Starting phenix.real_space_refine on Sun Aug 24 15:53:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mih_48290/08_2025/9mih_48290.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mih_48290/08_2025/9mih_48290.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mih_48290/08_2025/9mih_48290.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mih_48290/08_2025/9mih_48290.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mih_48290/08_2025/9mih_48290.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mih_48290/08_2025/9mih_48290.map" } resolution = 3.9 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= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 135 5.16 5 C 13133 2.51 5 N 3530 2.21 5 O 4157 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 20955 Number of models: 1 Model: "" Number of chains: 28 Chain: "L" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 773 Classifications: {'peptide': 102} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 96} Chain: "A" Number of atoms: 3386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3386 Classifications: {'peptide': 431} Link IDs: {'PTRANS': 22, 'TRANS': 408} Chain breaks: 3 Chain: "B" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 973 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 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: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "C" Number of atoms: 3393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3393 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 22, 'TRANS': 407} Chain breaks: 4 Chain: "D" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 979 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 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: "K" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "E" Number of atoms: 3389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3389 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 22, 'TRANS': 407} Chain breaks: 4 Chain: "F" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 973 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "M" 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: "N" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "H" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 921 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "O" 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: "P" 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: "Q" 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: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "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: 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: "U" 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: "V" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "D" 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: "E" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 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: 5.84, per 1000 atoms: 0.28 Number of scatterers: 20955 At special positions: 0 Unit cell: (124.068, 144.746, 150.949, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 135 16.00 O 4157 8.00 N 3530 7.00 C 13133 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.11 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=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.11 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.02 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.33 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.31 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=1.24 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " 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 U 3 " - " MAN U 4 " " BMA V 3 " - " MAN V 4 " ALPHA1-6 " BMA V 3 " - " MAN V 5 " BETA1-4 " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 160 " " NAG A 604 " - " ASN A 234 " " NAG A 605 " - " ASN A 301 " " NAG A 606 " - " ASN A 339 " " NAG A 607 " - " ASN A 392 " " NAG A 608 " - " ASN A 156 " " NAG A 609 " - " ASN A 197 " " NAG A 610 " - " ASN A 276 " " NAG A 611 " - " ASN A 448 " " NAG B 701 " - " ASN B 637 " " NAG C 601 " - " ASN C 88 " " NAG C 603 " - " ASN C 160 " " NAG C 604 " - " ASN C 234 " " NAG C 605 " - " ASN C 276 " " NAG C 606 " - " ASN C 295 " " NAG C 607 " - " ASN C 301 " " NAG C 608 " - " ASN C 332 " " NAG C 609 " - " ASN C 339 " " NAG C 610 " - " ASN C 355 " " NAG C 611 " - " ASN C 363 " " NAG C 612 " - " ASN C 392 " " NAG C 613 " - " ASN C 197 " " NAG C 614 " - " ASN C 448 " " NAG C 615 " - " ASN C 386 " " NAG D 701 " - " ASN D 611 " " NAG D 702 " - " ASN D 618 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 160 " " NAG E 603 " - " ASN E 234 " " NAG E 604 " - " ASN E 276 " " NAG E 605 " - " ASN E 295 " " NAG E 606 " - " ASN E 301 " " NAG E 607 " - " ASN E 332 " " NAG E 608 " - " ASN E 363 " " NAG E 609 " - " ASN E 156 " " NAG E 610 " - " ASN E 197 " " NAG E 611 " - " ASN E 386 " " NAG E 612 " - " ASN E 448 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 637 " " NAG F 703 " - " ASN F 618 " " NAG O 1 " - " ASN A 295 " " NAG P 1 " - " ASN A 332 " " NAG Q 1 " - " ASN A 363 " " NAG R 1 " - " ASN A 262 " " NAG S 1 " - " ASN A 386 " " NAG T 1 " - " ASN C 156 " " NAG U 1 " - " ASN C 262 " " NAG V 1 " - " ASN E 262 " Time building additional restraints: 2.16 Conformation dependent library (CDL) restraints added in 885.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 5042 Ramachandran restraints generated. 2521 Oldfield, 0 Emsley, 2521 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4724 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 49 sheets defined 19.1% alpha, 32.