Starting phenix.real_space_refine on Sat Jun 21 07:27:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sw3_40796/06_2025/8sw3_40796.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sw3_40796/06_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_40796/06_2025/8sw3_40796.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sw3_40796/06_2025/8sw3_40796.map" model { file = "/net/cci-nas-00/data/ceres_data/8sw3_40796/06_2025/8sw3_40796.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sw3_40796/06_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-5710/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: 14.34, per 1000 atoms: 0.58 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: 5.90 Conformation dependent library (CDL) restraints added in 2.8 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: 2.85 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: 8.04 Time building geometry restraints manager: 7.03 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: 0.15 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: 7.030 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: 0.870 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 52.660 Find NCS groups from input model: 0.420 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:14.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.470 ------------------------------------------------------------------------------- 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 : 2.631 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: 1.3594 time to fit residues: 950.5105 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 : 3.164 ------------------------------------------------------------------------------- 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): 0.3358 rms_B_bonded: 1.80 r_work: 0.3197 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 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 : 2.594 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: 0.7769 (mttt) cc_final: 0.7339 (mmtm) REVERT: A 136 ASN cc_start: 0.6210 (m-40) cc_final: 0.6009 (m110) REVERT: A 166 ARG cc_start: 0.7454 (mtp85) cc_final: 0.6871 (ttp80) REVERT: A 178 LYS cc_start: 0.7946 (tttt) cc_final: 0.7296 (ttpp) REVERT: A 232 LYS cc_start: 0.8385 (mttp) cc_final: 0.7775 (mmpt) REVERT: A 267 GLU cc_start: 0.7356 (mp0) cc_final: 0.7043 (mp0) REVERT: A 278 ARG cc_start: 0.8177 (mmt-90) cc_final: 0.7930 (mmt90) REVERT: A 347 LYS cc_start: 0.7894 (mttt) cc_final: 0.7494 (pttp) REVERT: A 490 LYS cc_start: 0.8755 (ttpp) cc_final: 0.7839 (tptt) REVERT: A 504 ARG cc_start: 0.6773 (tpp-160) cc_final: 0.6334 (mpp-170) REVERT: G 11 LEU cc_start: 0.7229 (OUTLIER) cc_final: 0.6948 (tt) REVERT: G 20 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7803 (mt) REVERT: I 47 MET cc_start: 0.8369 (mmm) cc_final: 0.8066 (mmt) REVERT: B 530 MET cc_start: 0.9203 (mtp) cc_final: 0.8969 (mtp) REVERT: B 542 ARG cc_start: 0.7558 (mmm-85) cc_final: 0.7163 (mtm110) REVERT: B 657 GLU cc_start: 0.8307 (mt-10) cc_final: 0.8036 (mm-30) REVERT: H 56 SER cc_start: 0.8300 (t) cc_final: 0.8097 (p) REVERT: H 100 ARG cc_start: 0.8382 (mtm180) cc_final: 0.7372 (mmm160) REVERT: C 97 LYS cc_start: 0.8484 (mmtm) cc_final: 0.8247 (mptt) REVERT: C 117 LYS cc_start: 0.7555 (mttt) cc_final: 0.7213 (mmtm) REVERT: C 136 ASN cc_start: 0.6681 (m-40) cc_final: 0.6322 (m-40) REVERT: C 166 ARG cc_start: 0.7399 (mtp85) cc_final: 0.6844 (ttp80) REVERT: C 178 LYS cc_start: 0.8115 (tttt) cc_final: 0.7535 (ttpp) REVERT: C 211 GLU cc_start: 0.7267 (tt0) cc_final: 0.6815 (tp30) REVERT: C 232 LYS cc_start: 0.8412 (mttp) cc_final: 0.7885 (mmtm) REVERT: C 267 GLU cc_start: 0.7482 (mp0) cc_final: 0.7103 (mp0) REVERT: C 325 ASP cc_start: 0.7484 (m-30) cc_final: 0.7215 (p0) REVERT: C 347 LYS cc_start: 0.7733 (mttt) cc_final: 0.7357 (pttp) REVERT: C 356 ASN cc_start: 0.8023 (OUTLIER) cc_final: 0.7543 (t0) REVERT: C 444 ARG cc_start: 0.7976 (mtt90) cc_final: 0.7680 (mmm160) REVERT: C 475 MET cc_start: 0.6824 (mpt) cc_final: 0.6365 (mpp) REVERT: C 490 LYS cc_start: 0.8686 (ttpp) cc_final: 0.7872 (tptp) REVERT: J 11 LEU cc_start: 0.7392 (OUTLIER) cc_final: 0.7031 (tt) REVERT: J 70 SER cc_start: 0.8471 (t) cc_final: 0.8219 (p) REVERT: J 81 GLN cc_start: 0.8512 (tp40) cc_final: 0.8216 (tp40) REVERT: J 90 TYR cc_start: 0.8430 (m-80) cc_final: 0.8069 (m-80) REVERT: J 91 TYR cc_start: 0.8437 (m-80) cc_final: 0.8188 (m-80) REVERT: O 54 ARG cc_start: 0.8534 (mtm-85) cc_final: 0.8220 (mtm110) REVERT: E 542 ARG cc_start: 0.7577 (mmm-85) cc_final: 0.6910 (mtm-85) REVERT: E 657 GLU cc_start: 0.8395 (mt-10) cc_final: 0.7952 (mm-30) REVERT: M 25 SER cc_start: 0.7892 (t) cc_final: 0.7313 (m) REVERT: M 56 SER cc_start: 0.8256 (t) cc_final: 0.8025 (p) REVERT: M 70 SER cc_start: 0.7989 (p) cc_final: 0.7672 (t) REVERT: M 100 ARG cc_start: 0.8446 (mtm180) cc_final: 0.7481 (mmm160) REVERT: Q 93 ASP cc_start: 0.8486 (m-30) cc_final: 0.8211 (m-30) REVERT: D 97 LYS cc_start: 0.8595 (mmtm) cc_final: 0.8285 (mttp) REVERT: D 106 THR cc_start: 0.8617 (m) cc_final: 0.8381 (m) REVERT: D 117 LYS cc_start: 0.7654 (mttt) cc_final: 0.7334 (mmtm) REVERT: D 136 ASN cc_start: 0.6691 (m-40) cc_final: 0.6338 (m-40) REVERT: D 166 ARG cc_start: 0.7536 (mtp85) cc_final: 0.6818 (ttp80) REVERT: D 232 LYS cc_start: 0.8244 (mttp) cc_final: 0.7640 (mmtm) REVERT: D 267 GLU cc_start: 0.7375 (mp0) cc_final: 0.7084 (mp0) REVERT: D 347 LYS cc_start: 0.7774 (mttt) cc_final: 0.7556 (pttp) REVERT: D 355 ASN cc_start: 0.6928 (m-40) cc_final: 0.6722 (t0) REVERT: D 444 ARG cc_start: 0.8077 (mtt90) cc_final: 0.7820 (mmm160) REVERT: D 475 MET cc_start: 0.7259 (mpt) cc_final: 0.6972 (mpp) REVERT: D 490 LYS cc_start: 0.8759 (ttpp) cc_final: 0.7901 (tptp) REVERT: P 97 ILE cc_start: 0.8142 (mt) cc_final: 0.7900 (mm) REVERT: F 542 ARG cc_start: 0.7604 (mmm-85) cc_final: 0.7162 (mtm110) REVERT: F 636 SER cc_start: 0.8467 (m) cc_final: 0.8089 (p) REVERT: F 653 GLN cc_start: 0.8552 (mt0) cc_final: 0.8322 (mt0) REVERT: F 657 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8169 (mt-10) REVERT: N 25 SER cc_start: 0.7818 (t) cc_final: 0.7321 (m) REVERT: N 56 SER cc_start: 0.8151 (t) cc_final: 0.7916 (p) REVERT: N 100 ARG cc_start: 0.8274 (mtm180) cc_final: 0.7377 (mmm160) outliers start: 55 outliers final: 16 residues processed: 461 average time/residue: 1.2805 time to fit residues: 691.2757 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 : 3.008 ------------------------------------------------------------------------------- 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: 0.0870 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: 0.4980 chunk 67 optimal weight: 0.5980 overall best weight: 0.8362 ------------------------------------------------------------------------------- 