Starting phenix.real_space_refine on Mon Aug 25 02:15:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sw3_40796/08_2025/8sw3_40796.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sw3_40796/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8sw3_40796/08_2025/8sw3_40796.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sw3_40796/08_2025/8sw3_40796.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sw3_40796/08_2025/8sw3_40796.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sw3_40796/08_2025/8sw3_40796.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 5.92, per 1000 atoms: 0.24 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: 2.25 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 1.2 microseconds 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: 0.79 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: 4.40 Time building geometry restraints manager: 2.95 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'I' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'H' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'L' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = chain 'S' selection = chain 'U' selection = chain 'W' } ncs_group { reference = chain 'T' selection = chain 'V' selection = chain 'X' } 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: 5.310 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.760 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.910 ------------------------------------------------------------------------------- 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 : 1.82 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (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 ARG 0.018 0.001 ARG A 360 TYR 0.018 0.003 TYR D 318 PHE 0.027 0.003 PHE C 53 TRP 0.031 0.003 TRP N 47 HIS 0.019 0.003 HIS M 50 Details of bonding type rmsd covalent geometry : bond 0.00640 (25335) covalent geometry : angle 1.05768 (34398) SS BOND : bond 0.00593 ( 45) SS BOND : angle 2.55238 ( 90) hydrogen bonds : bond 0.13677 ( 651) hydrogen bonds : angle 7.14903 ( 1656) link_ALPHA1-3 : bond 0.00370 ( 3) link_ALPHA1-3 : angle 1.44083 ( 9) link_BETA1-4 : bond 0.00414 ( 9) link_BETA1-4 : angle 1.41537 ( 27) link_NAG-ASN : bond 0.00574 ( 48) link_NAG-ASN : angle 3.10454 ( 144) *********************** 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 : 0.893 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: 0.7451 (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: 0.7222 (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: 0.7332 (tptp) REVERT: G 70 SER cc_start: 0.8137 (t) cc_final: 0.7936 (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: 0.8019 (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: 0.7838 (mm-40) REVERT: B 653 GLN cc_start: 0.8183 (mt0) cc_final: 0.7973 (mt0) REVERT: B 657 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7255 (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: 0.7578 (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: 0.6595 (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: 0.6832 (pttp) REVERT: C 355 ASN cc_start: 0.6668 (m-40) cc_final: 0.6397 (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: 0.7341 (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: 0.7285 (tptp) REVERT: J 67 PHE cc_start: 0.7987 (m-10) cc_final: 0.7775 (m-10) REVERT: J 70 SER cc_start: 0.8278 (t) cc_final: 0.7916 (p) REVERT: J 81 GLN cc_start: 0.8309 (tp40) cc_final: 0.7983 (tp40) REVERT: J 90 TYR cc_start: 0.8197 (m-80) cc_final: 0.7760 (m-80) REVERT: J 91 TYR cc_start: 0.8094 (m-80) cc_final: 0.7837 (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: 0.6206 (mtm-85) REVERT: E 657 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7235 (mm-30) REVERT: M 25 SER cc_start: 0.7767 (t) cc_final: 0.7064 (m) REVERT: M 27 ASN cc_start: 0.8612 (t0) cc_final: 0.8360 (t0) REVERT: M 56 SER cc_start: 0.8069 (t) cc_final: 0.7613 (p) REVERT: M 100 ARG cc_start: 0.7865 (mtm180) cc_final: 0.6945 (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: 0.7121 (t-100) REVERT: D 117 LYS cc_start: 0.7515 (mttt) cc_final: 0.6995 (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: 0.6499 (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: 0.7601 (mt0) REVERT: D 347 LYS cc_start: 0.7211 (mttt) cc_final: 0.6966 (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: 0.7162 (tptp) REVERT: K 70 SER cc_start: 0.8116 (t) cc_final: 0.7797 (p) REVERT: F 542 ARG cc_start: 0.6966 (mmm-85) cc_final: 0.6500 (mtm110) REVERT: F 653 GLN cc_start: 0.8275 (mt0) cc_final: 0.7950 (mt0) REVERT: F 657 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7242 (mm-30) 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: 0.5458 time to fit residues: 380.5023 Evaluate side-chains 435 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 433 time to evaluate : 1.034 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.4980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.165543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.130677 restraints weight = 24699.129| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.79 r_work: 0.3175 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1649 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= 0.163 Angle : 0.613 8.081 34668 Z= 0.316 Chirality : 0.046 0.164 4014 Planarity : 0.004 0.039 4329 Dihedral : 7.167 69.453 4572 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.18 % Favored : 98.72 % Rotamer: Outliers : 2.22 % Allowed : 7.26 % Favored : 90.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.15), residues: 3039 helix: 0.21 (0.28), residues: 393 sheet: 0.84 (0.16), residues: 915 loop : 0.39 (0.15), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 419 TYR 0.015 0.002 TYR N 91 PHE 0.018 0.002 PHE A 53 TRP 0.020 0.002 TRP D 479 HIS 0.007 0.002 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00378 (25335) covalent geometry : angle 0.58717 (34398) SS BOND : bond 0.00418 ( 45) SS BOND : angle 1.15886 ( 90) hydrogen bonds : bond 0.04438 ( 651) hydrogen bonds : angle 5.47381 ( 1656) link_ALPHA1-3 : bond 0.01351 ( 3) link_ALPHA1-3 : angle 2.74070 ( 9) link_BETA1-4 : bond 0.00636 ( 9) link_BETA1-4 : angle 1.78031 ( 27) link_NAG-ASN : bond 0.00303 ( 48) link_NAG-ASN : angle 2.51773 ( 144) *********************** 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 487 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 428 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7958 (tt0) REVERT: A 117 LYS cc_start: 0.7744 (mttt) cc_final: 0.7323 (mmtm) REVERT: A 136 ASN cc_start: 0.6217 (m-40) cc_final: 0.6015 (m110) REVERT: A 166 ARG cc_start: 0.7435 (mtp85) cc_final: 0.6863 (ttp80) REVERT: A 178 LYS cc_start: 0.7982 (tttt) cc_final: 0.7358 (ttpp) REVERT: A 232 LYS cc_start: 0.8378 (mttp) cc_final: 0.7751 (mmpt) REVERT: A 267 GLU cc_start: 0.7350 (mp0) cc_final: 0.7038 (mp0) REVERT: A 278 ARG cc_start: 0.8172 (mmt-90) cc_final: 0.7885 (mmt90) REVERT: A 347 LYS cc_start: 0.7878 (mttt) cc_final: 0.7474 (pttp) REVERT: A 490 LYS cc_start: 0.8732 (ttpp) cc_final: 0.7807 (tptp) REVERT: A 504 ARG cc_start: 0.6761 (OUTLIER) cc_final: 0.6302 (mpp-170) REVERT: G 11 LEU cc_start: 0.7241 (OUTLIER) cc_final: 0.6960 (tt) REVERT: G 20 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7808 (mt) REVERT: I 47 MET cc_start: 0.8361 (mmm) cc_final: 0.8084 (mmt) REVERT: B 530 MET cc_start: 0.9198 (mtp) cc_final: 0.8921 (mtp) REVERT: B 542 ARG cc_start: 0.7576 (mmm-85) cc_final: 0.7183 (mtm110) REVERT: H 56 SER cc_start: 0.8306 (t) cc_final: 0.8100 (p) REVERT: C 46 LYS cc_start: 0.8897 (mmtm) cc_final: 0.8691 (mptt) REVERT: C 95 MET cc_start: 0.9136 (ptm) cc_final: 0.8815 (ptm) REVERT: C 97 LYS cc_start: 0.8469 (mmtm) cc_final: 0.8229 (mptt) REVERT: C 117 LYS cc_start: 0.7516 (mttt) cc_final: 0.7154 (mmtm) REVERT: C 136 ASN cc_start: 0.6697 (m-40) cc_final: 0.6417 (m-40) REVERT: C 166 ARG cc_start: 0.7374 (mtp85) cc_final: 0.6834 (ttp80) REVERT: C 178 LYS cc_start: 0.8129 (tttt) cc_final: 