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.918A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.139A 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 387 through 390 Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.657A pdb=" N ARG A 429 " --> pdb=" O MET A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 481 removed outlier: 4.301A pdb=" N ASN A 478 " --> pdb=" O ASP A 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 535 removed outlier: 3.534A pdb=" N MET B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 543 removed outlier: 4.160A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 595 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 663 Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.581A pdb=" N THR G 87 " --> pdb=" O ASP G 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.650A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.658A pdb=" N LEU C 125 " --> pdb=" O LEU C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 388 through 392 Processing helix chain 'C' and resid 474 through 483 removed outlier: 3.744A pdb=" N ASN C 478 " --> pdb=" O ASP C 474 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 536 removed outlier: 3.695A pdb=" N THR D 536 " --> pdb=" O ALA D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 544 removed outlier: 4.630A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 595 Processing helix chain 'D' and resid 618 through 625 removed outlier: 3.588A pdb=" N ILE D 622 " --> pdb=" O ASN D 618 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 663 removed outlier: 3.746A pdb=" N LEU D 663 " --> pdb=" O ASP D 659 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.679A pdb=" N PHE J 32 " --> pdb=" O PHE J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 64 removed outlier: 3.540A pdb=" N LYS J 64 " --> pdb=" O ASP J 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 61 through 64' Processing helix chain 'E' and resid 94 through 97 Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.244A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 removed outlier: 3.688A pdb=" N LEU E 125 " --> pdb=" O LEU E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 198 Processing helix chain 'E' and resid 335 through 353 removed outlier: 3.842A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 475 through 483 removed outlier: 3.938A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 543 removed outlier: 4.115A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 595 Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 662 Processing helix chain 'M' and resid 28 through 32 removed outlier: 3.660A pdb=" N PHE M 32 " --> pdb=" O PHE M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 64 removed outlier: 4.047A pdb=" N LYS M 64 " --> pdb=" O ASP M 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 61 through 64' Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.573A pdb=" N CYS L 23 " --> pdb=" O PHE L 71 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.730A pdb=" N ASP L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA L 34 " --> pdb=" O GLN L 89 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 35 through 40 Processing sheet with id=AA4, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.360A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA6, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA7, first strand: chain 'A' and resid 169 through 172 Processing sheet with id=AA8, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.790A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 256 through 257 removed outlier: 3.684A pdb=" N SER A 375 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS A 421 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.284A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.229A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.691A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.625A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.308A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.952A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 260 through 261 removed outlier: 3.779A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 9.952A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.308A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.625A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.691A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.229A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.284A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 284 through 298 current: chain 'A' and resid 359 through 361 Processing sheet with id=AB2, first strand: chain 'A' and resid 305 through 308 Processing sheet with id=AB3, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AB4, first strand: chain 'G' and resid 57 through 59 removed outlier: 6.429A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N LEU G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N MET G 34 " --> pdb=" O LEU G 50 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N CYS G 92 " --> pdb=" O TRP G 103 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N TRP G 103 " --> pdb=" O CYS G 92 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N THR G 94 " --> pdb=" O ASP G 101 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 57 through 59 removed outlier: 6.429A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N LEU G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N MET G 34 " --> pdb=" O LEU G 50 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA G 88 " --> pdb=" O VAL G 109 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 9 through 13 removed outlier: 6.913A pdb=" N VAL I 11 " --> pdb=" O THR I 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'I' and resid 19 through 24 Processing sheet with id=AB8, first strand: chain 'I' and resid 45 through 48 removed outlier: 6.590A pdb=" N TRP I 35 " --> pdb=" O MET I 47 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA I 90 " --> pdb=" O ILE I 97 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE I 97 " --> pdb=" O ALA I 90 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 495 through 499 removed outlier: 5.836A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.622A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AC3, first strand: chain 'C' and resid 90 through 94 removed outlier: 4.228A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 170 through 177 Processing sheet with id=AC5, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.982A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 259 through 261 removed outlier: 3.897A pdb=" N GLY C 451 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 10.177A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.541A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.863A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.902A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.297A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.839A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.887A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.839A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.297A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.902A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.863A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.541A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.177A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 