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 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 Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.162815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.128227 restraints weight = 24371.400| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.75 r_work: 0.3120 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 25440 Z= 0.157 Angle : 0.569 6.649 34668 Z= 0.293 Chirality : 0.045 0.140 4014 Planarity : 0.004 0.037 4329 Dihedral : 6.242 58.386 4570 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.84 % Allowed : 9.07 % Favored : 89.09 % 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: 0.55 (0.15), residues: 3039 helix: 0.36 (0.28), residues: 393 sheet: 0.59 (0.16), residues: 945 loop : 0.37 (0.15), residues: 1701 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 0.019 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 0.00340 ( 48) link_NAG-ASN : angle 2.18087 ( 144) link_BETA1-4 : bond 0.00469 ( 9) link_BETA1-4 : angle 1.40018 ( 27) link_ALPHA1-3 : bond 0.01059 ( 3) link_ALPHA1-3 : angle 1.54338 ( 9) hydrogen bonds : bond 0.04108 ( 651) hydrogen bonds : angle 5.16279 ( 1656) SS BOND : bond 0.00360 ( 45) SS BOND : angle 1.08219 ( 90) covalent geometry : bond 0.00371 (25335) covalent geometry : angle 0.54848 (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 431 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 382 time to evaluate : 3.080 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: 0.7701 (mttt) cc_final: 0.7258 (mmtm) REVERT: A 166 ARG cc_start: 0.7495 (mtp85) cc_final: 0.6927 (ttp80) REVERT: A 178 LYS cc_start: 0.8037 (tttt) cc_final: 0.7458 (ttpp) REVERT: A 232 LYS cc_start: 0.8459 (mttp) cc_final: 0.7798 (mmpt) REVERT: A 267 GLU cc_start: 0.7353 (mp0) cc_final: 0.7024 (mp0) REVERT: A 278 ARG cc_start: 0.8228 (mmt-90) cc_final: 0.8008 (mmp80) REVERT: A 347 LYS cc_start: 0.7906 (mttt) cc_final: 0.7663 (ttpp) REVERT: A 474 ASP cc_start: 0.7094 (p0) cc_final: 0.6799 (p0) REVERT: A 476 ARG cc_start: 0.7291 (mtm-85) cc_final: 0.6805 (mtm180) REVERT: A 490 LYS cc_start: 0.8701 (ttpp) cc_final: 0.7771 (tptt) REVERT: G 11 LEU cc_start: 0.7307 (OUTLIER) cc_final: 0.7012 (tt) REVERT: G 20 LEU cc_start: 0.8016 (mp) cc_final: 0.7812 (mt) REVERT: B 530 MET cc_start: 0.9210 (mtp) cc_final: 0.8910 (mtp) REVERT: B 542 ARG cc_start: 0.7751 (mmm-85) cc_final: 0.7326 (mtm110) REVERT: B 657 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8069 (mm-30) REVERT: H 56 SER cc_start: 0.8373 (t) cc_final: 0.8165 (p) REVERT: C 95 MET cc_start: 0.9150 (ptm) cc_final: 0.8862 (ptm) REVERT: C 117 LYS cc_start: 0.7583 (mttt) cc_final: 0.7212 (mmtm) REVERT: C 136 ASN cc_start: 0.6803 (m-40) cc_final: 0.6576 (m110) REVERT: C 166 ARG cc_start: 0.7463 (mtp85) cc_final: 0.6947 (ttp80) REVERT: C 178 LYS cc_start: 0.8149 (tttt) cc_final: 0.7568 (ttpp) REVERT: C 211 GLU cc_start: 0.7227 (tt0) cc_final: 0.6816 (tp30) REVERT: C 232 LYS cc_start: 0.8466 (mttp) cc_final: 0.7918 (mmtm) REVERT: C 267 GLU cc_start: 0.7564 (mp0) cc_final: 0.7164 (mp0) REVERT: C 325 ASP cc_start: 0.7526 (m-30) cc_final: 0.7303 (p0) REVERT: C 347 LYS cc_start: 0.7737 (mttt) cc_final: 0.7408 (pttm) REVERT: C 444 ARG cc_start: 0.8034 (mtt90) cc_final: 0.7673 (mmm160) REVERT: C 475 MET cc_start: 0.6886 (mpt) cc_final: 0.6657 (mpp) REVERT: C 490 LYS cc_start: 0.8706 (ttpp) cc_final: 0.7860 (tptp) REVERT: J 11 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.7095 (tt) REVERT: J 70 SER cc_start: 0.8493 (t) cc_final: 0.8205 (p) REVERT: J 81 GLN cc_start: 0.8388 (tp40) cc_final: 0.8010 (tp40) REVERT: J 91 TYR cc_start: 0.8517 (m-80) cc_final: 0.8279 (m-80) REVERT: O 54 ARG cc_start: 0.8577 (mtm-85) cc_final: 0.8325 (mtm110) REVERT: E 542 ARG cc_start: 0.7833 (mmm-85) cc_final: 0.7421 (mtm110) REVERT: M 25 SER cc_start: 0.8091 (t) cc_final: 0.7525 (m) REVERT: M 56 SER cc_start: 0.8404 (t) cc_final: 0.8147 (p) REVERT: M 70 SER cc_start: 0.8051 (p) cc_final: 0.7725 (t) REVERT: M 100 ARG cc_start: 0.8513 (mtm180) cc_final: 0.7561 (mmm160) REVERT: D 97 LYS cc_start: 0.8665 (mmtm) cc_final: 0.8387 (mttp) REVERT: D 106 THR cc_start: 0.8556 (m) cc_final: 0.8281 (m) REVERT: D 117 LYS cc_start: 0.7598 (mttt) cc_final: 0.7288 (mmtm) REVERT: D 136 ASN cc_start: 0.6763 (m-40) cc_final: 0.6492 (m110) REVERT: D 166 ARG cc_start: 0.7528 (mtp85) cc_final: 0.6857 (ttp80) REVERT: D 232 LYS cc_start: 0.8385 (mttp) cc_final: 0.7695 (mmpt) REVERT: D 267 GLU cc_start: 0.7400 (mp0) cc_final: 0.7071 (mp0) REVERT: D 444 ARG cc_start: 0.8032 (mtt90) cc_final: 0.7672 (mmm160) REVERT: D 490 LYS cc_start: 0.8741 (ttpp) cc_final: 0.7863 (tptp) REVERT: P 97 ILE cc_start: 0.8126 (mt) cc_final: 0.7921 (mm) REVERT: F 542 ARG cc_start: 0.7780 (mmm-85) cc_final: 0.7409 (mtm110) REVERT: F 636 SER cc_start: 0.8398 (m) cc_final: 0.8157 (p) REVERT: F 640 GLN cc_start: 0.8780 (mm-40) cc_final: 0.8464 (tp40) REVERT: F 653 GLN cc_start: 0.8524 (mt0) cc_final: 0.8305 (mt0) REVERT: F 657 GLU cc_start: 0.8384 (mt-10) cc_final: 0.8151 (mt-10) REVERT: N 56 SER cc_start: 0.8221 (t) cc_final: 0.7967 (p) REVERT: N 100 ARG cc_start: 0.8417 (mtm180) cc_final: 0.7469 (mmm160) REVERT: R 72 SER cc_start: 0.7993 (p) cc_final: 0.7791 (t) outliers start: 49 outliers final: 29 residues processed: 414 average time/residue: 1.3654 time to fit residues: 656.2084 Evaluate side-chains 392 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 361 time to evaluate : 2.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 GLU 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 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: 0.5980 chunk 37 optimal weight: 4.9990 chunk 291 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 236 optimal weight: 0.9980 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: 1.0784 ------------------------------------------------------------------------------- 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 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.161355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.126023 restraints weight = 24537.640| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.78 r_work: 0.3069 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 25440 Z= 0.183 Angle : 0.578 8.707 34668 Z= 0.295 Chirality : 0.045 0.160 4014 Planarity : 0.004 0.039 4329 Dihedral : 5.769 58.774 4570 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.18 % Allowed : 9.74 % Favored : 88.07 % 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: 0.36 (0.15), residues: 3039 helix: 0.37 (0.28), residues: 393 sheet: 0.40 (0.15), residues: 939 loop : 0.24 (0.15), residues: 1707 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 0.017 0.002 TYR O 49 ARG 0.005 0.001 ARG D 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00284 ( 48) link_NAG-ASN : angle 2.25329 ( 144) link_BETA1-4 : bond 0.00408 ( 9) link_BETA1-4 : angle 1.45873 ( 27) link_ALPHA1-3 : bond 0.01053 ( 3) link_ALPHA1-3 : angle 1.68069 ( 9) hydrogen bonds : bond 0.04177 ( 651) hydrogen bonds : angle 5.12778 ( 1656) SS BOND : bond 0.00378 ( 45) SS BOND : angle 1.02932 ( 90) covalent geometry : bond 0.00435 (25335) covalent geometry : angle 0.55738 (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 424 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 366 time to evaluate : 2.