0.7530 (ttpp) REVERT: C 211 GLU cc_start: 0.7224 (tt0) cc_final: 0.6783 (tp30) REVERT: C 232 LYS cc_start: 0.8425 (mttp) cc_final: 0.7903 (mmtm) REVERT: C 267 GLU cc_start: 0.7463 (mp0) cc_final: 0.7090 (mp0) REVERT: C 325 ASP cc_start: 0.7480 (m-30) cc_final: 0.7225 (p0) REVERT: C 347 LYS cc_start: 0.7702 (mttt) cc_final: 0.7318 (pttp) REVERT: C 356 ASN cc_start: 0.8012 (OUTLIER) cc_final: 0.7519 (t0) REVERT: C 444 ARG cc_start: 0.7975 (mtt90) cc_final: 0.7665 (mmm160) REVERT: C 475 MET cc_start: 0.6803 (mpt) cc_final: 0.6401 (mpp) REVERT: C 490 LYS cc_start: 0.8670 (ttpp) cc_final: 0.7852 (tptp) REVERT: J 11 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.7040 (tt) REVERT: J 70 SER cc_start: 0.8455 (t) cc_final: 0.8192 (p) REVERT: J 81 GLN cc_start: 0.8464 (tp40) cc_final: 0.8158 (tp40) REVERT: J 91 TYR cc_start: 0.8448 (m-80) cc_final: 0.8195 (m-80) REVERT: O 54 ARG cc_start: 0.8523 (mtm-85) cc_final: 0.8199 (mtm110) REVERT: E 542 ARG cc_start: 0.7592 (mmm-85) cc_final: 0.7034 (mtm-85) REVERT: E 657 GLU cc_start: 0.8409 (mt-10) cc_final: 0.7918 (mm-30) REVERT: M 25 SER cc_start: 0.7904 (t) cc_final: 0.7331 (m) REVERT: M 56 SER cc_start: 0.8260 (t) cc_final: 0.7999 (p) REVERT: M 70 SER cc_start: 0.7985 (p) cc_final: 0.7675 (t) REVERT: M 100 ARG cc_start: 0.8453 (mtm180) cc_final: 0.7483 (mmm160) REVERT: Q 72 SER cc_start: 0.8197 (p) cc_final: 0.7885 (t) REVERT: Q 93 ASP cc_start: 0.8460 (m-30) cc_final: 0.8255 (m-30) REVERT: D 97 LYS cc_start: 0.8576 (mmtm) cc_final: 0.8267 (mttp) REVERT: D 106 THR cc_start: 0.8606 (m) cc_final: 0.8364 (m) REVERT: D 117 LYS cc_start: 0.7604 (mttt) cc_final: 0.7247 (mmtm) REVERT: D 136 ASN cc_start: 0.6702 (m-40) cc_final: 0.6352 (m-40) REVERT: D 166 ARG cc_start: 0.7537 (mtp85) cc_final: 0.6841 (ttp80) REVERT: D 232 LYS cc_start: 0.8263 (mttp) cc_final: 0.7640 (mmtm) REVERT: D 267 GLU cc_start: 0.7384 (mp0) cc_final: 0.7091 (mp0) REVERT: D 347 LYS cc_start: 0.7739 (mttt) cc_final: 0.7484 (pttp) REVERT: D 355 ASN cc_start: 0.6999 (m-40) cc_final: 0.6773 (t0) REVERT: D 444 ARG cc_start: 0.7983 (mtt90) cc_final: 0.7696 (mmm160) REVERT: D 475 MET cc_start: 0.7277 (mpt) cc_final: 0.7010 (mpp) REVERT: D 490 LYS cc_start: 0.8746 (ttpp) cc_final: 0.7879 (tptp) REVERT: F 542 ARG cc_start: 0.7602 (mmm-85) cc_final: 0.7178 (mtm110) REVERT: F 636 SER cc_start: 0.8478 (m) cc_final: 0.8134 (p) REVERT: F 653 GLN cc_start: 0.8535 (mt0) cc_final: 0.8297 (mt0) REVERT: F 657 GLU cc_start: 0.8360 (mt-10) cc_final: 0.8146 (mt-10) REVERT: N 25 SER cc_start: 0.7834 (t) cc_final: 0.7339 (m) REVERT: N 56 SER cc_start: 0.8151 (t) cc_final: 0.7917 (p) REVERT: N 100 ARG cc_start: 0.8330 (mtm180) cc_final: 0.7475 (mmm160) REVERT: R 72 SER cc_start: 0.8199 (p) cc_final: 0.7946 (t) REVERT: R 93 ASP cc_start: 0.8638 (m-30) cc_final: 0.8348 (m-30) outliers start: 59 outliers final: 16 residues processed: 461 average time/residue: 0.5223 time to fit residues: 280.5825 Evaluate side-chains 403 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 381 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 504 ARG 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 538 THR Chi-restraints excluded: chain E residue 660 LEU 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 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 271 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 286 optimal weight: 0.7980 chunk 295 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 187 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 292 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 103 GLN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 ASN O 31 ASN O 53 GLN M 27 ASN M 77 GLN D 103 GLN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 31 ASN P 53 GLN N 5 GLN N 27 ASN R 31 ASN R 53 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.163341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.128258 restraints weight = 24516.132| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.76 r_work: 0.3125 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2145 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= 0.156 Angle : 0.565 7.037 34668 Z= 0.291 Chirality : 0.045 0.169 4014 Planarity : 0.004 0.037 4329 Dihedral : 6.090 58.392 4570 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.03 % Allowed : 9.07 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.15), residues: 3039 helix: 0.38 (0.28), residues: 393 sheet: 0.55 (0.16), residues: 945 loop : 0.36 (0.15), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 71 TYR 0.020 0.002 TYR C 191 PHE 0.019 0.002 PHE H 78 TRP 0.016 0.002 TRP H 47 HIS 0.008 0.001 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00363 (25335) covalent geometry : angle 0.54579 (34398) SS BOND : bond 0.00448 ( 45) SS BOND : angle 1.11577 ( 90) hydrogen bonds : bond 0.04075 ( 651) hydrogen bonds : angle 5.12529 ( 1656) link_ALPHA1-3 : bond 0.00828 ( 3) link_ALPHA1-3 : angle 1.32187 ( 9) link_BETA1-4 : bond 0.00545 ( 9) link_BETA1-4 : angle 1.36525 ( 27) link_NAG-ASN : bond 0.00479 ( 48) link_NAG-ASN : angle 2.13969 ( 144) *********************** 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 438 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 384 time to evaluate : 0.769 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: 0.7694 (mttt) cc_final: 0.7239 (mmtm) REVERT: A 166 ARG cc_start: 0.7468 (mtp85) cc_final: 0.6906 (ttp80) REVERT: A 178 LYS cc_start: 0.8000 (tttt) cc_final: 0.7424 (ttpp) REVERT: A 232 LYS cc_start: 0.8474 (mttp) cc_final: 0.7810 (mmpt) REVERT: A 267 GLU cc_start: 0.7345 (mp0) cc_final: 0.7017 (mp0) REVERT: A 278 ARG cc_start: 0.8207 (mmt-90) cc_final: 0.8004 (mmp80) REVERT: A 347 LYS cc_start: 0.7891 (mttt) cc_final: 0.7469 (pttp) REVERT: A 474 ASP cc_start: 0.7131 (p0) cc_final: 0.6883 (p0) REVERT: A 476 ARG cc_start: 0.7289 (mtm-85) cc_final: 0.6796 (mtm180) REVERT: A 490 LYS cc_start: 0.8705 (ttpp) cc_final: 0.7779 (tptt) REVERT: G 11 LEU cc_start: 0.7313 (OUTLIER) cc_final: 0.7019 (tt) REVERT: B 530 MET cc_start: 0.9211 (mtp) cc_final: 0.8899 (mtp) REVERT: B 542 ARG cc_start: 0.7739 (mmm-85) cc_final: 0.7320 (mtm110) REVERT: H 56 SER cc_start: 0.8450 (t) cc_final: 0.8243 (p) REVERT: H 100 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.7222 (mmm160) REVERT: C 95 MET cc_start: 0.9145 (ptm) cc_final: 0.8863 (ptm) REVERT: C 117 LYS cc_start: 0.7564 (mttt) cc_final: 0.7193 (mmtm) REVERT: C 166 ARG cc_start: 0.7407 (mtp85) cc_final: 0.6891 (ttp80) REVERT: C 178 LYS cc_start: 0.8121 (tttt) cc_final: 0.7553 (ttpp) REVERT: C 211 GLU cc_start: 0.7218 (tt0) cc_final: 0.6802 (tp30) REVERT: C 232 LYS cc_start: 0.8468 (mttp) cc_final: 0.7921 (mmtm) REVERT: C 267 GLU cc_start: 0.7559 (mp0) cc_final: 0.7160 (mp0) REVERT: C 325 ASP cc_start: 0.7537 (m-30) cc_final: 0.7304 (p0) REVERT: C 347 LYS cc_start: 0.7797 (mttt) cc_final: 0.7383 (pttp) REVERT: C 444 ARG cc_start: 0.8034 (mtt90) cc_final: 0.7675 (mmm160) REVERT: C 475 MET cc_start: 0.6891 (mpt) cc_final: 0.6655 (mpp) REVERT: C 490 LYS cc_start: 0.8729 (ttpp) cc_final: 0.7798 (tptp) REVERT: J 11 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.7051 (tt) REVERT: J 70 SER cc_start: 0.8495 (t) cc_final: 0.8200 (p) REVERT: J 81 GLN cc_start: 0.8349 (tp40) cc_final: 0.8024 (tp40) REVERT: J 91 TYR cc_start: 0.8521 (m-80) cc_final: 0.8278 (m-80) REVERT: E 542 ARG cc_start: 0.7840 (mmm-85) cc_final: 0.7431 (mtm110) REVERT: E 617 ARG cc_start: 0.8633 (mtp85) cc_final: 0.8393 (mtp85) REVERT: M 25 SER cc_start: 0.8082 (t) cc_final: 0.7543 (m) REVERT: M 56 SER cc_start: 0.8411 (t) cc_final: 0.8156 (p) REVERT: M 100 ARG cc_start: 0.8523 (mtm180) cc_final: 0.7547 (mmm160) REVERT: D 97 LYS cc_start: 0.8660 (mmtm) cc_final: 0.8376 (mttp) REVERT: D 106 THR cc_start: 0.8547 (m) cc_final: 0.8274 (m) REVERT: D 117 LYS cc_start: 0.7535 (mttt) cc_final: 0.7206 (mmtm) REVERT: D 136 ASN cc_start: 0.6769 (m-40) cc_final: 0.6519 (m110) REVERT: D 166 ARG cc_start: 0.7510 (mtp85) cc_final: 0.6835 (ttp80) REVERT: D 232 LYS cc_start: 0.8386 (mttp) cc_final: 0.7772 (mmtm) REVERT: D 267 GLU cc_start: 0.7363 (mp0) cc_final: 0.7049 (mp0) REVERT: D 347 LYS cc_start: 0.7782 (mttt) cc_final: 0.7519 (pttp) REVERT: D 444 ARG cc_start: 0.8036 (mtt90) cc_final: 0.7672 (mmm160) REVERT: D 490 LYS cc_start: 0.8732 (ttpp) cc_final: 0.7839 (tptp) REVERT: F 542 ARG cc_start: 0.7854 (mmm-85) cc_final: 0.7413 (mtm110) REVERT: F 636 SER cc_start: 0.8472 (m) cc_final: 0.8246 (p) REVERT: F 640 GLN cc_start: 0.8814 (mm-40) cc_final: 0.8476 (tp40) REVERT: F 653 GLN cc_start: 0.8517 (mt0) cc_final: 0.8304 (mt0) REVERT: F 657 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8180 (mt-10) REVERT: N 56 SER cc_start: 0.8264 (t) cc_final: 0.7998 (p) REVERT: N 100 ARG cc_start: 0.8430 (mtm180) cc_final: 0.7463 (mmm160) outliers start: 54 outliers final: 29 residues processed: 416 average time/residue: 0.5737 time to fit residues: 274.7820 Evaluate side-chains 388 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 356 time to evaluate : 0.924 ------------------------------------------------------------------------------- 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 595 ILE Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain H residue 100 ARG 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 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 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 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 76 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 272 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 266 optimal weight: 0.9980 chunk 146 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 261 optimal weight: 7.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 ASN A 374 HIS A 440 GLN G 76 ASN G 100BGLN I 31 ASN I 53 GLN C 103 GLN C 374 HIS O 53 GLN E 652 GLN M 27 ASN 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: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.157966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.122780 restraints weight = 24433.637| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.74 r_work: 0.3059 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 25440 Z= 0.224 Angle : 0.630 9.131 34668 Z= 0.320 Chirality : 0.047 0.175 4014 Planarity : 0.004 0.040 4329 Dihedral : 5.809 59.076 4570 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.26 % Allowed : 9.82 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.15), residues: 3039 helix: 0.33 (0.28), residues: 390 sheet: 0.25 (0.15), residues: 945 loop : 0.17 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 456 TYR 0.021 0.002 TYR O 49 PHE 0.018 0.002 PHE H 78 TRP 0.017 0.002 TRP H 47 HIS 0.006 0.001 HIS M 99 Details of bonding type rmsd covalent geometry : bond 0.00536 (25335) covalent geometry : angle 0.60743 (34398) SS BOND : bond 0.00513 ( 45) SS BOND : angle 1.14054 ( 90) hydrogen bonds : bond 0.04471 ( 651) hydrogen bonds : angle 5.22544 ( 1656) link_ALPHA1-3 : bond 0.01182 ( 3) link_ALPHA1-3 : angle 1.64606 ( 9) link_BETA1-4 : bond 0.00320 ( 9) link_BETA1-4 : angle 1.54125 ( 27) link_NAG-ASN : bond 0.00451 ( 48) link_NAG-ASN : angle 2.42654 ( 144) *********************** 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 420 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 360 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LYS cc_start: 0.7718 (mttt) cc_final: 0.7252 (mmtm) REVERT: A 166 ARG cc_start: 0.7537 (mtp85) cc_final: 0.6926 (ttp80) REVERT: A 178 LYS cc_start: 0.8202 (tttt) cc_final: 0.7633 (ttpp) REVERT: A 232 LYS cc_start: 0.8505 (mttp) cc_final: 0.7814 (mmpt) REVERT: A 267 GLU cc_start: 0.7378 (mp0) cc_final: 0.7060 (mp0) REVERT: A 278 ARG cc_start: 0.8183 (mmt-90) cc_final: 0.7950 (mmp80) REVERT: A 347 LYS cc_start: 0.8027 (mttt) cc_final: 0.7532 (pttp) REVERT: A 474 ASP cc_start: 0.7132 (OUTLIER) cc_final: 0.6651 (p0) REVERT: A 490 LYS cc_start: 0.8724 (ttpp) cc_final: 0.7763 (tptt) REVERT: A 504 ARG cc_start: 0.6881 (tpp-160) cc_final: 0.6636 (mmt-90) REVERT: G 11 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.7078 (tt) REVERT: G 46 GLU cc_start: 0.8591 (tt0) cc_final: 0.8078 (tt0) REVERT: B 530 MET cc_start: 0.9214 (mtp) cc_final: 0.8936 (mtp) REVERT: B 542 ARG cc_start: 0.7888 (mmm-85) cc_final: 0.7507 (mtm110) REVERT: H 5 GLN cc_start: 0.7629 (tp40) cc_final: 0.7386 (tp40) REVERT: H 56 SER cc_start: 0.8506 (t) cc_final: 0.8192 (p) REVERT: C 95 MET cc_start: 0.9142 (ptm) cc_final: 0.8860 (ptm) REVERT: C 117 LYS cc_start: 0.7608 (mttt) cc_final: 0.7278 (mmtm) REVERT: C 166 ARG cc_start: 0.7524 (mtp85) cc_final: 0.6957 (ttp80) REVERT: C 171 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8332 (tmmt) REVERT: C 178 LYS cc_start: 0.8323 (tttt) cc_final: 0.7659 (tttm) REVERT: C 211 GLU cc_start: 0.7336 (tt0) cc_final: 0.6882 (tp30) REVERT: C 232 LYS cc_start: 0.8430 (mttp) cc_final: 0.7851 (mmtm) REVERT: C 267 GLU cc_start: 0.7671 (mp0) cc_final: 0.7261 (mp0) REVERT: C 325 ASP cc_start: 0.7726 (m-30) cc_final: 0.7444 (p0) REVERT: C 347 LYS cc_start: 0.7870 (mttt) cc_final: 0.7375 (pttp) REVERT: C 444 ARG cc_start: 0.8145 (mtt90) cc_final: 0.7708 (mmm160) REVERT: C 490 LYS cc_start: 0.8793 (ttpp) cc_final: 0.7853 (tptp) REVERT: C 504 ARG cc_start: 0.7686 (ttt180) cc_final: 0.7415 (tpp-160) REVERT: J 11 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.7153 (tt) REVERT: J 70 SER cc_start: 0.8671 (t) cc_final: 0.8405 (p) REVERT: J 81 GLN cc_start: 0.8331 (tp40) cc_final: 0.7997 (tp40) REVERT: J 91 TYR cc_start: 0.8679 (m-80) cc_final: 0.8394 (m-80) REVERT: E 542 ARG cc_start: 0.8069 (mmm-85) cc_final: 0.7658 (mtm110) REVERT: E 617 ARG cc_start: 0.8779 (mtp85) cc_final: 0.8533 (mtp85) REVERT: M 3 GLN cc_start: 0.7755 (OUTLIER) cc_final: 0.6903 (tm-30) REVERT: M 27 ASN cc_start: 0.8840 (OUTLIER) cc_final: 0.8633 (t0) REVERT: M 56 SER cc_start: 0.8478 (t) cc_final: 0.8140 (p) REVERT: M 100 ARG cc_start: 0.8539 (mtm180) cc_final: 0.7530 (mmm160) REVERT: D 97 LYS cc_start: 0.8647 (mmtm) cc_final: 0.8281 (mttp) REVERT: D 117 LYS cc_start: 0.7534 (mttt) cc_final: 0.7185 (mmtm) REVERT: D 166 ARG cc_start: 0.7627 (mtp85) cc_final: 0.6942 (ttp80) REVERT: D 232 LYS cc_start: 0.8386 (mttp) cc_final: 0.7773 (mmtm) REVERT: D 267 GLU cc_start: 0.7362 (mp0) cc_final: 0.7033 (mp0) REVERT: D 327 ARG cc_start: 0.7692 (mtm180) cc_final: 0.7180 (mtm180) REVERT: D 328 GLN cc_start: 0.8221 (tt0) cc_final: 0.7907 (tt0) REVERT: D 347 LYS cc_start: 0.7899 (mttt) cc_final: 0.7529 (pttp) REVERT: D 444 ARG cc_start: 0.8143 (mtt90) cc_final: 0.7843 (mmm-85) REVERT: D 490 LYS cc_start: 0.8709 (ttpp) cc_final: 0.7927 (tptp) REVERT: D 502 LYS cc_start: 0.8727 (tttm) cc_final: 0.8402 (tttt) REVERT: F 542 ARG cc_start: 0.8037 (mmm-85) cc_final: 0.7581 (mtm110) REVERT: F 657 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8250 (mt-10) REVERT: N 27 ASN cc_start: 0.9183 (OUTLIER) cc_final: 0.8776 (t0) REVERT: N 100 ARG cc_start: 0.8464 (mtm180) cc_final: 0.7453 (mmm160) outliers start: 60 outliers final: 36 residues processed: 398 average time/residue: 0.6024 time to fit residues: 274.6899 Evaluate side-chains 392 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 349 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 100 GLN Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain C residue 171 LYS Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 660 LEU Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 19 SER Chi-restraints excluded: chain M residue 27 ASN Chi-restraints excluded: chain M residue 101 ASP Chi-restraints excluded: chain Q residue 27 SER Chi-restraints excluded: chain Q residue 70 SER Chi-restraints excluded: chain Q residue 72 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 P residue 97 ILE 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 27 ASN Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain R residue 5 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 176 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 155 