304 through 308 Processing sheet with id=AC9, first strand: chain 'J' and resid 3 through 7 removed outlier: 3.950A pdb=" N SER J 82B" --> pdb=" O GLY J 15 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N SER J 17 " --> pdb=" O MET J 82 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N MET J 82 " --> pdb=" O SER J 17 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LYS J 19 " --> pdb=" O LEU J 80 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU J 80 " --> pdb=" O LYS J 19 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N SER J 21 " --> pdb=" O LEU J 78 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N LEU J 78 " --> pdb=" O SER J 21 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR J 77 " --> pdb=" O ASP J 72 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASP J 72 " --> pdb=" O THR J 77 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 10 through 11 removed outlier: 5.900A pdb=" N GLY J 10 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 10 through 11 removed outlier: 5.900A pdb=" N GLY J 10 " --> pdb=" O THR J 110 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 9 through 12 removed outlier: 7.298A pdb=" N VAL K 11 " --> pdb=" O THR K 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'K' and resid 18 through 24 removed outlier: 6.259A pdb=" N VAL K 19 " --> pdb=" O ILE K 75 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 46 through 49 removed outlier: 5.933A pdb=" N LEU K 46 " --> pdb=" O GLN K 37 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLN K 37 " --> pdb=" O LEU K 46 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE K 48 " --> pdb=" O TRP K 35 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA K 90 " --> pdb=" O ILE K 97 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE K 97 " --> pdb=" O ALA K 90 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.749A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.761A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AD9, first strand: chain 'E' and resid 90 through 92 removed outlier: 3.764A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AE2, first strand: chain 'E' and resid 259 through 261 removed outlier: 3.646A pdb=" N GLY E 451 " --> pdb=" O LEU E 260 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.938A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 12.199A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 12.385A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 10.608A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.061A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 271 through 273 removed outlier: 11.061A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 10.608A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 12.385A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 12.199A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 10.938A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 304 through 308 Processing sheet with id=AE5, first strand: chain 'E' and resid 423 through 424 Processing sheet with id=AE6, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AE7, first strand: chain 'M' and resid 11 through 12 removed outlier: 6.993A pdb=" N MET M 34 " --> pdb=" O LEU M 50 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N LEU M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'N' and resid 9 through 13 removed outlier: 6.442A pdb=" N VAL N 11 " --> pdb=" O THR N 105 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N TRP N 35 " --> pdb=" O MET N 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'N' and resid 9 through 13 removed outlier: 6.442A pdb=" N VAL N 11 " --> pdb=" O THR N 105 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'N' and resid 19 through 24 Processing sheet with id=AF2, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AF3, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.805A pdb=" N THR H 110 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N MET H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N TRP H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.805A pdb=" N THR H 110 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) 767 hydrogen bonds defined for protein. 1995 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: 4.27 Time building geometry restraints manager: 2.76 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: 4053 1.33 - 1.46: 6072 1.46 - 1.58: 11059 1.58 - 1.71: 0 1.71 - 1.84: 188 Bond restraints: 21372 Sorted by residual: bond pdb=" C ALA L 51 " pdb=" O ALA L 51 " ideal model delta sigma weight residual 1.242 1.202 0.040 1.00e-02 1.00e+04 1.60e+01 bond pdb=" CA TYR L 49 " pdb=" C TYR L 49 " ideal model delta sigma weight residual 1.522 1.479 0.043 1.27e-02 6.20e+03 1.16e+01 bond pdb=" CA SER A 463 " pdb=" CB SER A 463 " ideal model delta sigma weight residual 1.529 1.483 0.046 1.38e-02 5.25e+03 1.12e+01 bond pdb=" N ILE E 424 " pdb=" CA ILE E 424 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.17e-02 7.31e+03 1.05e+01 bond pdb=" N MET J 34 " pdb=" CA MET J 34 " ideal model delta sigma weight residual 1.455 1.490 -0.036 1.26e-02 6.30e+03 8.03e+00 ... (remaining 21367 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 28116 2.44 - 4.87: 735 4.87 - 7.31: 121 7.31 - 9.75: 17 9.75 - 12.19: 4 Bond angle restraints: 28993 Sorted by residual: angle pdb=" C ALA L 51 " pdb=" CA ALA L 51 " pdb=" CB ALA L 51 " ideal model delta sigma weight residual 116.63 107.91 8.72 1.16e+00 7.43e-01 5.65e+01 angle pdb=" N GLY A 459 " pdb=" CA GLY A 459 " pdb=" C GLY A 459 " ideal model delta sigma weight residual 115.36 108.58 6.78 1.33e+00 5.65e-01 2.60e+01 angle pdb=" CA ALA J 33 " pdb=" C ALA J 33 " pdb=" O ALA J 33 " ideal model delta sigma weight residual 121.89 117.29 4.60 1.17e+00 7.31e-01 1.55e+01 angle pdb=" N ARG C 298 " pdb=" CA ARG C 298 " pdb=" C ARG C 298 " ideal model delta sigma weight residual 108.47 101.61 6.86 1.79e+00 3.12e-01 1.47e+01 angle pdb=" CA LYS M 43 " pdb=" CB LYS M 43 " pdb=" CG LYS M 43 " ideal model delta sigma weight residual 114.10 121.76 -7.66 2.00e+00 2.50e-01 1.47e+01 ... (remaining 28988 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.02: 12091 18.02 - 36.04: 1174 36.04 - 54.06: 266 54.06 - 72.07: 59 72.07 - 90.09: 27 Dihedral angle restraints: 13617 sinusoidal: 6247 harmonic: 7370 Sorted by residual: dihedral pdb=" CB CYS A 54 " pdb=" SG CYS A 54 " pdb=" SG CYS A 74 " pdb=" CB CYS A 74 " ideal model delta sinusoidal sigma weight residual -86.00 -169.09 83.09 1 1.00e+01 1.00e-02 8.44e+01 dihedral pdb=" CB CYS C 119 " pdb=" SG CYS C 119 " pdb=" SG CYS C 205 " pdb=" CB CYS C 205 " ideal model delta sinusoidal sigma weight residual -86.00 -143.08 57.08 1 1.00e+01 1.00e-02 4.38e+01 dihedral pdb=" CB CYS E 126 " pdb=" SG CYS E 126 " pdb=" SG CYS E 196 " pdb=" CB CYS E 196 " ideal model delta sinusoidal sigma weight residual 93.00 147.07 -54.07 1 1.00e+01 1.00e-02 3.97e+01 ... (remaining 13614 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2803 0.063 - 0.126: 523 0.126 - 0.190: 99 0.190 - 0.253: 8 0.253 - 0.316: 1 Chirality restraints: 3434 Sorted by residual: chirality pdb=" CB ILE H 75 " pdb=" CA ILE H 75 " pdb=" CG1 ILE H 75 " pdb=" CG2 ILE H 75 " both_signs ideal model delta sigma weight residual False 2.64 2.96 -0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" C1 NAG C 603 " pdb=" ND2 ASN C 160 " pdb=" C2 NAG C 603 " pdb=" O5 NAG C 603 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" C1 NAG C 609 " pdb=" ND2 ASN C 339 " pdb=" C2 NAG C 609 " pdb=" O5 NAG C 609 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 3431 not shown) Planarity restraints: 3661 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 457 " -0.022 2.00e-02 2.50e+03 4.70e-02 2.20e+01 pdb=" C ASP A 457 " 0.081 2.00e-02 2.50e+03 pdb=" O ASP A 457 " -0.032 2.00e-02 2.50e+03 pdb=" N GLY A 458 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP M 36 " 0.025 2.00e-02 2.50e+03 1.80e-02 8.06e+00 pdb=" CG TRP M 36 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 TRP M 36 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP M 36 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP M 36 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP M 36 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP M 36 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP M 36 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP M 36 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP M 36 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 94 " 0.248 9.50e-02 1.11e+02 1.11e-01 7.82e+00 pdb=" NE ARG H 94 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ARG H 94 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG H 94 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG H 94 " 0.006 2.00e-02 2.50e+03 ... (remaining 3658 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.40: 95 2.40 - 3.02: 12955 3.02 - 3.65: 31302 3.65 - 4.27: 45227 4.27 - 4.90: 76158 Nonbonded interactions: 165737 Sorted by model distance: nonbonded pdb=" O LEU F 663 " pdb=" OD1 ASP F 664 " model vdw 1.775 3.040 nonbonded pdb=" NH2 ARG K 94 " pdb=" OD2 ASP F 664 " model vdw 1.795 3.120 nonbonded pdb=" O ASN C 425 " pdb=" OD1 ASN C 425 " model vdw 2.004 3.040 nonbonded pdb=" OD2 ASP E 107 " pdb=" OH TYR E 217 " model vdw 2.089 3.040 nonbonded pdb=" OG SER A 481 " pdb=" OE1 GLU A 482 " model vdw 2.103 3.040 ... (remaining 165732 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 396 or resid 412 through 457 or resid 463 throu \ gh 611)) selection = (chain 'C' and (resid 33 through 56 or resid 71 through 185 or resid 189 through \ 611)) selection = (chain 'E' and (resid 33 through 56 or resid 71 through 457 or resid 463 through \ 611)) } ncs_group { reference = chain 'B' selection = (chain 'D' and (resid 520 through 545 or resid 569 through 701)) selection = (chain 'F' and resid 520 through 701) } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'M' } ncs_group { reference = chain 'I' selection = chain 'K' selection = chain 'N' } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.250 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 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 : 0.008 0.792 21478 Z= 0.387 Angle : 1.067 59.158 29270 Z= 0.535 Chirality : 0.052 0.316 3434 Planarity : 0.007 0.111 3610 Dihedral : 15.087 90.093 8770 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.13 % Allowed : 21.68 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % 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: -1.14 (0.17), residues: 2521 helix: 0.81 (0.27), residues: 394 sheet: -0.65 (0.18), residues: 765 loop : -1.28 (0.17), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.002 ARG B 542 TYR 0.028 0.002 TYR E 217 PHE 0.026 0.002 PHE L 98 TRP 0.048 0.002 TRP M 36 HIS 0.021 0.002 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00532 (21372) covalent geometry : angle 0.94253 (28993) SS BOND : bond 0.14049 ( 41) SS BOND : angle 8.90810 ( 82) hydrogen bonds : bond 0.12478 ( 727) hydrogen bonds : angle 6.85360 ( 1995) link_ALPHA1-3 : bond 0.00634 ( 2) link_ALPHA1-3 : angle 2.39474 ( 6) link_ALPHA1-6 : bond 0.00707 ( 1) link_ALPHA1-6 : angle 1.46204 ( 3) link_BETA1-4 : bond 0.00297 ( 11) link_BETA1-4 : angle 2.09035 ( 33) link_NAG-ASN : bond 0.00343 ( 51) link_NAG-ASN : angle 2.39503 ( 153) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5042 Ramachandran restraints generated. 2521 Oldfield, 0 Emsley, 2521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5042 Ramachandran restraints generated. 2521 Oldfield, 0 Emsley, 2521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 416 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 62 PHE cc_start: 0.8603 (m-80) cc_final: 0.8330 (m-80) REVERT: L 73 LEU cc_start: 0.9188 (tp) cc_final: 0.8430 (tp) REVERT: L 85 THR cc_start: 0.9186 (m) cc_final: 0.8844 (p) REVERT: A 173 TYR cc_start: 0.7566 (m-80) cc_final: 0.7012 (m-10) REVERT: A 195 ASN cc_start: 0.9167 (p0) cc_final: 0.8489 (t0) REVERT: B 530 MET cc_start: 0.8584 (tpp) cc_final: 0.8216 (tpp) REVERT: G 23 ARG cc_start: 0.8242 (ttp80) cc_final: 0.7888 (ttp80) REVERT: G 51 ILE cc_start: 0.8895 (tt) cc_final: 0.8694 (tp) REVERT: G 56 LEU cc_start: 0.8714 (tp) cc_final: 0.8480 (tp) REVERT: G 72 ASP cc_start: 0.8813 (t0) cc_final: 0.8432 (t0) REVERT: G 81 GLN cc_start: 0.8881 (tp40) cc_final: 0.8270 (tp40) REVERT: I 38 GLN cc_start: 0.8449 (pm20) cc_final: 0.7704 (pm20) REVERT: I 85 ASP cc_start: 0.7268 (t0) cc_final: 0.6741 (t0) REVERT: I 94 ARG cc_start: 0.8761 (mtp180) cc_final: 0.8363 (ttt-90) REVERT: C 161 MET cc_start: 0.8552 (tpp) cc_final: 0.8251 (tpp) REVERT: C 271 MET cc_start: 0.8301 (mmm) cc_final: 0.8005 (mmm) REVERT: C 368 ASP cc_start: 0.8146 (p0) cc_final: 0.7287 (p0) REVERT: C 426 MET cc_start: 0.8272 (tpt) cc_final: 0.8007 (tpp) REVERT: D 529 THR cc_start: 0.8888 (m) cc_final: 0.8537 (m) REVERT: D 590 GLN cc_start: 0.8480 (tm-30) cc_final: 0.8189 (tm-30) REVERT: J 32 PHE cc_start: 0.8861 (m-10) cc_final: 0.8612 (m-10) REVERT: J 97 MET cc_start: 0.8380 (ttm) cc_final: 0.8054 (ttt) REVERT: K 31 ASN cc_start: 0.8249 (t0) cc_final: 0.7862 (t0) REVERT: E 207 LYS cc_start: 0.8668 (mttt) cc_final: 0.7835 (tptt) REVERT: E 315 GLN cc_start: 0.9075 (pm20) cc_final: 0.8740 (pm20) REVERT: E 434 MET cc_start: 0.8127 (tmm) cc_final: 0.7914 (tmm) REVERT: F 634 GLU cc_start: 0.8816 (tm-30) cc_final: 0.8577 (tm-30) REVERT: M 23 ARG cc_start: 0.8565 (tmm-80) cc_final: 0.7967 (ttp80) REVERT: M 46 GLU cc_start: 0.9073 (tp30) cc_final: 0.8869 (tp30) REVERT: M 81 GLN cc_start: 0.9057 (tt0) cc_final: 0.8635 (tm-30) REVERT: M 82 MET cc_start: 0.8083 (mpp) cc_final: 0.7880 (mpp) REVERT: M 102 PHE cc_start: 0.9246 (m-80) cc_final: 0.8936 (m-80) REVERT: N 86 TYR cc_start: 0.7388 (m-10) cc_final: 0.6963 (m-10) REVERT: H 36 TRP cc_start: 0.8815 (m100) cc_final: 0.7511 (m100) outliers start: 3 outliers final: 2 residues processed: 419 average time/residue: 0.1578 time to fit residues: 101.4626 Evaluate side-chains 360 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 358 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain E residue 446 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 7.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 20.0000 chunk 247 optimal weight: 0.6980 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 650 GLN ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 105 GLN ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 81 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.079487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.065215 restraints weight = 74601.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.067356 restraints weight = 37670.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.068796 restraints weight = 24083.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.069708 restraints weight = 17710.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.070370 restraints weight = 14430.875| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 21478 Z= 0.218 Angle : 0.722 10.057 29270 Z= 0.354 Chirality : 0.047 0.291 3434 Planarity : 0.005 0.059 3610 Dihedral : 7.312 75.211 4136 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 2.65 % Allowed : 20.78 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % 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: -0.94 (0.17), residues: 2521 helix: 1.30 (0.26), residues: 399 sheet: -0.54 (0.18), residues: 775 loop : -1.27 (0.17), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 542 TYR 0.025 0.002 TYR E 484 PHE 0.023 0.002 PHE L 83 TRP 0.017 0.002 TRP K 35 HIS 0.004 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00488 (21372) covalent geometry : angle 0.69520 (28993) SS BOND : bond 0.00394 ( 41) SS BOND : angle 1.01750 ( 82) hydrogen bonds : bond 0.04179 ( 727) hydrogen bonds : angle 5.65918 ( 1995) link_ALPHA1-3 : bond 0.01666 ( 2) link_ALPHA1-3 : angle 1.27455 ( 6) link_ALPHA1-6 : bond 0.00454 ( 1) link_ALPHA1-6 : angle 1.61949 ( 3) link_BETA1-4 : bond 0.00346 ( 11) link_BETA1-4 : angle 2.39107 ( 33) link_NAG-ASN : bond 0.00308 ( 51) link_NAG-ASN : angle 2.47759 ( 153) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5042 Ramachandran restraints generated. 2521 Oldfield, 0 Emsley, 2521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5042 Ramachandran restraints generated. 2521 Oldfield, 0 Emsley, 2521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 365 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 96 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7725 (pp20) REVERT: A 114 GLN cc_start: 0.8634 (pp30) cc_final: 0.8367 (pp30) REVERT: A 173 TYR cc_start: 0.7613 (m-80) cc_final: 0.7211 (m-80) REVERT: A 195 ASN cc_start: 0.9133 (p0) cc_final: 0.8442 (t0) REVERT: B 535 MET cc_start: 0.8250 (pmm) cc_final: 0.7855 (pmm) REVERT: B 542 ARG cc_start: 0.9184 (ttm110) cc_final: 0.8902 (ttm110) REVERT: G 72 ASP cc_start: 0.8761 (t0) cc_final: 0.8456 (t0) REVERT: G 81 GLN cc_start: 0.8836 (tp40) cc_final: 0.8467 (tp40) REVERT: I 38 GLN cc_start: 0.8270 (pm20) cc_final: 0.7522 (pm20) REVERT: C 271 MET cc_start: 0.8516 (mmm) cc_final: 0.8262 (mmm) REVERT: C 368 ASP cc_start: 0.8146 (OUTLIER) cc_final: 0.7579 (p0) REVERT: C 395 TRP cc_start: 0.7555 (OUTLIER) cc_final: 0.7224 (t60) REVERT: C 396 ILE cc_start: 0.8649 (OUTLIER) cc_final: 0.8374 (mt) REVERT: D 529 THR cc_start: 0.8827 (m) cc_final: 0.8605 (m) REVERT: D 590 GLN cc_start: 0.8648 (tm-30) cc_final: 0.8432 (tm-30) REVERT: D 626 MET cc_start: 0.8207 (ttm) cc_final: 0.7999 (ttt) REVERT: J 3 GLN cc_start: 0.8253 (tm-30) cc_final: 0.7959 (tm-30) REVERT: J 32 PHE cc_start: 0.8991 (m-10) cc_final: 0.8739 (m-10) REVERT: J 52 ASN cc_start: 0.8696 (p0) cc_final: 0.8153 (p0) REVERT: J 64 LYS cc_start: 0.9288 (tptm) cc_final: 0.8963 (ttmt) REVERT: K 31 ASN cc_start: 0.8228 (t0) cc_final: 0.7919 (t0) REVERT: K 47 MET cc_start: 0.7097 (mmm) cc_final: 0.6648 (mmt) REVERT: E 122 LEU cc_start: 0.9290 (tp) cc_final: 0.8993 (tt) REVERT: E 207 LYS cc_start: 0.8761 (mttt) cc_final: 0.7863 (tptt) REVERT: E 434 MET cc_start: 0.8319 (tmm) cc_final: 0.8118 (tmm) REVERT: F 530 MET cc_start: 0.7671 (tpp) cc_final: 0.7422 (tpp) REVERT: F 588 ARG cc_start: 0.8462 (mpt180) cc_final: 0.8176 (mpt180) REVERT: F 634 GLU cc_start: 0.8921 (tm-30) cc_final: 0.8687 (tm-30) REVERT: F 647 GLU cc_start: 0.8651 (tm-30) cc_final: 0.8437 (tm-30) REVERT: F 654 GLU cc_start: 0.8306 (mt-10) cc_final: 0.8101 (mt-10) REVERT: M 13 GLN cc_start: 0.8315 (pp30) cc_final: 0.8013 (pp30) REVERT: M 34 MET cc_start: 0.8776 (mmm) cc_final: 0.8362 (mmm) REVERT: M 46 GLU cc_start: 0.9165 (tp30) cc_final: 0.8921 (mm-30) REVERT: M 81 GLN cc_start: 0.9176 (tt0) cc_final: 0.8213 (tm-30) REVERT: M 82 MET cc_start: 0.8136 (mpp) cc_final: 0.7880 (mpp) REVERT: M 102 PHE cc_start: 0.9309 (m-80) cc_final: 0.8992 (m-80) REVERT: H 36 TRP cc_start: 0.8772 (m100) cc_final: 0.6889 (m100) REVERT: H 37 MET cc_start: 0.8899 (mmm) cc_final: 0.8636 (mmm) REVERT: H 52 ASN cc_start: 0.8890 (t0) cc_final: 0.8684 (t0) REVERT: H 102 TYR cc_start: 0.8603 (m-80) cc_final: 0.8264 (m-80) outliers start: 