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LYS cc_start: 0.7715 (mttt) cc_final: 0.7260 (mmtm) REVERT: A 166 ARG cc_start: 0.7525 (mtp85) cc_final: 0.6936 (ttp80) REVERT: A 178 LYS cc_start: 0.8168 (tttt) cc_final: 0.7572 (ttpp) REVERT: A 232 LYS cc_start: 0.8487 (mttp) cc_final: 0.7786 (mmpt) REVERT: A 267 GLU cc_start: 0.7425 (mp0) cc_final: 0.7114 (mp0) REVERT: A 278 ARG cc_start: 0.8219 (mmt-90) cc_final: 0.7999 (mmp80) REVERT: A 347 LYS cc_start: 0.7992 (mttt) cc_final: 0.7706 (ttpp) REVERT: A 474 ASP cc_start: 0.7157 (OUTLIER) cc_final: 0.6657 (p0) REVERT: A 490 LYS cc_start: 0.8728 (ttpp) cc_final: 0.7795 (tptt) REVERT: G 11 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.7023 (tt) REVERT: B 530 MET cc_start: 0.9221 (mtp) cc_final: 0.8954 (mtp) REVERT: B 542 ARG cc_start: 0.7878 (mmm-85) cc_final: 0.7431 (mtm110) REVERT: H 56 SER cc_start: 0.8482 (t) cc_final: 0.8215 (p) REVERT: C 95 MET cc_start: 0.9150 (ptm) cc_final: 0.8853 (ptm) REVERT: C 117 LYS cc_start: 0.7576 (mttt) cc_final: 0.7255 (mmtm) REVERT: C 166 ARG cc_start: 0.7501 (mtp85) cc_final: 0.6947 (ttp80) REVERT: C 178 LYS cc_start: 0.8282 (tttt) cc_final: 0.7613 (tttm) REVERT: C 211 GLU cc_start: 0.7341 (tt0) cc_final: 0.6863 (tp30) REVERT: C 232 LYS cc_start: 0.8484 (mttp) cc_final: 0.7905 (mmtm) REVERT: C 267 GLU cc_start: 0.7609 (mp0) cc_final: 0.7179 (mp0) REVERT: C 325 ASP cc_start: 0.7674 (m-30) cc_final: 0.7410 (p0) REVERT: C 347 LYS cc_start: 0.7856 (mttt) cc_final: 0.7606 (ttpp) REVERT: C 444 ARG cc_start: 0.8129 (mtt90) cc_final: 0.7751 (mmm160) REVERT: C 490 LYS cc_start: 0.8781 (ttpp) cc_final: 0.7828 (tptp) REVERT: J 11 LEU cc_start: 0.7457 (OUTLIER) cc_final: 0.7075 (tt) REVERT: J 70 SER cc_start: 0.8603 (t) cc_final: 0.8312 (p) REVERT: J 81 GLN cc_start: 0.8325 (tp40) cc_final: 0.7930 (tp40) REVERT: J 91 TYR cc_start: 0.8621 (m-80) cc_final: 0.8353 (m-80) REVERT: E 542 ARG cc_start: 0.7935 (mmm-85) cc_final: 0.7546 (mtm110) REVERT: M 25 SER cc_start: 0.8235 (t) cc_final: 0.7702 (m) REVERT: M 27 ASN cc_start: 0.8849 (OUTLIER) cc_final: 0.8623 (t0) REVERT: M 56 SER cc_start: 0.8460 (t) cc_final: 0.8161 (p) REVERT: M 100 ARG cc_start: 0.8489 (mtm180) cc_final: 0.7446 (mmm160) REVERT: D 97 LYS cc_start: 0.8654 (mmtm) cc_final: 0.8307 (mptt) REVERT: D 117 LYS cc_start: 0.7541 (mttt) cc_final: 0.7204 (mmtm) REVERT: D 166 ARG cc_start: 0.7575 (mtp85) cc_final: 0.6865 (ttp80) REVERT: D 232 LYS cc_start: 0.8430 (mttp) cc_final: 0.7800 (mmtm) REVERT: D 267 GLU cc_start: 0.7387 (mp0) cc_final: 0.7041 (mp0) REVERT: D 444 ARG cc_start: 0.8114 (mtt90) cc_final: 0.7830 (mmm-85) REVERT: D 490 LYS cc_start: 0.8730 (ttpp) cc_final: 0.7966 (tptp) REVERT: P 97 ILE cc_start: 0.8200 (mt) cc_final: 0.7982 (mm) REVERT: F 542 ARG cc_start: 0.7973 (mmm-85) cc_final: 0.7560 (mtm110) REVERT: F 640 GLN cc_start: 0.8910 (mm-40) cc_final: 0.8608 (tp40) REVERT: F 657 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8168 (mt-10) REVERT: N 56 SER cc_start: 0.8345 (t) cc_final: 0.8037 (p) REVERT: N 100 ARG cc_start: 0.8446 (mtm180) cc_final: 0.7461 (mmm160) outliers start: 58 outliers final: 32 residues processed: 402 average time/residue: 1.4901 time to fit residues: 693.1691 Evaluate side-chains 382 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 346 time to evaluate : 2.570 ------------------------------------------------------------------------------- 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 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 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 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 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 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: 0.8980 chunk 220 optimal weight: 3.9990 chunk 125 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 49 optimal weight: 0.4980 chunk 284 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 269 optimal weight: 0.9990 chunk 222 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 O 53 GLN M 27 ASN M 77 GLN ** 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.160315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.125104 restraints weight = 24537.669| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.78 r_work: 0.3087 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 25440 Z= 0.154 Angle : 0.549 8.576 34668 Z= 0.280 Chirality : 0.044 0.193 4014 Planarity : 0.004 0.039 4329 Dihedral : 5.490 59.496 4570 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.22 % Allowed : 10.84 % Favored : 86.95 % 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: 0.43 (0.28), residues: 393 sheet: 0.34 (0.15), residues: 933 loop : 0.21 (0.15), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 112 HIS 0.006 0.001 HIS H 50 PHE 0.017 0.002 PHE H 78 TYR 0.018 0.001 TYR O 49 ARG 0.004 0.000 ARG D 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00277 ( 48) link_NAG-ASN : angle 2.28364 ( 144) link_BETA1-4 : bond 0.00397 ( 9) link_BETA1-4 : angle 1.37427 ( 27) link_ALPHA1-3 : bond 0.01032 ( 3) link_ALPHA1-3 : angle 1.52978 ( 9) hydrogen bonds : bond 0.03983 ( 651) hydrogen bonds : angle 5.04736 ( 1656) SS BOND : bond 0.00406 ( 45) SS BOND : angle 0.96008 ( 90) covalent geometry : bond 0.00361 (25335) covalent geometry : angle 0.52660 (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 423 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 364 time to evaluate : 2.562 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: 0.7659 (mttt) cc_final: 0.7430 (mmtm) REVERT: A 166 ARG cc_start: 0.7474 (mtp85) cc_final: 0.6873 (ttp80) REVERT: A 178 LYS cc_start: 0.8130 (tttt) cc_final: 0.7565 (ttpp) REVERT: A 232 LYS cc_start: 0.8532 (mttp) cc_final: 0.7879 (mmpt) REVERT: A 267 GLU cc_start: 0.7368 (mp0) cc_final: 0.7054 (mp0) REVERT: A 278 ARG cc_start: 0.8219 (mmt-90) cc_final: 0.8002 (mmp80) REVERT: A 347 LYS cc_start: 0.7964 (mttt) cc_final: 0.7689 (ttpp) REVERT: A 476 ARG cc_start: 0.7411 (mtm-85) cc_final: 0.7046 (mtm180) REVERT: A 490 LYS cc_start: 0.8712 (ttpp) cc_final: 0.7776 (tptt) REVERT: G 11 LEU cc_start: 0.7365 (OUTLIER) cc_final: 0.7069 (tt) REVERT: B 530 MET cc_start: 0.9221 (mtp) cc_final: 0.8928 (mtp) REVERT: B 542 ARG cc_start: 0.7851 (mmm-85) cc_final: 0.7471 (mtm110) REVERT: H 5 GLN cc_start: 0.7686 (tp40) cc_final: 0.7462 (tp-100) REVERT: H 56 SER cc_start: 0.8447 (t) cc_final: 0.8177 (p) REVERT: C 95 MET cc_start: 0.9146 (ptm) cc_final: 0.8828 (ptm) REVERT: C 117 LYS cc_start: 0.7587 (mttt) cc_final: 0.7262 (mmtm) REVERT: C 166 ARG cc_start: 0.7431 (mtp85) cc_final: 0.6908 (ttp80) REVERT: C 171 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8428 (tmmt) REVERT: C 178 LYS cc_start: 0.8244 (tttt) cc_final: 0.7605 (tttm) REVERT: C 211 GLU cc_start: 0.7330 (tt0) cc_final: 0.6845 (tp30) REVERT: C 232 LYS cc_start: 0.8454 (mttp) cc_final: 0.7969 (mmpt) REVERT: C 267 GLU cc_start: 0.7627 (mp0) cc_final: 0.7227 (mp0) REVERT: C 325 ASP cc_start: 0.7696 (m-30) cc_final: 0.7412 (p0) REVERT: C 347 LYS cc_start: 0.7873 (mttt) cc_final: 0.7642 (ttpp) REVERT: C 444 ARG cc_start: 0.8106 (mtt90) cc_final: 0.7697 (mmm160) REVERT: C 490 LYS cc_start: 0.8786 (ttpp) cc_final: 0.7818 (tptp) REVERT: J 11 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.7105 (tt) REVERT: J 70 SER cc_start: 0.8564 (t) cc_final: 0.8257 (p) REVERT: J 81 GLN cc_start: 0.8303 (tp40) cc_final: 0.7892 (tp40) REVERT: J 91 TYR cc_start: 0.8636 (m-80) cc_final: 0.8358 (m-80) REVERT: E 542 ARG cc_start: 0.8025 (mmm-85) cc_final: 0.7602 (mtm110) REVERT: M 25 SER cc_start: 0.8251 (t) cc_final: 0.7716 (m) REVERT: M 56 SER cc_start: 0.8438 (t) cc_final: 0.8152 (p) REVERT: M 100 ARG cc_start: 0.8516 (mtm180) cc_final: 0.7439 (mmm160) REVERT: D 97 LYS cc_start: 0.8699 (mmtm) cc_final: 0.8365 (mptt) REVERT: D 117 LYS cc_start: 0.7603 (mttt) cc_final: 0.7262 (mmtm) REVERT: D 166 ARG cc_start: 0.7532 (mtp85) cc_final: 0.6849 (ttp80) REVERT: D 232 LYS cc_start: 0.8424 (mttp) cc_final: 0.7804 (mmtm) REVERT: D 267 GLU cc_start: 0.7363 (mp0) cc_final: 0.7016 (mp0) REVERT: D 444 ARG cc_start: 0.8111 (mtt90) cc_final: 0.7834 (mmm-85) REVERT: D 490 LYS cc_start: 0.8705 (ttpp) cc_final: 0.7933 (tptp) REVERT: F 542 ARG cc_start: 0.7952 (mmm-85) cc_final: 0.7548 (mtm110) REVERT: F 640 GLN cc_start: 0.8894 (mm-40) cc_final: 0.8540 (tp40) REVERT: F 657 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8227 (mt-10) REVERT: N 100 ARG cc_start: 0.8470 (mtm180) cc_final: 0.7475 (mmm160) outliers start: 59 outliers final: 33 residues processed: 401 average time/residue: 1.3828 time to fit residues: 638.3122 Evaluate side-chains 392 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 356 time to evaluate : 2.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 303 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 B residue 595 ILE 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 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 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 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 478 ASN Chi-restraints excluded: chain P residue 27 SER Chi-restraints excluded: chain F residue 538 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 241 optimal weight: 9.9990 chunk 143 optimal weight: 4.9990 chunk 291 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 191 optimal weight: 0.6980 chunk 108 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 167 optimal weight: 0.6980 chunk 135 optimal weight: 0.6980 chunk 168 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 GLN G 76 ASN G 100BGLN I 31 ASN I 53 GLN C 98 ASN ** C 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 53 GLN M 27 ASN M 77 GLN ** 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.160307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.125282 restraints weight = 24585.397| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.77 r_work: 0.3172 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2654 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= 0.146 Angle : 0.541 8.782 34668 Z= 0.275 Chirality : 0.044 0.188 4014 Planarity : 0.004 0.039 4329 Dihedral : 5.314 59.646 4570 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.14 % Allowed : 11.21 % Favored : 86.64 % 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: 0.49 (0.28), residues: 393 sheet: 0.27 (0.15), residues: 933 loop : 0.20 (0.15), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 112 HIS 0.005 0.001 HIS H 50 PHE 0.020 0.002 PHE D 53 TYR 0.020 0.001 TYR O 49 ARG 0.004 0.000 ARG E 585 Details of bonding type rmsd link_NAG-ASN : bond 0.00424 ( 48) link_NAG-ASN : angle 2.34453 ( 144) link_BETA1-4 : bond 0.00412 ( 9) link_BETA1-4 : angle 1.35255 ( 27) link_ALPHA1-3 : bond 0.01030 ( 3) link_ALPHA1-3 : angle 1.47648 ( 9) hydrogen bonds : bond 0.03901 ( 651) hydrogen bonds : angle 5.00254 ( 1656) SS BOND : bond 0.00386 ( 45) SS BOND : angle 0.92203 ( 90) covalent geometry : bond 0.00343 (25335) covalent geometry : angle 0.51744 (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 408 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 351 time to evaluate : 3.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ARG cc_start: 0.7497 (mtp85) cc_final: 0.6992 (ttp80) REVERT: A 178 LYS cc_start: 0.8125 (tttt) cc_final: 0.7636 (ttpp) REVERT: A 232 LYS cc_start: 0.8650 (mttp) cc_final: 0.8043 (mmpt) REVERT: A 267 GLU cc_start: 0.7405 (mp0) cc_final: 0.7105 (mp0) REVERT: A 490 LYS cc_start: 0.8717 (ttpp) cc_final: 0.7854 (tptt) REVERT: G 11 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.7071 (tt) REVERT: B 530 MET cc_start: 0.9220 (mtp) cc_final: 0.8886 (mtp) REVERT: B 542 ARG cc_start: 0.7972 (mmm-85) cc_final: 0.7649 (mtm110) REVERT: H 5 GLN cc_start: 0.7743 (tp40) cc_final: 0.7505 (tp40) REVERT: H 56 SER cc_start: 0.8528 (t) cc_final: 0.8292 (p) REVERT: C 95 MET cc_start: 0.9179 (ptm) cc_final: 0.8866 (ptm) REVERT: C 117 LYS cc_start: 0.7644 (mttt) cc_final: 0.7371 (mmtm) REVERT: C 166 ARG cc_start: 0.7404 (mtp85) cc_final: 0.7004 (ttp80) REVERT: C 171 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8401 (tmmt) REVERT: C 178 LYS cc_start: 0.8253 (tttt) cc_final: 0.7677 (tttm) REVERT: C 211 GLU cc_start: 0.7432 (tt0) cc_final: 0.7028 (tp30) REVERT: C 232 LYS cc_start: 0.8536 (mttp) cc_final: 0.8096 (mmpt) REVERT: C 267 GLU cc_start: 0.7674 (mp0) cc_final: 0.7311 (mp0) REVERT: C 321 ASP cc_start: 0.7630 (t0) cc_final: 0.7346 (t0) REVERT: C 325 ASP cc_start: 0.7725 (m-30) cc_final: 0.7483 (p0) REVERT: C 339 ASN cc_start: 0.8305 (t0) cc_final: 0.7495 (m-40) REVERT: C 444 ARG cc_start: 0.8101 (mtt90) cc_final: 0.7771 (mmm160) REVERT: C 490 LYS cc_start: 0.8829 (ttpp) cc_final: 0.7896 (tptp) REVERT: J 11 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7130 (tt) REVERT: J 70 SER cc_start: 0.8580 (t) cc_final: 0.8325 (p) REVERT: J 81 GLN cc_start: 0.8342 (tp40) cc_final: 0.8014 (tp40) REVERT: J 91 TYR cc_start: 0.8737 (m-80) cc_final: 0.8452 (m-80) REVERT: O 54 ARG cc_start: 0.8466 (mtm110) cc_final: 