241 (mmt-90) cc_final: 0.8025 (mmp80) REVERT: A 339 ASN cc_start: 0.8355 (t0) cc_final: 0.7558 (m110) REVERT: A 347 LYS cc_start: 0.8130 (mttt) cc_final: 0.7930 (ttpp) REVERT: A 490 LYS cc_start: 0.8774 (ttpp) cc_final: 0.7889 (tptt) REVERT: A 504 ARG cc_start: 0.7070 (tpp-160) cc_final: 0.6783 (mmt-90) REVERT: G 11 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.7074 (tt) REVERT: B 530 MET cc_start: 0.9241 (mtp) cc_final: 0.9015 (mtp) REVERT: B 542 ARG cc_start: 0.8002 (mmm-85) cc_final: 0.7674 (mtm110) REVERT: C 95 MET cc_start: 0.9184 (ptm) cc_final: 0.8886 (ptm) REVERT: C 117 LYS cc_start: 0.7677 (mttt) cc_final: 0.7477 (mmtm) REVERT: C 166 ARG cc_start: 0.7555 (mtp85) cc_final: 0.7115 (ttp80) REVERT: C 171 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8412 (tmmt) REVERT: C 178 LYS cc_start: 0.8311 (tttt) cc_final: 0.7810 (mmmt) REVERT: C 211 GLU cc_start: 0.7543 (tt0) cc_final: 0.7057 (tp30) REVERT: C 232 LYS cc_start: 0.8558 (mttp) cc_final: 0.8085 (mmpt) REVERT: C 267 GLU cc_start: 0.7644 (mp0) cc_final: 0.7295 (mp0) REVERT: C 275 LYS cc_start: 0.8629 (ttmt) cc_final: 0.8290 (tttm) REVERT: C 321 ASP cc_start: 0.7626 (t0) cc_final: 0.7396 (t0) REVERT: C 327 ARG cc_start: 0.7953 (mtm180) cc_final: 0.7723 (mtm-85) REVERT: C 444 ARG cc_start: 0.8104 (mtt90) cc_final: 0.7889 (tpt90) REVERT: C 490 LYS cc_start: 0.8869 (ttpp) cc_final: 0.7971 (tptp) REVERT: C 504 ARG cc_start: 0.7697 (ttt180) cc_final: 0.7475 (tpp-160) REVERT: J 11 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7057 (tt) REVERT: J 81 GLN cc_start: 0.8264 (tp40) cc_final: 0.7831 (tp40) REVERT: E 538 THR cc_start: 0.9320 (m) cc_final: 0.8887 (p) REVERT: E 542 ARG cc_start: 0.8177 (mmm-85) cc_final: 0.7806 (mtm110) REVERT: E 574 LYS cc_start: 0.8108 (mttt) cc_final: 0.7670 (mtmp) REVERT: M 27 ASN cc_start: 0.8847 (OUTLIER) cc_final: 0.8600 (t0) REVERT: D 97 LYS cc_start: 0.8787 (mmtm) cc_final: 0.8537 (mptt) REVERT: D 106 THR cc_start: 0.8667 (m) cc_final: 0.8413 (m) REVERT: D 117 LYS cc_start: 0.7703 (mttt) cc_final: 0.7484 (mmtm) REVERT: D 166 ARG cc_start: 0.7533 (mtp85) cc_final: 0.6973 (ttp80) REVERT: D 232 LYS cc_start: 0.8544 (mttp) cc_final: 0.8001 (mmtm) REVERT: D 267 GLU cc_start: 0.7459 (mp0) cc_final: 0.7167 (mp0) REVERT: D 328 GLN cc_start: 0.8312 (tt0) cc_final: 0.8080 (tt0) REVERT: D 356 ASN cc_start: 0.8030 (t0) cc_final: 0.7622 (m-40) REVERT: D 475 MET cc_start: 0.6659 (mtm) cc_final: 0.6280 (mtm) REVERT: D 490 LYS cc_start: 0.8709 (ttpp) cc_final: 0.8007 (tptp) REVERT: F 542 ARG cc_start: 0.8201 (mmm-85) cc_final: 0.7725 (mtm110) REVERT: N 100 ARG cc_start: 0.8538 (mtm180) cc_final: 0.7655 (mmm160) outliers start: 46 outliers final: 32 residues processed: 374 average time/residue: 1.3807 time to fit residues: 596.9682 Evaluate side-chains 374 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 338 time to evaluate : 2.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 100 GLN Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain C residue 171 LYS Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 464 THR Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain E residue 660 LEU Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 19 SER Chi-restraints excluded: chain M residue 27 ASN Chi-restraints excluded: chain M residue 101 ASP Chi-restraints excluded: chain Q residue 27 SER Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 275 LYS Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 478 ASN Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain R residue 27 SER Chi-restraints excluded: chain R residue 70 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 184 optimal weight: 3.9990 chunk 240 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 235 optimal weight: 1.9990 chunk 5 optimal weight: 0.0050 chunk 73 optimal weight: 1.9990 chunk 293 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 142 