59 outliers final: 35 residues processed: 408 average time/residue: 0.1436 time to fit residues: 90.8678 Evaluate side-chains 377 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 338 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 96 GLU Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 395 TRP Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 26 THR Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 664 ASP Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 73 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 150 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 183 optimal weight: 0.7980 chunk 126 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 231 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 225 optimal weight: 4.9990 chunk 247 optimal weight: 2.9990 chunk 230 optimal weight: 1.9990 chunk 245 optimal weight: 0.6980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 653 GLN J 3 GLN ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.079791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.065610 restraints weight = 73933.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.067787 restraints weight = 36799.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.069234 restraints weight = 23245.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.070198 restraints weight = 17000.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.070847 restraints weight = 13659.689| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 21478 Z= 0.163 Angle : 0.668 12.508 29270 Z= 0.326 Chirality : 0.045 0.242 3434 Planarity : 0.004 0.050 3610 Dihedral : 6.672 59.705 4136 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 3.73 % Allowed : 20.47 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % 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: -0.89 (0.17), residues: 2521 helix: 1.38 (0.26), residues: 407 sheet: -0.49 (0.18), residues: 787 loop : -1.28 (0.17), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 178 TYR 0.026 0.002 TYR H 33 PHE 0.024 0.002 PHE J 102 TRP 0.020 0.001 TRP M 36 HIS 0.005 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00368 (21372) covalent geometry : angle 0.64063 (28993) SS BOND : bond 0.00585 ( 41) SS BOND : angle 1.56752 ( 82) hydrogen bonds : bond 0.03686 ( 727) hydrogen bonds : angle 5.28447 ( 1995) link_ALPHA1-3 : bond 0.01311 ( 2) link_ALPHA1-3 : angle 1.66163 ( 6) link_ALPHA1-6 : bond 0.00891 ( 1) link_ALPHA1-6 : angle 1.70811 ( 3) link_BETA1-4 : bond 0.00311 ( 11) link_BETA1-4 : angle 2.21703 ( 33) link_NAG-ASN : bond 0.00293 ( 51) link_NAG-ASN : angle 2.26121 ( 153) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5042 Ramachandran restraints generated. 2521 Oldfield, 0 Emsley, 2521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5042 Ramachandran restraints generated. 2521 Oldfield, 0 Emsley, 2521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 364 time to evaluate : 0.848 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: L 82 ASP cc_start: 0.8342 (m-30) cc_final: 0.8125 (m-30) REVERT: L 85 THR cc_start: 0.9062 (m) cc_final: 0.8760 (p) REVERT: A 114 GLN cc_start: 0.8651 (pp30) cc_final: 0.8333 (pp30) REVERT: A 173 TYR cc_start: 0.7551 (m-80) cc_final: 0.7134 (m-80) REVERT: A 195 ASN cc_start: 0.9146 (p0) cc_final: 0.8445 (t0) REVERT: A 308 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7695 (ttm110) REVERT: A 482 GLU cc_start: 0.8116 (mp0) cc_final: 0.7663 (mp0) REVERT: B 535 MET cc_start: 0.8008 (pmm) cc_final: 0.7645 (pmm) REVERT: G 72 ASP cc_start: 0.8694 (t0) cc_final: 0.8376 (t0) REVERT: G 83 ARG cc_start: 0.8208 (tpp80) cc_final: 0.7520 (mmt-90) REVERT: G 92 CYS cc_start: 0.7238 (OUTLIER) cc_final: 0.6625 (m) REVERT: I 35 TRP cc_start: 0.7857 (m-90) cc_final: 0.7396 (m-10) REVERT: I 38 GLN cc_start: 0.8257 (pm20) cc_final: 0.7501 (pm20) REVERT: C 271 MET cc_start: 0.8553 (mmm) cc_final: 0.8304 (mmm) REVERT: C 368 ASP cc_start: 0.8205 (OUTLIER) cc_final: 0.7652 (p0) REVERT: C 395 TRP cc_start: 0.7555 (OUTLIER) cc_final: 0.7170 (t60) REVERT: C 396 ILE cc_start: 0.8639 (OUTLIER) cc_final: 0.8363 (mt) REVERT: D 529 THR cc_start: 0.8872 (m) cc_final: 0.8595 (m) REVERT: D 584 GLU cc_start: 0.8748 (tt0) cc_final: 0.8370 (tt0) REVERT: D 590 GLN cc_start: 0.8711 (tm-30) cc_final: 0.8501 (tm-30) REVERT: D 626 MET cc_start: 0.8217 (ttm) cc_final: 0.8015 (ttt) REVERT: J 32 PHE cc_start: 0.9024 (m-10) cc_final: 0.8713 (m-10) REVERT: J 36 TRP cc_start: 0.8456 (m100) cc_final: 0.6944 (m100) REVERT: J 52 ASN cc_start: 0.8709 (p0) cc_final: 0.8365 (p0) REVERT: J 64 LYS cc_start: 0.9273 (tptm) cc_final: 0.8955 (ttmt) REVERT: K 31 ASN cc_start: 0.8160 (t0) cc_final: 0.7864 (t0) REVERT: K 47 MET cc_start: 0.6875 (mmm) cc_final: 0.6444 (mmt) REVERT: E 122 LEU cc_start: 0.9362 (tp) cc_final: 0.9054 (tt) REVERT: E 207 LYS cc_start: 0.8736 (mttt) cc_final: 0.7835 (tptt) REVERT: E 256 SER cc_start: 0.9291 (p) cc_final: 0.8810 (t) REVERT: E 259 LEU cc_start: 0.9544 (tp) cc_final: 0.9159 (tp) REVERT: E 475 MET cc_start: 0.8815 (mmm) cc_final: 0.8525 (mmm) REVERT: F 634 GLU cc_start: 0.8880 (tm-30) cc_final: 0.8663 (tm-30) REVERT: F 647 GLU cc_start: 0.8603 (tm-30) cc_final: 0.8347 (tm-30) REVERT: F 654 GLU cc_start: 0.8298 (mt-10) cc_final: 0.8035 (mt-10) REVERT: M 13 GLN cc_start: 0.8473 (pp30) cc_final: 0.8050 (pp30) REVERT: M 23 ARG cc_start: 0.8648 (tmm-80) cc_final: 0.7709 (tmm-80) REVERT: M 46 GLU cc_start: 0.9172 (tp30) cc_final: 0.8950 (mm-30) REVERT: M 81 GLN cc_start: 0.9178 (tt0) cc_final: 0.8178 (tm-30) REVERT: M 82 MET cc_start: 0.8336 (mpp) cc_final: 0.7947 (mpp) REVERT: N 49 TYR cc_start: 0.8481 (OUTLIER) cc_final: 0.7912 (p90) REVERT: H 36 TRP cc_start: 0.8878 (m100) cc_final: 0.7200 (m100) REVERT: H 47 TRP cc_start: 0.8604 (t60) cc_final: 0.7738 (t60) REVERT: H 102 TYR cc_start: 0.8740 (m-80) cc_final: 0.8155 (m-80) outliers start: 83 outliers final: 46 residues processed: 423 average time/residue: 0.1315 time to fit residues: 87.3056 Evaluate side-chains 394 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 342 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 395 TRP Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 82 ASP Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 664 ASP Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain N residue 37 GLN Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 82 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 72 optimal weight: 0.3980 chunk 211 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 chunk 232 optimal weight: 0.9980 chunk 171 optimal weight: 0.9980 chunk 36 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 142 optimal weight: 7.9990 chunk 84 optimal weight: 6.