0.8250 (ttp-110) REVERT: E 542 ARG cc_start: 0.8126 (mmm-85) cc_final: 0.7740 (mtm110) REVERT: M 25 SER cc_start: 0.8250 (t) cc_final: 0.7750 (m) REVERT: M 27 ASN cc_start: 0.8946 (OUTLIER) cc_final: 0.8686 (t0) REVERT: M 56 SER cc_start: 0.8543 (t) cc_final: 0.8306 (p) REVERT: M 100 ARG cc_start: 0.8536 (mtm180) cc_final: 0.7598 (mmm160) REVERT: D 97 LYS cc_start: 0.8728 (mmtm) cc_final: 0.8451 (mptt) REVERT: D 117 LYS cc_start: 0.7650 (mttt) cc_final: 0.7393 (mmtm) REVERT: D 166 ARG cc_start: 0.7538 (mtp85) cc_final: 0.6983 (ttp80) REVERT: D 171 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.7559 (tmmt) REVERT: D 232 LYS cc_start: 0.8537 (mttp) cc_final: 0.7970 (mmtm) REVERT: D 267 GLU cc_start: 0.7383 (mp0) cc_final: 0.7069 (mp0) REVERT: D 490 LYS cc_start: 0.8735 (ttpp) cc_final: 0.8005 (tptp) REVERT: F 542 ARG cc_start: 0.8051 (mmm-85) cc_final: 0.7665 (mtm110) REVERT: F 640 GLN cc_start: 0.8896 (mm-40) cc_final: 0.8523 (tp40) REVERT: N 100 ARG cc_start: 0.8510 (mtm180) cc_final: 0.7620 (mmm160) outliers start: 57 outliers final: 30 residues processed: 385 average time/residue: 1.4435 time to fit residues: 646.8390 Evaluate side-chains 371 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 336 time to evaluate : 2.809 ------------------------------------------------------------------------------- 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 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 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 11 LEU Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain O residue 97 ILE 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 45 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 chunk 95 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 159 optimal weight: 0.1980 chunk 284 optimal weight: 6.9990 chunk 251 optimal weight: 0.3980 chunk 207 optimal weight: 0.1980 chunk 296 optimal weight: 3.9990 chunk 185 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 76 ASN G 100BGLN I 31 ASN I 53 GLN ** C 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 53 GLN M 27 ASN D 283 ASN K 81 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 = 0.3691 r_free = 0.3691 target = 0.160264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.125138 restraints weight = 24682.891| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.78 r_work: 0.3102 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25440 Z= 0.135 Angle : 0.535 8.717 34668 Z= 0.272 Chirality : 0.043 0.188 4014 Planarity : 0.004 0.039 4329 Dihedral : 5.182 58.402 4570 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.11 % Allowed : 11.66 % Favored : 86.23 % 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: 0.27 (0.15), residues: 3039 helix: 0.59 (0.28), residues: 393 sheet: 0.12 (0.15), residues: 951 loop : 0.25 (0.15), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 112 HIS 0.005 0.001 HIS H 50 PHE 0.024 0.002 PHE D 53 TYR 0.017 0.001 TYR O 49 ARG 0.009 0.000 ARG C 327 Details of bonding type rmsd link_NAG-ASN : bond 0.00300 ( 48) link_NAG-ASN : angle 2.40443 ( 144) link_BETA1-4 : bond 0.00399 ( 9) link_BETA1-4 : angle 1.32784 ( 27) link_ALPHA1-3 : bond 0.00997 ( 3) link_ALPHA1-3 : angle 1.39468 ( 9) hydrogen bonds : bond 0.03811 ( 651) hydrogen bonds : angle 4.94214 ( 1656) SS BOND : bond 0.00391 ( 45) SS BOND : angle 0.94297 ( 90) covalent geometry : bond 0.00316 (25335) covalent geometry : angle 0.50994 (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 410 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 354 time to evaluate : 2.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.7480 (ttm-80) cc_final: 0.6784 (ttm170) REVERT: A 166 ARG cc_start: 0.7434 (mtp85) cc_final: 0.6869 (ttp80) REVERT: A 178 LYS cc_start: 0.8103 (tttt) cc_final: 0.7567 (ttpp) REVERT: A 232 LYS cc_start: 0.8545 (mttp) cc_final: 0.7894 (mmpt) REVERT: A 267 GLU cc_start: 0.7340 (mp0) cc_final: 0.7062 (mp0) REVERT: A 476 ARG cc_start: 0.7333 (mtm-85) cc_final: 0.7071 (mtt90) REVERT: A 490 LYS cc_start: 0.8710 (ttpp) cc_final: 0.7778 (tptt) REVERT: A 504 ARG cc_start: 0.7094 (tpp-160) cc_final: 0.6839 (mmt-90) REVERT: G 11 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.7031 (tt) REVERT: B 530 MET cc_start: 0.9225 (mtp) cc_final: 0.8878 (mtp) REVERT: B 542 ARG cc_start: 0.7777 (mmm-85) cc_final: 0.7450 (mtm110) REVERT: H 5 GLN cc_start: 0.7579 (tp40) cc_final: 0.7320 (tp40) REVERT: H 56 SER cc_start: 0.8421 (t) cc_final: 0.8140 (p) REVERT: C 95 MET cc_start: 0.9139 (ptm) cc_final: 0.8822 (ptm) REVERT: C 117 LYS cc_start: 0.7557 (mttt) cc_final: 0.7333 (mmtm) REVERT: C 166 ARG cc_start: 0.7397 (mtp85) cc_final: 0.6954 (ttp80) REVERT: C 171 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8406 (tmmt) REVERT: C 178 LYS cc_start: 0.8234 (tttt) cc_final: 0.7618 (tttm) REVERT: C 211 GLU cc_start: 0.7421 (tt0) cc_final: 0.6865 (tp30) REVERT: C 232 LYS cc_start: 0.8454 (mttp) cc_final: 0.7965 (mmpt) REVERT: C 267 GLU cc_start: 0.7649 (mp0) cc_final: 0.7249 (mp0) REVERT: C 321 ASP cc_start: 0.7600 (t0) cc_final: 0.7291 (t0) REVERT: C 325 ASP cc_start: 0.7722 (m-30) cc_final: 0.7425 (p0) REVERT: C 444 ARG cc_start: 0.8066 (mtt90) cc_final: 0.7652 (mmm160) REVERT: C 490 LYS cc_start: 0.8802 (ttpp) cc_final: 0.7807 (tptp) REVERT: J 11 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7112 (tt) REVERT: J 70 SER cc_start: 0.8540 (t) cc_final: 0.8242 (p) REVERT: J 81 GLN cc_start: 0.8200 (tp40) cc_final: 0.7806 (tp40) REVERT: J 91 TYR cc_start: 0.8661 (m-80) cc_final: 0.8369 (m-80) REVERT: O 54 ARG cc_start: 0.8390 (mtm110) cc_final: 0.8176 (ttp-110) REVERT: E 542 ARG cc_start: 0.8035 (mmm-85) cc_final: 0.7619 (mtm110) REVERT: M 25 SER cc_start: 0.8237 (t) cc_final: 0.7746 (m) REVERT: M 56 SER cc_start: 0.8483 (t) cc_final: 0.8208 (p) REVERT: M 100 ARG cc_start: 0.8511 (mtm180) cc_final: 0.7450 (mmm160) REVERT: D 97 LYS cc_start: 0.8684 (mmtm) cc_final: 0.8352 (mttp) REVERT: D 106 THR cc_start: 0.8527 (m) cc_final: 0.8254 (m) REVERT: D 117 LYS cc_start: 0.7600 (mttt) cc_final: 0.7277 (mmtm) REVERT: D 166 ARG cc_start: 0.7541 (mtp85) cc_final: 0.6890 (ttp80) REVERT: D 171 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.7525 (tmmt) REVERT: D 232 LYS cc_start: 0.8367 (mttp) cc_final: 0.7783 (mmtm) REVERT: D 267 GLU cc_start: 0.7342 (mp0) cc_final: 0.7006 (mp0) REVERT: D 339 ASN cc_start: 0.8132 (t0) cc_final: 0.7390 (m110) REVERT: D 490 LYS cc_start: 0.8716 (ttpp) cc_final: 0.7935 (tptp) REVERT: F 542 ARG cc_start: 0.7962 (mmm-85) cc_final: 0.7504 (mtm110) REVERT: F 640 GLN cc_start: 0.8898 (mm-40) cc_final: 0.8499 (tp40) REVERT: F 657 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8168 (mt-10) REVERT: N 100 ARG cc_start: 0.8441 (mtm180) cc_final: 0.7463 (mmm160) outliers start: 56 outliers final: 