optimal weight: 0.1980 chunk 204 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 266 optimal weight: 3.9990 chunk 167 optimal weight: 0.7980 chunk 96 optimal weight: 10.0000 chunk 185 optimal weight: 3.9990 chunk 282 optimal weight: 0.4980 chunk 59 optimal weight: 0.6980 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 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 GLN G 76 ASN G 100BGLN I 31 ASN I 53 GLN C 103 GLN C 440 GLN O 53 GLN M 27 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 81 GLN P 31 ASN P 53 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.159157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.124210 restraints weight = 24556.584| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.75 r_work: 0.3066 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 25440 Z= 0.156 Angle : 0.558 8.670 34668 Z= 0.284 Chirality : 0.044 0.149 4014 Planarity : 0.004 0.040 4329 Dihedral : 5.499 59.751 4570 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.29 % Allowed : 10.76 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.15), residues: 3039 helix: 0.36 (0.28), residues: 393 sheet: 0.09 (0.15), residues: 951 loop : 0.19 (0.15), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 327 TYR 0.017 0.001 TYR C 191 PHE 0.019 0.002 PHE D 53 TRP 0.015 0.001 TRP D 112 HIS 0.006 0.001 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00366 (25335) covalent geometry : angle 0.53398 (34398) SS BOND : bond 0.00418 ( 45) SS BOND : angle 0.98713 ( 90) hydrogen bonds : bond 0.04046 ( 651) hydrogen bonds : angle 5.08126 ( 1656) link_ALPHA1-3 : bond 0.01046 ( 3) link_ALPHA1-3 : angle 1.49024 ( 9) link_BETA1-4 : bond 0.00406 ( 9) link_BETA1-4 : angle 1.38611 ( 27) link_NAG-ASN : bond 0.00347 ( 48) link_NAG-ASN : angle 2.38931 ( 144) *********************** 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 424 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 363 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LYS cc_start: 0.7662 (mttt) cc_final: 0.7205 (mmtm) REVERT: A 166 ARG cc_start: 0.7497 (mtp85) cc_final: 0.6908 (ttp80) REVERT: A 178 LYS cc_start: 0.8151 (tttt) cc_final: 0.7607 (ttpp) REVERT: A 232 LYS cc_start: 0.8514 (mttp) cc_final: 0.7809 (mmpt) REVERT: A 267 GLU cc_start: 0.7368 (mp0) cc_final: 0.7053 (mp0) REVERT: A 278 ARG cc_start: 0.8243 (mmt-90) cc_final: 0.8034 (mmp80) REVERT: A 347 LYS cc_start: 0.8022 (mttt) cc_final: 0.7542 (pttp) REVERT: A 476 ARG cc_start: 0.7300 (mtm-85) cc_final: 0.6963 (mtm180) REVERT: A 490 LYS cc_start: 0.8725 (ttpp) cc_final: 0.7777 (tptt) REVERT: A 504 ARG cc_start: 0.6854 (tpp-160) cc_final: 0.6602 (mmt-90) REVERT: G 11 LEU cc_start: 0.7384 (OUTLIER) cc_final: 0.7082 (tt) REVERT: G 46 GLU cc_start: 0.8598 (tt0) cc_final: 0.8188 (tt0) REVERT: B 530 MET cc_start: 0.9222 (mtp) cc_final: 0.8921 (mtp) REVERT: B 542 ARG cc_start: 0.7805 (mmm-85) cc_final: 0.7467 (mtm110) REVERT: H 5 GLN cc_start: 0.7599 (tp40) cc_final: 0.7349 (tp-100) REVERT: H 56 SER cc_start: 0.8481 (t) cc_final: 0.8160 (p) REVERT: H 100 ARG cc_start: 0.8518 (mtp180) cc_final: 0.7364 (mmm160) REVERT: C 95 MET cc_start: 0.9145 (ptm) cc_final: 0.8836 (ptm) REVERT: C 117 LYS cc_start: 0.7516 (mttt) cc_final: 0.7213 (mmtm) REVERT: C 166 ARG cc_start: 0.7484 (mtp85) cc_final: 0.6961 (ttp80) REVERT: C 171 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8416 (tmmt) REVERT: C 178 LYS cc_start: 0.8265 (tttt) cc_final: 0.7671 (mmmt) REVERT: C 211 GLU cc_start: 0.7340 (tt0) cc_final: 0.6870 (tp30) REVERT: C 232 LYS cc_start: 0.8415 (mttp) cc_final: 0.7892 (mmpt) REVERT: C 267 GLU cc_start: 0.7639 (mp0) cc_final: 0.7248 (mp0) REVERT: C 325 ASP cc_start: 0.7751 (m-30) cc_final: 0.7503 (p0) REVERT: C 347 LYS cc_start: 0.7869 (mttt) cc_final: 0.7367 (pttp) REVERT: C 444 ARG cc_start: 0.8172 (mtt90) cc_final: 0.7773 (mmm160) REVERT: C 490 LYS cc_start: 0.8856 (ttpp) cc_final: 0.7887 (tptp) REVERT: C 504 ARG cc_start: 0.7740 (ttt180) cc_final: 0.7427 (tpp-160) REVERT: J 11 LEU cc_start: 0.7519 (OUTLIER) cc_final: 0.7129 (tt) REVERT: J 70 SER cc_start: 0.8615 (t) cc_final: 0.8374 (p) REVERT: J 81 GLN cc_start: 0.8347 (tp40) cc_final: 0.8013 (tp40) REVERT: J 91 TYR cc_start: 0.8676 (m-80) cc_final: 0.8393 (m-80) REVERT: E 542 ARG cc_start: 0.8051 (mmm-85) cc_final: 0.7623 (mtm110) REVERT: E 617 ARG cc_start: 0.8751 (mtp85) cc_final: 0.8501 (mtp85) REVERT: M 56 SER cc_start: 0.8508 (t) cc_final: 0.8214 (p) REVERT: M 100 ARG cc_start: 0.8506 (mtm180) cc_final: 0.7446 (mmm160) REVERT: D 97 LYS cc_start: 0.8689 (mmtm) cc_final: 0.8357 (mptt) REVERT: D 117 LYS cc_start: 0.7590 (mttt) cc_final: 0.7230 (mmtm) REVERT: D 166 ARG cc_start: 0.7576 (mtp85) cc_final: 0.6906 (ttp80) REVERT: D 232 LYS cc_start: 0.8393 (mttp) cc_final: 0.7796 (mmtm) REVERT: D 267 GLU cc_start: 0.7346 (mp0) cc_final: 0.7040 (mp0) REVERT: D 327 ARG cc_start: 0.7575 (mtm180) cc_final: 0.7327 (mtm180) REVERT: D 328 GLN cc_start: 0.8232 (tt0) cc_final: 0.7933 (tt0) REVERT: D 347 LYS cc_start: 0.7880 (mttt) cc_final: 0.7517 (pttp) REVERT: D 444 ARG cc_start: 0.8105 (mtt90) cc_final: 0.7846 (mmm-85) REVERT: D 490 LYS cc_start: 0.8744 (ttpp) cc_final: 0.7946 (tptp) REVERT: F 542 ARG cc_start: 0.8024 (mmm-85) cc_final: 0.7525 (mtm110) REVERT: F 640 GLN cc_start: 0.8920 (mm-40) cc_final: 0.8576 (tp40) REVERT: F 657 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8172 (mt-10) REVERT: N 100 ARG cc_start: 0.8479 (mtm180) cc_final: 0.7454 (mmm160) outliers start: 61 outliers final: 31 residues processed: 405 average time/residue: 0.5696 time to fit residues: 264.6780 Evaluate side-chains 382 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 348 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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 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 5 VAL Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain O residue 27 SER 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 Q residue 72 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 P residue 27 ASP Chi-restraints excluded: chain P residue 97 ILE Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain R residue 27 SER Chi-restraints excluded: chain R residue 70 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 220 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 173 optimal weight: 0.5980 chunk 138 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 chunk 83 optimal weight: 0.0980 chunk 279 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN A 440 GLN G 100BGLN I 31 ASN I 53 GLN C 98 ASN C 103 GLN C 440 GLN M 27 ASN ** D 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3674 r_free = 0.3674 target = 0.158563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.123339 restraints weight = 24612.854| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.77 r_work: 0.3078 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 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 : 0.004 0.051 25440 Z= 0.162 Angle : 0.560 8.749 34668 Z= 0.284 Chirality : 0.044 0.153 4014 Planarity : 0.004 0.040 4329 Dihedral : 5.361 58.996 4570 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.41 % Allowed : 10.76 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.15), residues: 3039 helix: 0.43 (0.28), residues: 393 sheet: 0.04 (0.15), residues: 951 loop : 0.18 (0.15), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 327 TYR 0.017 0.001 TYR C 191 PHE 0.023 0.002 PHE D 53 TRP 0.018 0.001 TRP D 112 HIS 0.006 0.001 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00383 (25335) covalent geometry : angle 0.53641 (34398) SS BOND : bond 0.00432 ( 45) SS BOND : angle 0.97059 ( 90) hydrogen bonds : bond 0.04012 ( 651) hydrogen bonds : angle 5.04579 ( 1656) link_ALPHA1-3 : bond 0.00993 ( 3) link_ALPHA1-3 : angle 1.42758 ( 9) link_BETA1-4 : bond 0.00394 ( 9) link_BETA1-4 : angle 1.38046 ( 27) link_NAG-ASN : bond 0.00312 ( 48) link_NAG-ASN : angle 2.40602 ( 144) *********************** 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 