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 653 GLN J 3 GLN J 105 GLN ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.080349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.066013 restraints weight = 73717.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.068174 restraints weight = 37189.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.069628 restraints weight = 23767.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.070587 restraints weight = 17466.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.071192 restraints weight = 14119.683| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 21478 Z= 0.149 Angle : 0.648 10.817 29270 Z= 0.316 Chirality : 0.044 0.231 3434 Planarity : 0.004 0.043 3610 Dihedral : 5.926 48.149 4136 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 4.08 % Allowed : 21.01 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % 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: -0.78 (0.17), residues: 2521 helix: 1.54 (0.27), residues: 408 sheet: -0.46 (0.18), residues: 796 loop : -1.21 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 480 TYR 0.028 0.001 TYR H 33 PHE 0.024 0.002 PHE L 83 TRP 0.019 0.001 TRP C 112 HIS 0.007 0.001 HIS K 39 Details of bonding type rmsd covalent geometry : bond 0.00341 (21372) covalent geometry : angle 0.62306 (28993) SS BOND : bond 0.00496 ( 41) SS BOND : angle 1.38814 ( 82) hydrogen bonds : bond 0.03442 ( 727) hydrogen bonds : angle 5.14835 ( 1995) link_ALPHA1-3 : bond 0.01335 ( 2) link_ALPHA1-3 : angle 1.77036 ( 6) link_ALPHA1-6 : bond 0.01433 ( 1) link_ALPHA1-6 : angle 1.30165 ( 3) link_BETA1-4 : bond 0.00306 ( 11) link_BETA1-4 : angle 2.15529 ( 33) link_NAG-ASN : bond 0.00249 ( 51) link_NAG-ASN : angle 2.12661 ( 153) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5042 Ramachandran restraints generated. 2521 Oldfield, 0 Emsley, 2521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5042 Ramachandran restraints generated. 2521 Oldfield, 0 Emsley, 2521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 370 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 54 LEU cc_start: 0.8138 (tp) cc_final: 0.7915 (pp) REVERT: L 85 THR cc_start: 0.9020 (m) cc_final: 0.8724 (p) REVERT: L 96 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7464 (pp20) REVERT: A 114 GLN cc_start: 0.8659 (pp30) cc_final: 0.8449 (pp30) REVERT: A 150 MET cc_start: 0.8509 (ppp) cc_final: 0.8306 (ppp) REVERT: A 173 TYR cc_start: 0.7560 (m-80) cc_final: 0.7105 (m-80) REVERT: A 195 ASN cc_start: 0.9151 (p0) cc_final: 0.8483 (t0) REVERT: A 308 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7762 (ttm110) REVERT: A 482 GLU cc_start: 0.8102 (mp0) cc_final: 0.7646 (mp0) REVERT: B 530 MET cc_start: 0.9003 (tpp) cc_final: 0.8453 (tpp) REVERT: B 535 MET cc_start: 0.7888 (pmm) cc_final: 0.7593 (pmm) REVERT: G 72 ASP cc_start: 0.8704 (t0) cc_final: 0.8388 (t0) REVERT: G 81 GLN cc_start: 0.8993 (tp40) cc_final: 0.8488 (tp40) REVERT: G 83 ARG cc_start: 0.8203 (tpp80) cc_final: 0.7810 (mmt-90) REVERT: G 92 CYS cc_start: 0.7226 (OUTLIER) cc_final: 0.6671 (m) REVERT: I 35 TRP cc_start: 0.7952 (OUTLIER) cc_final: 0.7481 (m-10) REVERT: I 38 GLN cc_start: 0.8240 (pm20) cc_final: 0.7469 (pm20) REVERT: C 271 MET cc_start: 0.8562 (mmm) cc_final: 0.8111 (mmm) REVERT: C 368 ASP cc_start: 0.8285 (OUTLIER) cc_final: 0.7879 (p0) REVERT: C 395 TRP cc_start: 0.7569 (OUTLIER) cc_final: 0.7131 (t60) REVERT: C 396 ILE cc_start: 0.8644 (OUTLIER) cc_final: 0.8341 (mt) REVERT: C 475 MET cc_start: 0.8983 (mmp) cc_final: 0.8754 (mmm) REVERT: D 529 THR cc_start: 0.8877 (m) cc_final: 0.8606 (m) REVERT: D 543 ASN cc_start: 0.9254 (t0) cc_final: 0.8883 (t0) REVERT: D 584 GLU cc_start: 0.8748 (tt0) cc_final: 0.8353 (tt0) REVERT: D 590 GLN cc_start: 0.8746 (tm-30) cc_final: 0.8541 (tm-30) REVERT: J 32 PHE cc_start: 0.8976 (m-10) cc_final: 0.8680 (m-10) REVERT: J 52 ASN cc_start: 0.8634 (p0) cc_final: 0.8355 (p0) REVERT: J 64 LYS cc_start: 0.9245 (tptm) cc_final: 0.8930 (ttmt) REVERT: J 82 MET cc_start: 0.9216 (pmm) cc_final: 0.8760 (pmm) REVERT: J 109 VAL cc_start: 0.9151 (t) cc_final: 0.8951 (p) REVERT: K 31 ASN cc_start: 0.8140 (t0) cc_final: 0.7835 (t0) REVERT: K 47 MET cc_start: 0.6903 (mmm) cc_final: 0.6492 (mmt) REVERT: E 42 VAL cc_start: 0.9205 (t) cc_final: 0.8859 (p) REVERT: E 122 LEU cc_start: 0.9354 (tp) cc_final: 0.9027 (tt) REVERT: E 207 LYS cc_start: 0.8767 (mttt) cc_final: 0.7845 (tptt) REVERT: E 256 SER cc_start: 0.9340 (p) cc_final: 0.8833 (t) REVERT: E 271 MET cc_start: 0.9270 (mmm) cc_final: 0.8937 (mmm) REVERT: E 421 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8384 (ttpt) REVERT: E 475 MET cc_start: 0.8864 (mmm) cc_final: 0.8585 (mmm) REVERT: F 634 GLU cc_start: 0.8880 (tm-30) cc_final: 0.8655 (tm-30) REVERT: F 647 GLU cc_start: 0.8620 (tm-30) cc_final: 0.8343 (tm-30) REVERT: F 654 GLU cc_start: 0.8278 (mt-10) cc_final: 0.8003 (mt-10) REVERT: M 13 GLN cc_start: 0.8550 (pp30) cc_final: 0.8199 (pp30) REVERT: M 23 ARG cc_start: 0.8679 (tmm-80) cc_final: 0.7753 (tmm-80) REVERT: M 46 GLU cc_start: 0.9128 (tp30) cc_final: 0.8902 (mm-30) REVERT: M 81 GLN cc_start: 0.9151 (tt0) cc_final: 0.8236 (tm-30) REVERT: M 82 MET cc_start: 0.8449 (mpp) cc_final: 0.8093 (mpp) REVERT: N 49 TYR cc_start: 0.8444 (OUTLIER) cc_final: 0.7901 (p90) REVERT: N 81 ASP cc_start: 0.9101 (t0) cc_final: 0.8888 (m-30) REVERT: H 36 TRP cc_start: 0.8924 (m100) cc_final: 0.7268 (m100) REVERT: H 37 MET cc_start: 0.8976 (mmm) cc_final: 0.8477 (mmm) REVERT: H 47 TRP cc_start: 0.8615 (t60) cc_final: 0.7987 (t60) REVERT: H 52 ASN cc_start: 0.8718 (t0) cc_final: 0.8481 (t0) REVERT: H 102 TYR cc_start: 0.8800 (m-80) cc_final: 0.8195 (m-80) outliers start: 91 outliers final: 59 residues processed: 434 average time/residue: 0.1175 time to fit residues: 80.5654 Evaluate side-chains 414 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 346 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 96 GLU Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 35 TRP Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 395 TRP Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 419 ARG Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 