32 residues processed: 388 average time/residue: 1.4385 time to fit residues: 642.3413 Evaluate side-chains 380 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 344 time to evaluate : 2.687 ------------------------------------------------------------------------------- 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 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 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 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 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: 1.9990 chunk 129 optimal weight: 1.9990 chunk 96 optimal weight: 9.9990 chunk 257 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 173 optimal weight: 0.6980 chunk 184 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 162 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 273 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 GLN G 76 ASN G 100BGLN I 31 ASN I 53 GLN B 652 GLN C 103 GLN ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 53 GLN D 283 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 81 GLN P 31 ASN P 53 GLN N 27 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.157250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.122033 restraints weight = 24685.330| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.77 r_work: 0.3041 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 25440 Z= 0.206 Angle : 0.607 9.534 34668 Z= 0.306 Chirality : 0.046 0.215 4014 Planarity : 0.004 0.040 4329 Dihedral : 5.405 56.155 4570 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.96 % Allowed : 12.04 % Favored : 86.00 % 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: 0.11 (0.15), residues: 3039 helix: 0.06 (0.26), residues: 426 sheet: 0.13 (0.15), residues: 948 loop : 0.20 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 112 HIS 0.006 0.001 HIS A 105 PHE 0.030 0.002 PHE D 53 TYR 0.020 0.002 TYR C 191 ARG 0.008 0.001 ARG C 327 Details of bonding type rmsd link_NAG-ASN : bond 0.00436 ( 48) link_NAG-ASN : angle 2.62873 ( 144) link_BETA1-4 : bond 0.00351 ( 9) link_BETA1-4 : angle 1.44398 ( 27) link_ALPHA1-3 : bond 0.00908 ( 3) link_ALPHA1-3 : angle 1.33885 ( 9) hydrogen bonds : bond 0.04286 ( 651) hydrogen bonds : angle 5.09331 ( 1656) SS BOND : bond 0.00487 ( 45) SS BOND : angle 1.17717 ( 90) covalent geometry : bond 0.00492 (25335) covalent geometry : angle 0.58069 (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 399 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 347 time to evaluate : 2.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.7427 (ttm-80) cc_final: 0.6738 (ttm170) REVERT: A 166 ARG cc_start: 0.7479 (mtp85) cc_final: 0.6883 (ttp80) REVERT: A 178 LYS cc_start: 0.8211 (tttt) cc_final: 0.7681 (mmmt) REVERT: A 232 LYS cc_start: 0.8524 (mttp) cc_final: 0.7838 (mmpt) REVERT: A 267 GLU cc_start: 0.7370 (mp0) cc_final: 0.7075 (mp0) REVERT: A 339 ASN cc_start: 0.8359 (t0) cc_final: 0.7519 (m110) REVERT: A 490 LYS cc_start: 0.8759 (ttpp) cc_final: 0.7798 (tptt) REVERT: A 504 ARG cc_start: 0.7066 (tpp-160) cc_final: 0.6752 (mmt-90) REVERT: G 11 LEU cc_start: 0.7308 (OUTLIER) cc_final: 0.7014 (tt) REVERT: B 530 MET cc_start: 0.9237 (mtp) cc_final: 0.8999 (mtp) REVERT: B 542 ARG cc_start: 0.7893 (mmm-85) cc_final: 0.7537 (mtm110) REVERT: H 5 GLN cc_start: 0.7657 (tp40) cc_final: 0.7410 (tp40) REVERT: H 56 SER cc_start: 0.8460 (t) cc_final: 0.8015 (p) REVERT: C 95 MET cc_start: 0.9143 (ptm) cc_final: 0.8850 (ptm) REVERT: C 117 LYS cc_start: 0.7525 (mttt) cc_final: 0.7276 (mmtm) REVERT: C 166 ARG cc_start: 0.7565 (mtp85) cc_final: 0.7007 (ttp80) REVERT: C 171 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8364 (tmmt) REVERT: C 178 LYS cc_start: 0.8299 (tttt) cc_final: 0.7750 (mmmt) REVERT: C 211 GLU cc_start: 0.7326 (tt0) cc_final: 0.6836 (tp30) REVERT: C 232 LYS cc_start: 0.8472 (mttp) cc_final: 0.7915 (mmtm) REVERT: C 267 GLU cc_start: 0.7661 (mp0) cc_final: 0.7248 (mp0) REVERT: C 321 ASP cc_start: 0.7678 (t0) cc_final: 0.7383 (t0) REVERT: C 325 ASP cc_start: 0.7862 (m-30) cc_final: 0.7608 (p0) REVERT: C 339 ASN cc_start: 0.8062 (t0) cc_final: 0.7278 (m-40) REVERT: C 444 ARG cc_start: 0.8149 (mtt90) cc_final: 0.7735 (mmm160) REVERT: C 490 LYS cc_start: 0.8846 (ttpp) cc_final: 0.7885 (tptp) REVERT: C 504 ARG cc_start: 0.7707 (ttt180) cc_final: 0.7378 (tpp-160) REVERT: J 11 LEU cc_start: 0.7504 (OUTLIER) cc_final: 0.7099 (tt) REVERT: J 70 SER cc_start: 0.8671 (t) cc_final: 0.8394 (p) REVERT: J 81 GLN cc_start: 0.8171 (tp40) cc_final: 0.7804 (tp40) REVERT: J 91 TYR cc_start: 0.8670 (m-80) cc_final: 0.8384 (m-80) REVERT: E 542 ARG cc_start: 0.8116 (mmm-85) cc_final: 0.7696 (mtm110) REVERT: M 25 SER cc_start: 0.8424 (t) cc_final: 0.7839 (m) REVERT: M 56 SER cc_start: 0.8542 (t) cc_final: 0.8196 (p) REVERT: M 100 ARG cc_start: 0.8507 (mtm180) cc_final: 0.7428 (mmm160) REVERT: D 97 LYS cc_start: 0.8704 (mmtm) cc_final: 0.8387 (mptt) REVERT: D 117 LYS cc_start: 0.7654 (mttt) cc_final: 0.7355 (mmtm) REVERT: D 166 ARG cc_start: 0.7537 (mtp85) cc_final: 0.6842 (ttp80) REVERT: D 232 LYS cc_start: 0.8391 (mttp) cc_final: 0.7771 (mmtm) REVERT: D 267 GLU cc_start: 0.7406 (mp0) cc_final: 0.7061 (mp0) REVERT: D 328 GLN cc_start: 0.8231 (tt0) cc_final: 0.7940 (tt0) REVERT: D 356 ASN cc_start: 0.8002 (t0) cc_final: 0.7580 (m-40) REVERT: D 474 ASP cc_start: 0.6774 (p0) cc_final: 0.6528 (p0) REVERT: D 475 MET cc_start: 0.6881 (mtm) cc_final: 0.6615 (mtm) REVERT: D 490 LYS cc_start: 0.8734 (ttpp) cc_final: 0.7931 (tptp) REVERT: F 542 ARG cc_start: 0.8077 (mmm-85) cc_final: 0.7567 (mtm110) REVERT: F 653 GLN cc_start: 0.8022 (mt0) cc_final: 0.7793 (pt0) REVERT: N 100 ARG cc_start: 0.8482 (mtm180) cc_final: 0.7472 (mmm160) outliers start: 52 outliers final: 31 residues processed: 382 average time/residue: 1.6747 time to fit residues: 740.0170 Evaluate side-chains 370 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 336 time to evaluate : 2.602 ------------------------------------------------------------------------------- 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 20 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 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 538 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 19 SER 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 52 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 152 optimal weight: 0.8980 chunk 257 optimal weight: 3.9990 chunk 296 optimal weight: 0.4980 chunk 165 optimal weight: 2.9990 chunk 226 optimal weight: 2.9990 chunk 198 optimal weight: 0.9980 chunk 245 optimal weight: 0.0470 chunk 209 optimal weight: 0.5980 overall best weight: 0.6078 ------------------------------------------------------------------------------- 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** D 