415 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 351 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LYS cc_start: 0.7680 (mttt) cc_final: 0.7453 (mmtm) REVERT: A 151 ARG cc_start: 0.7484 (ttm-80) cc_final: 0.6804 (ttm170) REVERT: A 166 ARG cc_start: 0.7441 (mtp85) cc_final: 0.6905 (ttp80) REVERT: A 178 LYS cc_start: 0.8168 (tttt) cc_final: 0.7687 (mmmt) REVERT: A 232 LYS cc_start: 0.8524 (mttp) cc_final: 0.7826 (mmpt) REVERT: A 267 GLU cc_start: 0.7363 (mp0) cc_final: 0.7071 (mp0) REVERT: A 278 ARG cc_start: 0.8269 (mmt-90) cc_final: 0.8025 (mmp80) REVERT: A 347 LYS cc_start: 0.7999 (mttt) cc_final: 0.7710 (ttpp) REVERT: A 490 LYS cc_start: 0.8707 (ttpp) cc_final: 0.7757 (tptt) REVERT: A 504 ARG cc_start: 0.6945 (tpp-160) cc_final: 0.6663 (mmt-90) REVERT: G 11 LEU cc_start: 0.7368 (OUTLIER) cc_final: 0.7070 (tt) REVERT: G 46 GLU cc_start: 0.8583 (tt0) cc_final: 0.8079 (tt0) REVERT: B 530 MET cc_start: 0.9230 (mtp) cc_final: 0.8886 (mtp) REVERT: B 542 ARG cc_start: 0.7853 (mmm-85) cc_final: 0.7519 (mtm110) REVERT: H 56 SER cc_start: 0.8480 (t) cc_final: 0.8142 (p) REVERT: C 95 MET cc_start: 0.9135 (ptm) cc_final: 0.8832 (ptm) REVERT: C 117 LYS cc_start: 0.7553 (mttt) cc_final: 0.7328 (mmtm) REVERT: C 166 ARG cc_start: 0.7512 (mtp85) cc_final: 0.6999 (ttp80) REVERT: C 171 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8385 (tmmt) REVERT: C 178 LYS cc_start: 0.8254 (tttt) cc_final: 0.7655 (mmmt) REVERT: C 211 GLU cc_start: 0.7308 (tt0) cc_final: 0.6835 (tp30) REVERT: C 232 LYS cc_start: 0.8431 (mttp) cc_final: 0.7910 (mmpt) REVERT: C 267 GLU cc_start: 0.7627 (mp0) cc_final: 0.7243 (mp0) REVERT: C 275 LYS cc_start: 0.8508 (ttmt) cc_final: 0.8097 (tttm) REVERT: C 321 ASP cc_start: 0.7601 (t0) cc_final: 0.7349 (t0) REVERT: C 325 ASP cc_start: 0.7741 (m-30) cc_final: 0.7521 (p0) REVERT: C 339 ASN cc_start: 0.8157 (t0) cc_final: 0.7337 (m-40) REVERT: C 347 LYS cc_start: 0.7894 (mttt) cc_final: 0.7421 (pttp) REVERT: C 444 ARG cc_start: 0.8156 (mtt90) cc_final: 0.7745 (mmm160) REVERT: C 490 LYS cc_start: 0.8842 (ttpp) cc_final: 0.7837 (tptp) REVERT: J 11 LEU cc_start: 0.7537 (OUTLIER) cc_final: 0.7139 (tt) REVERT: J 70 SER cc_start: 0.8610 (t) cc_final: 0.8356 (p) REVERT: J 81 GLN cc_start: 0.8306 (tp40) cc_final: 0.7954 (tp40) REVERT: J 91 TYR cc_start: 0.8676 (m-80) cc_final: 0.8392 (m-80) REVERT: E 542 ARG cc_start: 0.8035 (mmm-85) cc_final: 0.7633 (mtm110) REVERT: E 617 ARG cc_start: 0.8673 (mtp85) cc_final: 0.8421 (mtp85) REVERT: M 56 SER cc_start: 0.8510 (t) cc_final: 0.8207 (p) REVERT: M 100 ARG cc_start: 0.8528 (mtm180) cc_final: 0.7459 (mmm160) REVERT: D 97 LYS cc_start: 0.8678 (mmtm) cc_final: 0.8375 (mptt) REVERT: D 117 LYS cc_start: 0.7609 (mttt) cc_final: 0.7234 (mmtm) REVERT: D 166 ARG cc_start: 0.7572 (mtp85) cc_final: 0.6875 (ttp80) REVERT: D 171 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.7625 (tmmt) REVERT: D 232 LYS cc_start: 0.8394 (mttp) cc_final: 0.7803 (mmtm) REVERT: D 267 GLU cc_start: 0.7357 (mp0) cc_final: 0.7038 (mp0) REVERT: D 328 GLN cc_start: 0.8221 (tt0) cc_final: 0.7914 (tt0) REVERT: D 347 LYS cc_start: 0.7870 (mttt) cc_final: 0.7564 (pttm) REVERT: D 444 ARG cc_start: 0.8092 (mtt90) cc_final: 0.7838 (mmm-85) REVERT: D 490 LYS cc_start: 0.8724 (ttpp) cc_final: 0.7948 (tptp) REVERT: F 542 ARG cc_start: 0.8049 (mmm-85) cc_final: 0.7528 (mtm110) REVERT: N 100 ARG cc_start: 0.8474 (mtm180) cc_final: 0.7469 (mmm160) outliers start: 64 outliers final: 37 residues processed: 394 average time/residue: 0.6843 time to fit residues: 308.1097 Evaluate side-chains 376 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 335 time to evaluate : 0.857 ------------------------------------------------------------------------------- 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 443 ILE Chi-restraints excluded: chain C residue 464 THR Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain O residue 97 ILE Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain E residue 660 LEU Chi-restraints excluded: chain M residue 19 SER Chi-restraints excluded: chain M residue 101 ASP Chi-restraints excluded: chain Q residue 27 SER Chi-restraints excluded: chain Q residue 70 SER Chi-restraints excluded: chain Q residue 72 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 P residue 27 ASP Chi-restraints excluded: chain P residue 97 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 271 optimal weight: 1.9990 chunk 176 optimal weight: 4.9990 chunk 225 optimal weight: 0.0970 chunk 43 optimal weight: 9.9990 chunk 79 optimal weight: 0.9990 chunk 241 optimal weight: 9.9990 chunk 269 optimal weight: 0.9990 chunk 63 optimal weight: 0.4980 chunk 75 optimal weight: 0.9990 chunk 274 optimal weight: 1.9990 chunk 250 optimal weight: 0.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.158787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.123878 restraints weight = 24603.424| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.76 r_work: 0.3091 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25440 Z= 0.139 Angle : 0.543 9.020 34668 Z= 0.276 Chirality : 0.044 0.204 4014 Planarity : 0.004 0.040 4329 Dihedral : 5.230 57.107 4570 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.07 % Allowed : 12.00 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.15), residues: 3039 helix: 0.07 (0.26), residues: 429 sheet: 0.11 (0.15), residues: 936 loop : 0.18 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 327 TYR 0.018 0.001 TYR C 191 PHE 0.026 0.002 PHE D 53 TRP 0.022 0.001 TRP D 112 HIS 0.005 0.001 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00326 (25335) covalent geometry : angle 0.51764 (34398) SS BOND : bond 0.00392 ( 45) SS BOND : angle 0.94929 ( 90) hydrogen bonds : bond 0.03850 ( 651) hydrogen bonds : angle 4.98108 ( 1656) link_ALPHA1-3 : bond 0.00959 ( 3) link_ALPHA1-3 : angle 1.35674 ( 9) link_BETA1-4 : bond 0.00387 ( 9) link_BETA1-4 : angle 1.33620 ( 27) link_NAG-ASN : bond 0.00278 ( 48) link_NAG-ASN : angle 2.42007 ( 144) *********************** 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 418 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 363 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LYS cc_start: 0.7623 (mttt) cc_final: 0.7405 (mmtm) REVERT: A 151 ARG cc_start: 0.7395 (ttm-80) cc_final: 0.6707 (ttm170) REVERT: A 166 ARG cc_start: 0.7388 (mtp85) cc_final: 0.6835 (ttp80) REVERT: A 178 LYS cc_start: 0.8155 (tttt) cc_final: 0.7664 (mmmt) REVERT: A 208 VAL cc_start: 0.7485 (t) cc_final: 0.7212 (m) REVERT: A 232 LYS cc_start: 0.8506 (mttp) cc_final: 0.7827 (mmpt) REVERT: A 267 GLU cc_start: 0.7345 (mp0) cc_final: 0.7066 (mp0) REVERT: A 278 ARG cc_start: 0.8191 (mmt-90) cc_final: 0.7976 (mmp80) REVERT: A 339 ASN cc_start: 0.8121 (t0) cc_final: 0.7358 (m110) REVERT: A 347 LYS cc_start: 0.7942 (mttt) cc_final: 0.7695 (ttpp) REVERT: A 490 LYS cc_start: 0.8717 (ttpp) cc_final: 0.7763 (tptt) REVERT: A 504 ARG cc_start: 0.7024 (tpp-160) cc_final: 0.6727 (mmt-90) REVERT: G 11 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.7076 (tt) REVERT: B 530 MET cc_start: 0.9219 (mtp) cc_final: 0.8866 (mtp) REVERT: B 542 ARG cc_start: 0.7853 (mmm-85) cc_final: 0.7516 (mtm110) REVERT: H 5 GLN cc_start: 0.7743 (tp-100) cc_final: 0.7430 (tp40) REVERT: H 56 SER cc_start: 0.8451 (t) cc_final: 0.8117 (p) REVERT: C 95 MET cc_start: 0.9127 (ptm) cc_final: 0.8812 (ptm) REVERT: C 117 LYS cc_start: 0.7531 (mttt) cc_final: 0.7316 (mmtm) REVERT: C 166 ARG cc_start: 0.7441 (mtp85) cc_final: 0.6967 (ttp80) REVERT: C 169 ARG cc_start: 0.8118 (mmt-90) cc_final: 0.7881 (mmt-90) REVERT: C 171 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8411 (tmmt) REVERT: C 178 LYS cc_start: 0.8237 (tttt) cc_final: 0.7644 (mmmt) REVERT: C 211 GLU cc_start: 0.7384 (tt0) cc_final: 0.6818 (tp30) REVERT: C 232 LYS cc_start: 0.8436 (mttp) cc_final: 0.7910 (mmpt) REVERT: C 267 GLU cc_start: 0.7638 (mp0) cc_final: 0.7252 (mp0) REVERT: C 321 ASP cc_start: 0.7572 (t0) cc_final: 0.7304 (t0) REVERT: C 325 ASP cc_start: 0.7758 (m-30) cc_final: 0.7519 (p0) REVERT: C 347 LYS cc_start: 0.7831 (mttt) cc_final: 0.7399 (pttp) REVERT: C 444 ARG cc_start: 0.8050 (mtt90) cc_final: 0.7692 (mmm160) REVERT: C 490 LYS cc_start: 0.8818 (ttpp) cc_final: 0.7855 (tptp) REVERT: J 11 LEU cc_start: 0.7539 (OUTLIER) cc_final: 0.7130 (tt) REVERT: J 70 SER cc_start: 0.8590 (t) cc_final: 0.8326 (p) REVERT: J 81 GLN cc_start: 0.8268 (tp40) cc_final: 0.7896 (tp40) REVERT: J 91 TYR cc_start: 0.8667 (m-80) cc_final: 0.8387 (m-80) REVERT: E 542 ARG cc_start: 0.8034 (mmm-85) cc_final: 0.7629 (mtm110) REVERT: E 617 ARG cc_start: 0.8651 (mtp85) cc_final: 0.8379 (mtp85) REVERT: M 56 SER cc_start: 0.8493 (t) cc_final: 0.8204 (p) REVERT: M 100 ARG cc_start: 0.8564 (mtm180) cc_final: 0.7503 (mmm160) REVERT: D 97 LYS cc_start: 0.8685 (mmtm) cc_final: 0.8406 (mttp) REVERT: D 117 LYS cc_start: 0.7641 (mttt) cc_final: 0.7312 (mmtm) REVERT: D 166 ARG cc_start: 0.7464 (mtp85) cc_final: 0.6830 (ttp80) REVERT: D 171 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.7733 (tmmt) REVERT: D 232 LYS cc_start: 0.8369 (mttp) cc_final: 0.7781 (mmtm) REVERT: D 267 GLU cc_start: 0.7369 (mp0) cc_final: 0.7034 (mp0) REVERT: D 328 GLN cc_start: 0.8228 (tt0) cc_final: 0.7878 (tt0) REVERT: D 339 ASN cc_start: 0.8120 (t0) cc_final: 0.7325 (m110) REVERT: D 347 LYS cc_start: 0.7761 (mttt) cc_final: 0.7483 (pttm) REVERT: D 444 ARG cc_start: 0.8080 (mtt90) cc_final: 0.7674 (mmm160) REVERT: D 474 ASP cc_start: 0.6809 (p0) cc_final: 0.6603 (p0) REVERT: D 478 ASN cc_start: 0.7044 (OUTLIER) cc_final: 0.6499 (m110) REVERT: D 490 LYS cc_start: 0.8707 (ttpp) cc_final: 0.7945 (tptp) REVERT: P 54 ARG cc_start: 0.8515 (mtm110) cc_final: 0.8211 (ttm110) REVERT: F 542 ARG cc_start: 0.8071 (mmm-85) cc_final: 0.7557 (mtm110) REVERT: F 657 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8273 (mt-10) REVERT: N 100 ARG cc_start: 0.8449 (mtm180) cc_final: 0.7458 (mmm160) outliers start: 55 outliers final: 39 residues processed: 399 average time/residue: 0.6831 time to fit residues: 312.2969 Evaluate side-chains 397 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 353 time to evaluate : 0.874 ------------------------------------------------------------------------------- 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 G residue 100 GLN Chi-restraints excluded: chain I residue 27 ASP Chi-restraints excluded: chain I residue 97 ILE 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 464 THR Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain O residue 27 SER 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 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 Q residue 70 SER Chi-restraints excluded: chain Q residue 72 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 P residue 27 ASP Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain R residue 27 SER Chi-restraints excluded: chain R residue 70 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 42 optimal weight: 0.1980 chunk 118 optimal weight: 2.9990 chunk 206 optimal weight: 0.0670 chunk 212 optimal weight: 0.5980 chunk 205 optimal weight: 0.9990 chunk 117 optimal weight: 0.5980 chunk 49 optimal weight: 0.0370 chunk 73 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 279 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 overall best weight: 0.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 103 GLN ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 GLN G 100BGLN I 31 ASN I 53 GLN L 53 GLN C 103 GLN ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 27 ASN D 283 ASN K 81 GLN P 31 ASN P 53 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.162245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.127967 restraints weight = 24645.630| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.71 r_work: 0.3143 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 25440 Z= 0.099 Angle : 0.510 9.242 34668 Z= 0.258 Chirality : 0.043 0.309 4014 Planarity : 0.004 0.039 4329 Dihedral : 5.012 54.707 4570 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.84 % Allowed : 12.68 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.15), residues: 3039 helix: 0.44 (0.27), residues: 411 sheet: -0.02 (0.15), residues: 969 loop : 0.37 (0.16), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 327 TYR 0.018 0.001 TYR A 191 PHE 0.024 0.001 PHE D 53 TRP 0.018 0.001 TRP D 112 HIS 0.006 0.001 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00220 (25335) covalent geometry : angle 0.48332 (34398) SS BOND : bond 0.00361 ( 45) SS BOND : angle 0.88956 ( 90) hydrogen bonds : bond 0.03498 ( 651) hydrogen bonds : angle 4.85810 ( 1656) link_ALPHA1-3 : bond 0.00922 ( 3) link_ALPHA1-3 : angle 1.31147 ( 9) link_BETA1-4 : bond 0.00417 ( 9) link_BETA1-4 : angle 1.24709 ( 27) link_NAG-ASN : bond 0.00217 ( 48) link_NAG-ASN : angle 2.42722 ( 144) *********************** 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 427 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 378 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LYS cc_start: 0.7645 (mttt) cc_final: 0.7442 (mmtm) REVERT: A 151 ARG cc_start: 0.7295 (ttm-80) cc_final: 0.6577 (ttm170) REVERT: A 166 ARG cc_start: 0.7355 (mtp85) cc_final: 0.7086 (ptt90) REVERT: A 178 LYS cc_start: 0.8069 (tttt) cc_final: 0.7602 (mmmt) REVERT: A 208 VAL cc_start: 0.7463 (t) cc_final: 0.7198 (m) REVERT: A 232 LYS cc_start: 0.8496 (mttp) cc_final: 0.7813 (mmpt) REVERT: A 267 GLU cc_start: 0.7354 (mp0) cc_final: 0.7025 (mp0) REVERT: A 278 ARG cc_start: 0.8161 (mmt-90) cc_final: 0.7945 (mmp80) REVERT: A 339 ASN cc_start: 0.8119 (t0) cc_final: 0.7355 (m110) REVERT: A 347 LYS cc_start: 0.7861 (mttt) cc_final: 0.7646 (ttpp) REVERT: A 490 LYS cc_start: 0.8692 (ttpp) cc_final: 0.7761 (tptt) REVERT: A 504 ARG cc_start: 0.7000 (tpp-160) cc_final: 0.6742 (mmt-90) REVERT: G 11 LEU cc_start: 0.7361 (OUTLIER) cc_final: 0.7059 (tt) REVERT: G 46 GLU cc_start: 0.8570 (tt0) cc_final: 0.8136 (tt0) REVERT: G 76 ASN cc_start: 0.8396 (m-40) cc_final: 0.8176 (m-40) REVERT: B 530 MET cc_start: 0.9207 (mtp) cc_final: 0.8848 (mtp) REVERT: B 542 ARG cc_start: 0.7778 (mmm-85) cc_final: 0.7441 (mtm110) REVERT: H 5 GLN cc_start: 0.7657 (tp-100) cc_final: 0.7327 (tp40) REVERT: H 56 SER cc_start: 0.8398 (t) cc_final: 0.8140 (p) REVERT: C 95 MET cc_start: 0.9094 (ptm) cc_final: 0.8772 (ptm) REVERT: C 117 LYS cc_start: 0.7575 (mttt) cc_final: 0.7337 (mmtm) REVERT: C 178 LYS cc_start: 0.8165 (tttt) cc_final: 0.7583 (mmmt) REVERT: C 208 VAL cc_start: 0.7180 (t) cc_final: 0.6957 (m) REVERT: C 211 GLU cc_start: 0.7391 (tt0) cc_final: 0.6855 (tp30) REVERT: C 232 LYS cc_start: 0.8453 (mttp) cc_final: 0.7890 (mmtm) REVERT: C 267 GLU cc_start: 0.7629 (mp0) cc_final: 0.7244 (mp0) REVERT: C 321 ASP cc_start: 0.7514 (t0) cc_final: 0.7255 (t0) REVERT: C 325 ASP cc_start: 0.7757 (m-30) cc_final: 0.7511 (p0) REVERT: C 339 ASN cc_start: 0.7911 (t0) cc_final: 0.7143 (m-40) REVERT: C 347 LYS cc_start: 0.7668 (mttt) cc_final: 0.7284 (pttp) REVERT: C 444 ARG cc_start: 0.8018 (mtt90) cc_final: 0.7727 (tpt90) REVERT: C 490 LYS cc_start: 0.8795 (ttpp) cc_final: 0.7784 (tptp) REVERT: J 11 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.7045 (tt) REVERT: J 70 SER cc_start: 0.8482 (t) cc_final: 0.8204 (p) REVERT: J 81 GLN cc_start: 0.8138 (tp40) cc_final: 0.7747 (tp40) REVERT: J 91 TYR cc_start: 0.8646 (m-80) cc_final: 0.8346 (m-80) REVERT: E 542 ARG cc_start: 0.8034 (mmm-85) cc_final: 0.7644 (mtm110) REVERT: E 574 LYS cc_start: 0.7891 (mttt) cc_final: 0.7424 (mtmp) REVERT: M 56 SER cc_start: 0.8330 (t) cc_final: 0.8106 (p) REVERT: M 100 ARG cc_start: 0.8506 (mtm180) cc_final: 0.7439 (mmm160) REVERT: D 97 LYS cc_start: 0.8681 (mmtm) cc_final: 0.8350 (mttp) REVERT: D 106 THR cc_start: 0.8497 (m) cc_final: 0.8224 (m) REVERT: D 117 LYS cc_start: 0.7621 (mttt) cc_final: 0.7335 (mmtm) REVERT: D 166 ARG cc_start: 0.7323 (mtp85) cc_final: 0.7021 (ptt90) REVERT: D 171 