optimal weight: 9.9990 chunk 267 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 GLN G 100BGLN I 31 ASN I 53 GLN C 103 GLN ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 53 GLN M 27 ASN D 283 ASN D 440 GLN P 31 ASN P 53 GLN N 27 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.156263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.121663 restraints weight = 24659.373| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.68 r_work: 0.3178 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 25440 Z= 0.222 Angle : 0.635 11.239 34668 Z= 0.319 Chirality : 0.046 0.284 4014 Planarity : 0.004 0.054 4329 Dihedral : 5.540 54.056 4570 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.69 % Allowed : 13.21 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.15), residues: 3039 helix: -0.09 (0.26), residues: 426 sheet: 0.08 (0.15), residues: 903 loop : 0.02 (0.15), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 112 HIS 0.006 0.001 HIS H 50 PHE 0.018 0.002 PHE C 53 TYR 0.026 0.002 TYR O 49 ARG 0.010 0.001 ARG P 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00431 ( 48) link_NAG-ASN : angle 2.70674 ( 144) link_BETA1-4 : bond 0.00362 ( 9) link_BETA1-4 : angle 1.44977 ( 27) link_ALPHA1-3 : bond 0.00868 ( 3) link_ALPHA1-3 : angle 1.31113 ( 9) hydrogen bonds : bond 0.04369 ( 651) hydrogen bonds : angle 5.16679 ( 1656) SS BOND : bond 0.00537 ( 45) SS BOND : angle 1.48268 ( 90) covalent geometry : bond 0.00535 (25335) covalent geometry : angle 0.60695 (34398) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 334 time to evaluate : 2.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8523 (m-30) cc_final: 0.8321 (m-30) REVERT: A 151 ARG cc_start: 0.7391 (ttm-80) cc_final: 0.6692 (ttm170) REVERT: A 166 ARG cc_start: 0.7502 (mtp85) cc_final: 0.6910 (ttp80) REVERT: A 178 LYS cc_start: 0.8196 (tttt) cc_final: 0.7731 (mmmt) REVERT: A 232 LYS cc_start: 0.8604 (mttp) cc_final: 0.7941 (mmpt) REVERT: A 267 GLU cc_start: 0.7372 (mp0) cc_final: 0.7074 (mp0) REVERT: A 278 ARG cc_start: 0.8190 (mmt-90) cc_final: 0.7971 (mmp80) REVERT: A 347 LYS cc_start: 0.8021 (mttt) cc_final: 0.7819 (ttpp) REVERT: A 490 LYS cc_start: 0.8777 (ttpp) cc_final: 0.7825 (tptt) REVERT: A 504 ARG cc_start: 0.6891 (tpp-160) cc_final: 0.6644 (mmt-90) REVERT: G 11 LEU cc_start: 0.7424 (OUTLIER) cc_final: 0.7100 (tt) REVERT: B 530 MET cc_start: 0.9243 (mtp) cc_final: 0.9002 (mtp) REVERT: B 542 ARG cc_start: 0.7944 (mmm-85) cc_final: 0.7621 (mtm110) REVERT: C 95 MET cc_start: 0.9160 (ptm) cc_final: 0.8894 (ptm) REVERT: C 117 LYS cc_start: 0.7645 (mttt) cc_final: 0.7429 (mmtm) REVERT: C 166 ARG cc_start: 0.7574 (mtp85) cc_final: 0.7091 (ttp80) REVERT: C 171 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8357 (tmmt) REVERT: C 178 LYS cc_start: 0.8285 (tttt) cc_final: 0.7789 (mmmt) REVERT: C 211 GLU cc_start: 0.7358 (tt0) cc_final: 0.6959 (tp30) REVERT: C 232 LYS cc_start: 0.8520 (mttp) cc_final: 0.7966 (mmtm) REVERT: C 267 GLU cc_start: 0.7622 (mp0) cc_final: 0.7262 (mp0) REVERT: C 275 LYS cc_start: 0.8559 (ttmt) cc_final: 0.8212 (tttm) REVERT: C 327 ARG cc_start: 0.7927 (mtm180) cc_final: 0.7687 (mtm-85) REVERT: C 339 ASN cc_start: 0.8072 (t0) cc_final: 0.7250 (m-40) REVERT: C 444 ARG cc_start: 0.8068 (mtt90) cc_final: 0.7824 (tpt90) REVERT: C 475 MET cc_start: 0.6941 (mtm) cc_final: 0.6484 (mtm) REVERT: C 490 LYS cc_start: 0.8846 (ttpp) cc_final: 0.7899 (tptp) REVERT: C 504 ARG cc_start: 0.7636 (ttt180) cc_final: 0.7415 (tpp-160) REVERT: J 11 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.7083 (tt) REVERT: J 81 GLN cc_start: 0.8087 (tp40) cc_final: 0.7730 (tp40) REVERT: J 91 TYR cc_start: 0.8529 (m-80) cc_final: 0.8321 (m-80) REVERT: E 538 THR cc_start: 0.9317 (m) cc_final: 0.8888 (p) REVERT: E 542 ARG cc_start: 0.8168 (mmm-85) cc_final: 0.7767 (mtm110) REVERT: E 574 LYS cc_start: 0.8078 (mttt) cc_final: 0.7622 (mtmp) REVERT: M 27 ASN cc_start: 0.8838 (OUTLIER) cc_final: 0.8578 (t0) REVERT: D 97 LYS cc_start: 0.8739 (mmtm) cc_final: 0.8475 (mptt) REVERT: D 106 THR cc_start: 0.8627 (m) cc_final: 0.8361 (m) REVERT: D 117 LYS cc_start: 0.7689 (mttt) cc_final: 0.7437 (mmtm) REVERT: D 166 ARG cc_start: 0.7524 (mtp85) cc_final: 0.6910 (ttp80) REVERT: D 232 LYS cc_start: 0.8498 (mttp) cc_final: 0.7920 (mmtm) REVERT: D 267 GLU cc_start: 0.7504 (mp0) cc_final: 0.7152 (mp0) REVERT: D 328 GLN cc_start: 0.8260 (tt0) cc_final: 0.7976 (tt0) REVERT: D 356 ASN cc_start: 0.8018 (t0) cc_final: 0.7613 (m-40) REVERT: D 475 MET cc_start: 0.6787 (mtm) cc_final: 0.6417 (mtm) REVERT: D 490 LYS cc_start: 0.8696 (ttpp) cc_final: 0.7939 (tptp) REVERT: D 502 LYS cc_start: 0.8761 (tttm) cc_final: 0.8414 (tttt) REVERT: F 542 ARG cc_start: 0.8162 (mmm-85) cc_final: 0.7665 (mtm110) REVERT: N 100 ARG cc_start: 0.8508 (mtm180) cc_final: 0.7564 (mmm160) outliers start: 45 outliers final: 34 residues processed: 366 average time/residue: 1.3785 time to fit residues: 580.5267 Evaluate side-chains 370 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 332 time to evaluate : 2.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 100 GLN Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain C residue 171 LYS Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 464 THR Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain E residue 660 LEU Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 19 SER Chi-restraints excluded: chain M residue 27 ASN Chi-restraints excluded: chain M residue 101 ASP Chi-restraints excluded: chain Q residue 27 SER Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain D residue 275 LYS Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain R residue 27 SER Chi-restraints excluded: chain R residue 70 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 36 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 239 optimal weight: 1.9990 chunk 185 optimal weight: 5.9990 chunk 70 optimal weight: 0.6980 chunk 241 optimal weight: 9.9990 chunk 260 optimal weight: 8.9990 chunk 96 optimal weight: 9.9990 chunk 181 optimal weight: 0.7980 chunk 115 optimal weight: 0.0870 chunk 289 optimal weight: 0.6980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN A 114 GLN ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 GLN G 100BGLN I 31 ASN I 53 GLN C 103 GLN ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 31 ASN O 53 GLN M 27 ASN M 77 GLN D 283 ASN P 31 ASN P 53 GLN N 27 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.158939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.124312 restraints weight = 24628.615| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.76 r_work: 0.3215 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25440 Z= 0.129 Angle : 0.559 11.568 34668 Z= 0.283 Chirality : 0.044 0.559 4014 Planarity : 0.004 0.047 4329 Dihedral : 5.281 49.401 4570 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.69 % Allowed : 13.21 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.15), residues: 3039 helix: 0.01 (0.26), residues: 429 sheet: 0.08 (0.16), residues: 903 loop : 0.06 (0.15), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 112 HIS 0.006 0.001 HIS H 50 PHE 0.015 0.001 PHE C 53 TYR 0.021 0.001 TYR O 49 ARG 0.007 0.000 ARG P 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00293 ( 48) link_NAG-ASN : angle 2.56712 ( 144) link_BETA1-4 : bond 0.00372 ( 9) link_BETA1-4 : angle 1.33869 ( 27) link_ALPHA1-3 : bond 0.00863 ( 3) link_ALPHA1-3 : angle 1.29434 ( 9) hydrogen bonds : bond 0.03892 ( 651) hydrogen bonds : angle 5.05976 ( 1656) SS BOND : bond 0.00418 ( 45) SS BOND : angle 1.21430 ( 90) covalent geometry : bond 0.00299 (25335) covalent geometry : angle 0.53103 (34398) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18960.26 seconds wall clock time: 326 minutes 47.56 seconds (19607.56 seconds total)