283 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 81 GLN P 31 ASN P 53 GLN N 27 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.160107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.124980 restraints weight = 24702.221| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.79 r_work: 0.3098 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 25440 Z= 0.129 Angle : 0.541 10.451 34668 Z= 0.274 Chirality : 0.044 0.342 4014 Planarity : 0.004 0.039 4329 Dihedral : 5.253 56.123 4570 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.47 % Allowed : 13.02 % Favored : 85.52 % 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: 0.16 (0.15), residues: 3039 helix: 0.35 (0.27), residues: 411 sheet: -0.06 (0.15), residues: 969 loop : 0.31 (0.15), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 112 HIS 0.006 0.001 HIS A 105 PHE 0.024 0.001 PHE D 53 TYR 0.019 0.001 TYR A 191 ARG 0.010 0.000 ARG C 327 Details of bonding type rmsd link_NAG-ASN : bond 0.00236 ( 48) link_NAG-ASN : angle 2.61022 ( 144) link_BETA1-4 : bond 0.00376 ( 9) link_BETA1-4 : angle 1.30629 ( 27) link_ALPHA1-3 : bond 0.00871 ( 3) link_ALPHA1-3 : angle 1.28132 ( 9) hydrogen bonds : bond 0.03799 ( 651) hydrogen bonds : angle 4.96811 ( 1656) SS BOND : bond 0.00397 ( 45) SS BOND : angle 0.98253 ( 90) covalent geometry : bond 0.00300 (25335) covalent geometry : angle 0.51203 (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 394 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 355 time to evaluate : 2.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.7326 (ttm-80) cc_final: 0.6632 (ttm170) REVERT: A 166 ARG cc_start: 0.7431 (mtp85) cc_final: 0.7050 (ptt90) REVERT: A 178 LYS cc_start: 0.8166 (tttt) cc_final: 0.7663 (mmmt) REVERT: A 208 VAL cc_start: 0.7417 (t) cc_final: 0.7188 (m) REVERT: A 232 LYS cc_start: 0.8503 (mttp) cc_final: 0.7823 (mmpt) REVERT: A 267 GLU cc_start: 0.7343 (mp0) cc_final: 0.7053 (mp0) REVERT: A 339 ASN cc_start: 0.8217 (t0) cc_final: 0.7393 (m110) REVERT: A 490 LYS cc_start: 0.8715 (ttpp) cc_final: 0.7775 (tptt) REVERT: A 504 ARG cc_start: 0.7094 (tpp-160) cc_final: 0.6803 (mmt-90) REVERT: G 11 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.7081 (tt) REVERT: G 46 GLU cc_start: 0.8547 (tt0) cc_final: 0.8177 (tt0) REVERT: B 530 MET cc_start: 0.9228 (mtp) cc_final: 0.8912 (mtp) REVERT: B 542 ARG cc_start: 0.7849 (mmm-85) cc_final: 0.7515 (mtm110) REVERT: H 5 GLN cc_start: 0.7636 (tp40) cc_final: 0.7375 (tp40) REVERT: H 56 SER cc_start: 0.8428 (t) cc_final: 0.8085 (p) REVERT: C 95 MET cc_start: 0.9120 (ptm) cc_final: 0.8789 (ptm) REVERT: C 117 LYS cc_start: 0.7604 (mttt) cc_final: 0.7350 (mmtm) REVERT: C 166 ARG cc_start: 0.7398 (mtp85) cc_final: 0.7117 (ptt90) REVERT: C 171 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8395 (tmmt) REVERT: C 178 LYS cc_start: 0.8206 (tttt) cc_final: 0.7566 (tttm) REVERT: C 208 VAL cc_start: 0.7189 (t) cc_final: 0.6916 (m) REVERT: C 211 GLU cc_start: 0.7370 (tt0) cc_final: 0.6813 (tp30) REVERT: C 232 LYS cc_start: 0.8413 (mttp) cc_final: 0.7902 (mmpt) REVERT: C 267 GLU cc_start: 0.7644 (mp0) cc_final: 0.7236 (mp0) REVERT: C 321 ASP cc_start: 0.7602 (t0) cc_final: 0.7297 (t0) REVERT: C 325 ASP cc_start: 0.7874 (m-30) cc_final: 0.7597 (p0) REVERT: C 339 ASN cc_start: 0.8081 (t0) cc_final: 0.7281 (m-40) REVERT: C 444 ARG cc_start: 0.8082 (mtt90) cc_final: 0.7796 (tpt90) REVERT: C 490 LYS cc_start: 0.8807 (ttpp) cc_final: 0.7855 (tptp) REVERT: J 11 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.7026 (tt) REVERT: J 70 SER cc_start: 0.8564 (t) cc_final: 0.8258 (p) REVERT: J 81 GLN cc_start: 0.7992 (tp40) cc_final: 0.7656 (tp40) REVERT: J 91 TYR cc_start: 0.8640 (m-80) cc_final: 0.8357 (m-80) REVERT: E 542 ARG cc_start: 0.8087 (mmm-85) cc_final: 0.7666 (mtm110) REVERT: E 574 LYS cc_start: 0.7919 (mttt) cc_final: 0.7437 (mtmp) REVERT: M 25 SER cc_start: 0.8394 (t) cc_final: 0.7837 (m) REVERT: M 56 SER cc_start: 0.8476 (t) cc_final: 0.8191 (p) REVERT: M 100 ARG cc_start: 0.8528 (mtm180) cc_final: 0.7418 (mmm160) REVERT: D 97 LYS cc_start: 0.8687 (mmtm) cc_final: 0.8369 (mptt) REVERT: D 117 LYS cc_start: 0.7621 (mttt) cc_final: 0.7348 (mmtm) REVERT: D 166 ARG cc_start: 0.7439 (mtp85) cc_final: 0.7057 (ptt90) REVERT: D 232 LYS cc_start: 0.8368 (mttp) cc_final: 0.7773 (mmtm) REVERT: D 267 GLU cc_start: 0.7403 (mp0) cc_final: 0.7035 (mp0) REVERT: D 328 GLN cc_start: 0.8164 (tt0) cc_final: 0.7882 (tt0) REVERT: D 356 ASN cc_start: 0.7976 (t0) cc_final: 0.7540 (m-40) REVERT: D 475 MET cc_start: 0.6887 (mtm) cc_final: 0.6656 (mtm) REVERT: D 490 LYS cc_start: 0.8702 (ttpp) cc_final: 0.7918 (tptp) REVERT: D 504 ARG cc_start: 0.6811 (tpp-160) cc_final: 0.6580 (mmt-90) REVERT: F 542 ARG cc_start: 0.8070 (mmm-85) cc_final: 0.7543 (mtm110) REVERT: N 100 ARG cc_start: 0.8430 (mtm180) cc_final: 0.7424 (mmm160) outliers start: 39 outliers final: 26 residues processed: 383 average time/residue: 1.5216 time to fit residues: 679.7488 Evaluate side-chains 369 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 340 time to evaluate : 2.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU 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 H residue 20 LEU Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain C residue 171 LYS Chi-restraints excluded: chain C residue 202 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 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 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 478 ASN Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain F residue 538 THR 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: 1.9990 chunk 240 optimal weight: 0.9990 chunk 83 optimal weight: 0.3980 chunk 235 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 293 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 142 optimal weight: 10.0000 chunk 267 optimal weight: 2.9990 chunk 155 optimal weight: 0.0270 overall best weight: 0.8642 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 GLN G 100BGLN I 31 ASN I 53 GLN L 53 GLN C 103 GLN ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 440 GLN K 81 GLN P 53 GLN F 650 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 = 0.3668 r_free = 0.3668 target = 0.158407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.123477 restraints weight = 24684.885| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.74 r_work: 0.3086 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 25440 Z= 0.159 Angle : 0.579 12.193 34668 Z= 0.292 Chirality : 0.052 1.671 4014 Planarity : 0.004 0.040 4329 Dihedral : 5.424 59.978 4570 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.50 % Allowed : 13.13 % Favored : 85.36 % 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: 0.10 (0.15), residues: 3039 helix: 0.10 (0.26), residues: 429 sheet: 0.07 (0.15), residues: 948 loop : 0.21 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 112 HIS 0.005 0.001 HIS H 50 PHE 0.025 0.002 PHE D 53 TYR 0.019 0.001 TYR O 49 ARG 0.009 0.000 ARG C 327 Details of bonding type rmsd link_NAG-ASN : bond 0.00353 ( 48) link_NAG-ASN : angle 2.59408 ( 144) link_BETA1-4 : bond 0.00361 ( 9) link_BETA1-4 : angle 1.34947 ( 27) link_ALPHA1-3 : bond 0.00770 ( 3) link_ALPHA1-3 : angle 1.21966 ( 9) hydrogen bonds : bond 0.04031 ( 651) hydrogen bonds : angle 4.97802 ( 1656) SS BOND : bond 0.00440 ( 45) SS BOND : angle 1.06846 ( 90) covalent geometry : bond 0.00376 (25335) covalent geometry : angle 0.55187 (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 389 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 349 time to evaluate : 3.