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.7692 (tmmt) REVERT: D 232 LYS cc_start: 0.8349 (mttp) cc_final: 0.7779 (mmtm) REVERT: D 267 GLU cc_start: 0.7379 (mp0) cc_final: 0.7003 (mp0) REVERT: D 328 GLN cc_start: 0.8206 (tt0) cc_final: 0.7957 (tt0) REVERT: D 347 LYS cc_start: 0.7693 (mttt) cc_final: 0.7468 (pttp) REVERT: D 356 ASN cc_start: 0.7978 (t0) cc_final: 0.7514 (m-40) REVERT: D 444 ARG cc_start: 0.8051 (mtt90) cc_final: 0.7783 (mmm-85) REVERT: D 474 ASP cc_start: 0.6812 (p0) cc_final: 0.6485 (p0) REVERT: D 490 LYS cc_start: 0.8663 (ttpp) cc_final: 0.7947 (tptp) REVERT: D 504 ARG cc_start: 0.6782 (tpp-160) cc_final: 0.6576 (mmt-90) REVERT: P 54 ARG cc_start: 0.8466 (mtm110) cc_final: 0.8164 (ttm110) REVERT: F 542 ARG cc_start: 0.7996 (mmm-85) cc_final: 0.7527 (mtm110) REVERT: F 640 GLN cc_start: 0.8801 (mm-40) cc_final: 0.8577 (mm110) REVERT: N 100 ARG cc_start: 0.8399 (mtm180) cc_final: 0.7389 (mmm160) outliers start: 49 outliers final: 30 residues processed: 408 average time/residue: 0.6443 time to fit residues: 301.3694 Evaluate side-chains 387 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 354 time to evaluate : 1.028 ------------------------------------------------------------------------------- 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 G residue 100 GLN Chi-restraints excluded: chain I residue 27 ASP Chi-restraints excluded: chain I residue 85 ASP 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 202 THR Chi-restraints excluded: chain C residue 464 THR Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain O residue 97 ILE Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain 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 72 SER Chi-restraints excluded: chain D residue 171 LYS Chi-restraints excluded: chain D residue 275 LYS Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain R residue 27 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 14 optimal weight: 1.9990 chunk 211 optimal weight: 0.4980 chunk 111 optimal weight: 0.6980 chunk 278 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 287 optimal weight: 0.3980 chunk 50 optimal weight: 0.6980 chunk 165 optimal weight: 3.9990 chunk 254 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 280 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 440 GLN G 100BGLN I 31 ASN I 53 GLN C 103 GLN ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 27 ASN Q 31 ASN D 283 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3684 r_free = 0.3684 target = 0.159524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.124795 restraints weight = 24649.027| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.73 r_work: 0.3227 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 25440 Z= 0.155 Angle : 0.565 11.576 34668 Z= 0.284 Chirality : 0.045 0.377 4014 Planarity : 0.004 0.040 4329 Dihedral : 5.150 55.370 4570 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.84 % Allowed : 12.90 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.15), residues: 3039 helix: 0.20 (0.27), residues: 429 sheet: 0.08 (0.15), residues: 954 loop : 0.31 (0.16), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 327 TYR 0.021 0.001 TYR O 49 PHE 0.016 0.002 PHE C 53 TRP 0.019 0.001 TRP A 112 HIS 0.006 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00366 (25335) covalent geometry : angle 0.53780 (34398) SS BOND : bond 0.00446 ( 45) SS BOND : angle 1.10002 ( 90) hydrogen bonds : bond 0.03838 ( 651) hydrogen bonds : angle 4.90749 ( 1656) link_ALPHA1-3 : bond 0.00776 ( 3) link_ALPHA1-3 : angle 1.21958 ( 9) link_BETA1-4 : bond 0.00389 ( 9) link_BETA1-4 : angle 1.34782 ( 27) link_NAG-ASN : bond 0.00284 ( 48) link_NAG-ASN : angle 2.54289 ( 144) *********************** 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 404 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 355 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.7437 (ttm-80) cc_final: 0.6752 (ttm170) REVERT: A 178 LYS cc_start: 0.8248 (tttt) cc_final: 0.7802 (mmmt) REVERT: A 208 VAL cc_start: 0.7636 (t) cc_final: 0.7305 (m) REVERT: A 232 LYS cc_start: 0.8609 (mttp) cc_final: 0.7989 (mmpt) REVERT: A 267 GLU cc_start: 0.7379 (mp0) cc_final: 0.7117 (mp0) REVERT: A 278 ARG cc_start: 0.8257 (mmt-90) cc_final: 0.8055 (mmp80) REVERT: A 490 LYS cc_start: 0.8751 (ttpp) cc_final: 0.7879 (tptt) REVERT: A 504 ARG cc_start: 0.7064 (tpp-160) cc_final: 0.6779 (mmt-90) REVERT: G 11 LEU cc_start: 0.7369 (OUTLIER) cc_final: 0.7060 (tt) REVERT: G 46 GLU cc_start: 0.8585 (tt0) cc_final: 0.8222 (tt0) REVERT: B 530 MET cc_start: 0.9230 (mtp) cc_final: 0.8979 (mtp) REVERT: B 542 ARG cc_start: 0.7956 (mmm-85) cc_final: 0.7646 (mtm110) REVERT: H 56 SER cc_start: 0.8511 (t) cc_final: 0.8253 (p) REVERT: C 95 MET cc_start: 0.9173 (ptm) cc_final: 0.8893 (ptm) REVERT: C 178 LYS cc_start: 0.8265 (tttt) cc_final: 0.7769 (mmmt) REVERT: C 211 GLU cc_start: 0.7503 (tt0) cc_final: 0.7015 (tp30) REVERT: C 232 LYS cc_start: 0.8540 (mttp) cc_final: 0.7995 (mmtm) REVERT: C 267 GLU cc_start: 0.7603 (mp0) cc_final: 0.7261 (mp0) REVERT: C 321 ASP cc_start: 0.7656 (t0) cc_final: 0.7366 (t0) REVERT: C 325 ASP cc_start: 0.7818 (m-30) cc_final: 0.7606 (p0) REVERT: C 339 ASN cc_start: 0.8174 (t0) cc_final: 0.7389 (m-40) REVERT: C 347 LYS cc_start: 0.7886 (mttt) cc_final: 0.7541 (pttp) REVERT: C 490 LYS cc_start: 0.8798 (ttpp) cc_final: 0.7921 (tptp) REVERT: J 11 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7090 (tt) REVERT: J 70 SER cc_start: 0.8572 (t) cc_final: 0.8363 (p) REVERT: J 81 GLN cc_start: 0.8213 (tp40) cc_final: 0.7871 (tp40) REVERT: E 542 ARG cc_start: 0.8145 (mmm-85) cc_final: 0.7783 (mtm110) REVERT: E 574 LYS cc_start: 0.8086 (mttt) cc_final: 0.7646 (mtmp) REVERT: M 27 ASN cc_start: 0.8706 (OUTLIER) cc_final: 0.8457 (t0) REVERT: M 56 SER cc_start: 0.8501 (t) cc_final: 0.8281 (p) REVERT: M 100 ARG cc_start: 0.8585 (mtm180) cc_final: 0.7662 (mmm160) REVERT: D 97 LYS cc_start: 0.8745 (mmtm) cc_final: 0.8486 (mttp) REVERT: D 106 THR cc_start: 0.8649 (m) cc_final: 0.8378 (m) REVERT: D 117 LYS cc_start: 0.7729 (mttt) cc_final: 0.7505 (mmtm) REVERT: D 166 ARG cc_start: 0.7418 (mtp85) cc_final: 0.6885 (ttp80) REVERT: D 171 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.7666 (tmmt) REVERT: D 232 LYS cc_start: 0.8512 (mttp) cc_final: 0.7988 (mmtm) REVERT: D 267 GLU cc_start: 0.7511 (mp0) cc_final: 0.7177 (mp0) REVERT: D 328 GLN cc_start: 0.8299 (tt0) cc_final: 0.7975 (tt0) REVERT: D 356 ASN cc_start: 0.8033 (t0) cc_final: 0.7579 (m-40) REVERT: D 490 LYS cc_start: 0.8695 (ttpp) cc_final: 0.8013 (tptp) REVERT: P 54 ARG cc_start: 0.8584 (mtm110) cc_final: 0.8317 (ttm110) REVERT: F 542 ARG cc_start: 0.8164 (mmm-85) cc_final: 0.7691 (mtm110) REVERT: F 657 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8304 (mt-10) REVERT: N 100 ARG cc_start: 0.8512 (mtm180) cc_final: 0.7634 (mmm160) outliers start: 49 outliers final: 34 residues processed: 391 average time/residue: 0.7189 time to fit residues: 321.3900 Evaluate side-chains 383 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 345 time to evaluate : 0.959 ------------------------------------------------------------------------------- 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 I residue 27 ASP 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 202 THR Chi-restraints excluded: chain C residue 464 THR Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain O residue 97 ILE Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 19 SER Chi-restraints excluded: chain M residue 27 ASN Chi-restraints excluded: chain M residue 101 ASP Chi-restraints excluded: chain Q residue 27 SER Chi-restraints excluded: chain Q residue 72 SER Chi-restraints excluded: chain D residue 171 LYS 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 478 ASN Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain P residue 27 SER Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain R residue 27 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 254 