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.7327 (ttm-80) cc_final: 0.6632 (ttm170) REVERT: A 166 ARG cc_start: 0.7440 (mtp85) cc_final: 0.7077 (ptt90) REVERT: A 178 LYS cc_start: 0.8173 (tttt) cc_final: 0.7645 (mmmt) REVERT: A 208 VAL cc_start: 0.7444 (t) cc_final: 0.7173 (m) REVERT: A 232 LYS cc_start: 0.8516 (mttp) cc_final: 0.7839 (mmpt) REVERT: A 267 GLU cc_start: 0.7331 (mp0) cc_final: 0.7048 (mp0) REVERT: A 339 ASN cc_start: 0.8258 (t0) cc_final: 0.7408 (m110) REVERT: A 490 LYS cc_start: 0.8717 (ttpp) cc_final: 0.7772 (tptt) REVERT: A 504 ARG cc_start: 0.7012 (tpp-160) cc_final: 0.6742 (mmt-90) REVERT: G 11 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.7056 (tt) REVERT: G 46 GLU cc_start: 0.8556 (tt0) cc_final: 0.8194 (tt0) REVERT: B 530 MET cc_start: 0.9228 (mtp) cc_final: 0.8993 (mtp) REVERT: B 542 ARG cc_start: 0.7850 (mmm-85) cc_final: 0.7528 (mtm110) REVERT: H 5 GLN cc_start: 0.7651 (tp40) cc_final: 0.7391 (tp40) REVERT: H 56 SER cc_start: 0.8449 (t) cc_final: 0.8100 (p) REVERT: C 95 MET cc_start: 0.9119 (ptm) cc_final: 0.8819 (ptm) REVERT: C 117 LYS cc_start: 0.7607 (mttt) cc_final: 0.7362 (mmtm) REVERT: C 166 ARG cc_start: 0.7432 (mtp85) cc_final: 0.6946 (ttp80) REVERT: C 171 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8372 (tmmt) REVERT: C 178 LYS cc_start: 0.8230 (tttt) cc_final: 0.7700 (mmmt) REVERT: C 211 GLU cc_start: 0.7364 (tt0) cc_final: 0.6852 (tp30) REVERT: C 232 LYS cc_start: 0.8468 (mttp) cc_final: 0.7969 (mmpt) REVERT: C 267 GLU cc_start: 0.7576 (mp0) cc_final: 0.7183 (mp0) REVERT: C 321 ASP cc_start: 0.7619 (t0) cc_final: 0.7322 (t0) REVERT: C 325 ASP cc_start: 0.7886 (m-30) cc_final: 0.7628 (p0) REVERT: C 339 ASN cc_start: 0.8122 (t0) cc_final: 0.7316 (m-40) REVERT: C 444 ARG cc_start: 0.8025 (mtt90) cc_final: 0.7754 (tpt90) REVERT: C 475 MET cc_start: 0.6609 (mtm) cc_final: 0.6293 (mtm) REVERT: C 490 LYS cc_start: 0.8823 (ttpp) cc_final: 0.7864 (tptp) REVERT: J 11 LEU cc_start: 0.7492 (OUTLIER) cc_final: 0.7047 (tt) REVERT: J 70 SER cc_start: 0.8602 (t) cc_final: 0.8292 (p) REVERT: J 81 GLN cc_start: 0.8014 (tp40) cc_final: 0.7708 (tp40) REVERT: J 91 TYR cc_start: 0.8676 (m-80) cc_final: 0.8392 (m-80) REVERT: E 542 ARG cc_start: 0.8064 (mmm-85) cc_final: 0.7685 (mtm110) REVERT: E 574 LYS cc_start: 0.8003 (mttt) cc_final: 0.7535 (mtmp) REVERT: M 25 SER cc_start: 0.8414 (t) cc_final: 0.7873 (m) REVERT: M 56 SER cc_start: 0.8500 (t) cc_final: 0.8190 (p) REVERT: M 100 ARG cc_start: 0.8467 (mtm180) cc_final: 0.7400 (mmm160) REVERT: D 97 LYS cc_start: 0.8680 (mmtm) cc_final: 0.8375 (mptt) REVERT: D 117 LYS cc_start: 0.7621 (mttt) cc_final: 0.7373 (mmtm) REVERT: D 166 ARG cc_start: 0.7469 (mtp85) cc_final: 0.6831 (ttp80) REVERT: D 232 LYS cc_start: 0.8373 (mttp) cc_final: 0.7764 (mmtm) REVERT: D 267 GLU cc_start: 0.7471 (mp0) cc_final: 0.7125 (mp0) REVERT: D 328 GLN cc_start: 0.8217 (tt0) cc_final: 0.7849 (tt0) REVERT: D 356 ASN cc_start: 0.7981 (t0) cc_final: 0.7557 (m-40) REVERT: D 490 LYS cc_start: 0.8703 (ttpp) cc_final: 0.7922 (tptp) REVERT: F 542 ARG cc_start: 0.8065 (mmm-85) cc_final: 0.7573 (mtm110) REVERT: N 100 ARG cc_start: 0.8442 (mtm180) cc_final: 0.7454 (mmm160) outliers start: 40 outliers final: 31 residues processed: 376 average time/residue: 1.5552 time to fit residues: 675.6231 Evaluate side-chains 378 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 344 time to evaluate : 2.569 ------------------------------------------------------------------------------- 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 H residue 20 LEU Chi-restraints excluded: chain H residue 101 ASP 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 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 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 339 ASN 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 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: 0.3980 chunk 47 optimal weight: 0.2980 chunk 239 optimal weight: 0.1980 chunk 185 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 241 optimal weight: 9.9990 chunk 260 optimal weight: 10.0000 chunk 96 optimal weight: 8.9990 chunk 181 optimal weight: 1.9990 chunk 115 optimal weight: 0.0470 chunk 289 optimal weight: 0.5980 overall best weight: 0.3078 ------------------------------------------------------------------------------- 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 98 ASN C 103 GLN ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 31 ASN O 53 GLN D 283 ASN D 440 GLN K 81 GLN P 53 GLN N 27 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.161872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.127271 restraints weight = 24745.392| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.78 r_work: 0.3127 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 25440 Z= 0.102 Angle : 0.529 12.926 34668 Z= 0.267 Chirality : 0.049 1.362 4014 Planarity : 0.004 0.039 4329 Dihedral : 5.069 49.321 4570 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.32 % Allowed : 13.17 % Favored : 85.52 % 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: 0.18 (0.15), residues: 3039 helix: 0.13 (0.26), residues: 435 sheet: 0.09 (0.15), residues: 954 loop : 0.30 (0.16), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D 112 HIS 0.005 0.001 HIS H 50 PHE 0.023 0.001 PHE D 53 TYR 0.018 0.001 TYR A 191 ARG 0.010 0.000 ARG C 327 Details of bonding type rmsd link_NAG-ASN : bond 0.00232 ( 48) link_NAG-ASN : angle 2.53915 ( 144) link_BETA1-4 : bond 0.00399 ( 9) link_BETA1-4 : angle 1.24724 ( 27) link_ALPHA1-3 : bond 0.00829 ( 3) link_ALPHA1-3 : angle 1.26500 ( 9) hydrogen bonds : bond 0.03620 ( 651) hydrogen bonds : angle 4.87466 ( 1656) SS BOND : bond 0.00369 ( 45) SS BOND : angle 0.92170 ( 90) covalent geometry : bond 0.00228 (25335) covalent geometry : angle 0.50094 (34398) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20887.81 seconds wall clock time: 364 minutes 59.36 seconds (21899.36 seconds total)