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 182 optimal weight: 1.9990 chunk 264 optimal weight: 1.9990 chunk 224 optimal weight: 1.9990 chunk 223 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 240 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 1 optimal weight: 0.0770 overall best weight: 0.9942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN A 440 GLN G 100BGLN I 31 ASN I 53 GLN C 103 GLN ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 31 ASN M 27 ASN 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.158207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.122791 restraints weight = 24707.634| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.82 r_work: 0.3072 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3157 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= 0.172 Angle : 0.595 11.647 34668 Z= 0.299 Chirality : 0.053 1.733 4014 Planarity : 0.004 0.048 4329 Dihedral : 5.426 59.895 4570 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.73 % Allowed : 13.66 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.15), residues: 3039 helix: 0.11 (0.26), residues: 429 sheet: 0.04 (0.15), residues: 954 loop : 0.28 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG P 94 TYR 0.025 0.002 TYR O 49 PHE 0.016 0.002 PHE C 53 TRP 0.020 0.002 TRP D 112 HIS 0.005 0.001 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00408 (25335) covalent geometry : angle 0.56657 (34398) SS BOND : bond 0.00465 ( 45) SS BOND : angle 1.11388 ( 90) hydrogen bonds : bond 0.04047 ( 651) hydrogen bonds : angle 4.95622 ( 1656) link_ALPHA1-3 : bond 0.00864 ( 3) link_ALPHA1-3 : angle 1.28733 ( 9) link_BETA1-4 : bond 0.00356 ( 9) link_BETA1-4 : angle 1.36021 ( 27) link_NAG-ASN : bond 0.00370 ( 48) link_NAG-ASN : angle 2.71216 ( 144) ********************** 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 390 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 344 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.7323 (ttm-80) cc_final: 0.6631 (ttm170) REVERT: A 178 LYS cc_start: 0.8233 (tttt) cc_final: 0.7729 (mmmt) REVERT: A 232 LYS cc_start: 0.8511 (mttp) cc_final: 0.7819 (mmpt) REVERT: A 267 GLU cc_start: 0.7347 (mp0) cc_final: 0.7065 (mp0) REVERT: A 278 ARG cc_start: 0.8175 (mmt-90) cc_final: 0.7956 (mmp80) REVERT: A 490 LYS cc_start: 0.8743 (ttpp) cc_final: 0.7783 (tptt) REVERT: A 504 ARG cc_start: 0.6986 (tpp-160) cc_final: 0.6723 (mmt-90) REVERT: G 11 LEU cc_start: 0.7351 (OUTLIER) cc_final: 0.7054 (tt) REVERT: G 46 GLU cc_start: 0.8573 (tt0) cc_final: 0.8145 (tt0) REVERT: B 542 ARG cc_start: 0.7863 (mmm-85) cc_final: 0.7519 (mtm110) REVERT: H 56 SER cc_start: 0.8446 (t) cc_final: 0.8094 (p) REVERT: C 95 MET cc_start: 0.9125 (ptm) cc_final: 0.8852 (ptm) REVERT: C 178 LYS cc_start: 0.8270 (tttt) cc_final: 0.7698 (mmmt) REVERT: C 208 VAL cc_start: 0.7177 (t) cc_final: 0.6907 (m) REVERT: C 211 GLU cc_start: 0.7380 (tt0) cc_final: 0.6813 (tp30) REVERT: C 232 LYS cc_start: 0.8424 (mttp) cc_final: 0.7875 (mmpt) REVERT: C 267 GLU cc_start: 0.7567 (mp0) cc_final: 0.7172 (mp0) REVERT: C 321 ASP cc_start: 0.7684 (t0) cc_final: 0.7377 (t0) REVERT: C 325 ASP cc_start: 0.7821 (m-30) cc_final: 0.7555 (p0) REVERT: C 339 ASN cc_start: 0.8152 (t0) cc_final: 0.7332 (m-40) REVERT: C 347 LYS cc_start: 0.7850 (mttt) cc_final: 0.7404 (pttp) REVERT: C 475 MET cc_start: 0.6565 (mtm) cc_final: 0.6211 (mtm) REVERT: C 490 LYS cc_start: 0.8790 (ttpp) cc_final: 0.7824 (tptp) REVERT: J 11 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.7039 (tt) REVERT: J 70 SER cc_start: 0.8545 (t) cc_final: 0.8270 (p) REVERT: J 81 GLN cc_start: 0.8088 (tp40) cc_final: 0.7715 (tp40) REVERT: J 91 TYR cc_start: 0.8480 (m-80) cc_final: 0.8267 (m-80) REVERT: E 542 ARG cc_start: 0.8109 (mmm-85) cc_final: 0.7678 (mtm110) REVERT: E 574 LYS cc_start: 0.8013 (mttt) cc_final: 0.7537 (mtmp) REVERT: M 56 SER cc_start: 0.8488 (t) cc_final: 0.8186 (p) REVERT: M 100 ARG cc_start: 0.8542 (mtm180) cc_final: 0.7480 (mmm160) REVERT: D 97 LYS cc_start: 0.8679 (mmtm) cc_final: 0.8364 (mptt) REVERT: D 106 THR cc_start: 0.8506 (m) cc_final: 0.8248 (m) REVERT: D 117 LYS cc_start: 0.7631 (mttt) cc_final: 0.7362 (mmtm) REVERT: D 166 ARG cc_start: 0.7438 (mtp85) cc_final: 0.6791 (ttp80) REVERT: D 171 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.7673 (tmmt) REVERT: D 232 LYS cc_start: 0.8400 (mttp) cc_final: 0.7797 (mmtm) REVERT: D 267 GLU cc_start: 0.7492 (mp0) cc_final: 0.7136 (mp0) REVERT: D 328 GLN cc_start: 0.8227 (tt0) cc_final: 0.7909 (tt0) REVERT: D 356 ASN cc_start: 0.8014 (t0) cc_final: 0.7524 (m-40) REVERT: D 474 ASP cc_start: 0.6643 (p0) cc_final: 0.6271 (p0) REVERT: D 475 MET cc_start: 0.6559 (mtm) cc_final: 0.6251 (mtm) REVERT: D 490 LYS cc_start: 0.8683 (ttpp) cc_final: 0.7925 (tptp) REVERT: P 54 ARG cc_start: 0.8534 (mtm110) cc_final: 0.8215 (ttm110) REVERT: F 542 ARG cc_start: 0.8092 (mmm-85) cc_final: 0.7562 (mtm110) REVERT: F 657 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8281 (mt-10) REVERT: N 100 ARG cc_start: 0.8455 (mtm180) cc_final: 0.7448 (mmm160) outliers start: 46 outliers final: 38 residues processed: 378 average time/residue: 0.7290 time to fit residues: 314.5016 Evaluate side-chains 379 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 338 time to evaluate : 1.005 ------------------------------------------------------------------------------- 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 I residue 27 ASP Chi-restraints excluded: chain I residue 85 ASP 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 202 THR Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 464 THR Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain O residue 97 ILE Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 19 SER Chi-restraints excluded: chain M residue 27 ASN Chi-restraints excluded: chain M residue 101 ASP Chi-restraints excluded: chain Q residue 27 SER Chi-restraints excluded: chain Q residue 72 SER Chi-restraints excluded: chain D residue 171 LYS 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 287 optimal weight: 0.0060 chunk 59 optimal weight: 0.0470 chunk 212 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 36 optimal weight: 0.0570 chunk 48 optimal weight: 0.0170 chunk 22 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 238 optimal weight: 0.0040 chunk 95 optimal weight: 8.9990 overall best weight: 0.0262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN A 440 GLN I 31 ASN I 53 GLN L 53 GLN C 103 GLN ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 31 ASN D 283 ASN K 81 GLN P 31 ASN 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 = 0.3763 r_free = 0.3763 target = 0.166189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.132366 restraints weight = 24618.005| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.75 r_work: 0.3325 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 25440 Z= 0.089 Angle : 0.544 14.275 34668 Z= 0.272 Chirality : 0.053 1.325 4014 Planarity : 0.004 0.047 4329 Dihedral : 5.217 57.731 4570 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.47 % Allowed : 13.92 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.15), residues: 3039 helix: 0.35 (0.27), residues: 414 sheet: 0.15 (0.15), residues: 972 loop : 0.38 (0.16), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 327 TYR 0.021 0.001 TYR A 191 PHE 0.014 0.001 PHE G 32 TRP 0.027 0.001 TRP A 338 HIS 0.005 0.001 HIS M 50 Details of bonding type rmsd covalent geometry : bond 0.00184 (25335) covalent geometry : angle 0.51534 (34398) SS BOND : bond 0.00297 ( 45) SS BOND : angle 0.80654 ( 90) hydrogen bonds : bond 0.03557 ( 651) hydrogen bonds : angle 4.84078 ( 1656) link_ALPHA1-3 : bond 0.00860 ( 3) link_ALPHA1-3 : angle 1.28950 ( 9) link_BETA1-4 : bond 0.00432 ( 9) link_BETA1-4 : angle 1.21674 ( 27) link_NAG-ASN : bond 0.00296 ( 48) link_NAG-ASN : angle 2.65688 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9258.64 seconds wall clock time: 158 minutes 29.30 seconds (9509.30 seconds total)