26 THR Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 82 ASP Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 421 LYS Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain F residue 664 ASP Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain N residue 37 GLN Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 82 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 168 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 chunk 196 optimal weight: 0.7980 chunk 194 optimal weight: 10.0000 chunk 192 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 190 optimal weight: 6.9990 chunk 149 optimal weight: 0.6980 chunk 47 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 89 GLN ** I 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 287 GLN D 653 GLN J 105 GLN ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN H 105 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.078245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.063968 restraints weight = 74446.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.066071 restraints weight = 37647.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.067497 restraints weight = 24175.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.068398 restraints weight = 17796.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.069058 restraints weight = 14518.025| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 21478 Z= 0.237 Angle : 0.699 11.892 29270 Z= 0.339 Chirality : 0.045 0.251 3434 Planarity : 0.004 0.045 3610 Dihedral : 6.049 47.459 4136 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 4.89 % Allowed : 21.14 % Favored : 73.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % 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: -0.83 (0.17), residues: 2521 helix: 1.44 (0.26), residues: 404 sheet: -0.43 (0.18), residues: 773 loop : -1.25 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 585 TYR 0.018 0.002 TYR H 33 PHE 0.032 0.002 PHE M 102 TRP 0.018 0.002 TRP C 69 HIS 0.006 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00531 (21372) covalent geometry : angle 0.67494 (28993) SS BOND : bond 0.00464 ( 41) SS BOND : angle 1.18048 ( 82) hydrogen bonds : bond 0.03683 ( 727) hydrogen bonds : angle 5.23955 ( 1995) link_ALPHA1-3 : bond 0.01358 ( 2) link_ALPHA1-3 : angle 1.75052 ( 6) link_ALPHA1-6 : bond 0.00881 ( 1) link_ALPHA1-6 : angle 1.30875 ( 3) link_BETA1-4 : bond 0.00248 ( 11) link_BETA1-4 : angle 2.23599 ( 33) link_NAG-ASN : bond 0.00311 ( 51) link_NAG-ASN : angle 2.25010 ( 153) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5042 Ramachandran restraints generated. 2521 Oldfield, 0 Emsley, 2521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5042 Ramachandran restraints generated. 2521 Oldfield, 0 Emsley, 2521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 348 time to evaluate : 0.852 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: L 62 PHE cc_start: 0.8522 (m-80) cc_final: 0.8263 (m-80) REVERT: L 79 GLN cc_start: 0.7534 (mp10) cc_final: 0.7143 (mp10) REVERT: L 82 ASP cc_start: 0.8295 (m-30) cc_final: 0.8051 (m-30) REVERT: L 96 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7419 (pp20) REVERT: A 114 GLN cc_start: 0.8666 (pp30) cc_final: 0.8456 (pp30) REVERT: A 173 TYR cc_start: 0.7584 (m-80) cc_final: 0.7204 (m-80) REVERT: A 195 ASN cc_start: 0.9205 (p0) cc_final: 0.8534 (t0) REVERT: A 308 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.7941 (ttm110) REVERT: A 482 GLU cc_start: 0.8164 (mp0) cc_final: 0.7684 (mp0) REVERT: B 535 MET cc_start: 0.7934 (pmm) cc_final: 0.7612 (pmm) REVERT: G 72 ASP cc_start: 0.8698 (t0) cc_final: 0.8360 (t0) REVERT: G 81 GLN cc_start: 0.9069 (tp40) cc_final: 0.8579 (tp40) REVERT: G 92 CYS cc_start: 0.7339 (OUTLIER) cc_final: 0.6762 (m) REVERT: I 35 TRP cc_start: 0.7980 (OUTLIER) cc_final: 0.7498 (m-10) REVERT: I 38 GLN cc_start: 0.8226 (pm20) cc_final: 0.7163 (pm20) REVERT: C 368 ASP cc_start: 0.8274 (OUTLIER) cc_final: 0.8017 (p0) REVERT: C 395 TRP cc_start: 0.7700 (OUTLIER) cc_final: 0.7115 (t60) REVERT: C 396 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8421 (mt) REVERT: D 529 THR cc_start: 0.8991 (m) cc_final: 0.8728 (m) REVERT: D 543 ASN cc_start: 0.9271 (t0) cc_final: 0.8908 (t0) REVERT: D 584 GLU cc_start: 0.8792 (tt0) cc_final: 0.8365 (tt0) REVERT: D 590 GLN cc_start: 0.8820 (tm-30) cc_final: 0.8591 (tm-30) REVERT: J 52 ASN cc_start: 0.8731 (p0) cc_final: 0.8400 (p0) REVERT: J 64 LYS cc_start: 0.9265 (tptm) cc_final: 0.8976 (ttmt) REVERT: J 82 MET cc_start: 0.9154 (pmm) cc_final: 0.8738 (pmm) REVERT: K 31 ASN cc_start: 0.8212 (t0) cc_final: 0.7928 (t0) REVERT: K 47 MET cc_start: 0.7012 (mmm) cc_final: 0.6599 (mmt) REVERT: E 122 LEU cc_start: 0.9418 (tp) cc_final: 0.9108 (tt) REVERT: E 207 LYS cc_start: 0.8761 (mttt) cc_final: 0.7860 (tptt) REVERT: E 256 SER cc_start: 0.9433 (p) cc_final: 0.9134 (t) REVERT: E 421 LYS cc_start: 0.9065 (OUTLIER) cc_final: 0.8537 (ttpt) REVERT: F 626 MET cc_start: 0.8451 (ttt) cc_final: 0.8228 (ttt) REVERT: F 634 GLU cc_start: 0.8934 (tm-30) cc_final: 0.8715 (tm-30) REVERT: F 647 GLU cc_start: 0.8664 (tm-30) cc_final: 0.8411 (tm-30) REVERT: F 654 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7995 (mt-10) REVERT: M 13 GLN cc_start: 0.8597 (pp30) cc_final: 0.8202 (pp30) REVERT: M 23 ARG cc_start: 0.8704 (tmm-80) cc_final: 0.7868 (tmm-80) REVERT: M 46 GLU cc_start: 0.9083 (tp30) cc_final: 0.8813 (mm-30) REVERT: M 81 GLN cc_start: 0.9192 (tt0) cc_final: 0.8735 (tp-100) REVERT: N 49 TYR cc_start: 0.8540 (OUTLIER) cc_final: 0.8073 (p90) REVERT: N 81 ASP cc_start: 0.9147 (t0) cc_final: 0.8828 (m-30) REVERT: H 36 TRP cc_start: 0.8954 (m100) cc_final: 0.7773 (m100) REVERT: H 47 TRP cc_start: 0.8618 (t60) cc_final: 0.7942 (t60) REVERT: H 52 ASN cc_start: 0.8782 (t0) cc_final: 0.8468 (t0) REVERT: H 101 ASP cc_start: 0.8346 (p0) cc_final: 0.8087 (p0) REVERT: H 102 TYR cc_start: 0.8837 (m-80) cc_final: 0.8157 (m-80) outliers start: 109 outliers final: 78 residues processed: 428 average time/residue: 0.1536 time to fit residues: 102.7100 Evaluate side-chains 424 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 337 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 96 GLU Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 35 TRP Chi-restraints excluded: chain I residue 49 TYR Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 395 TRP Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 419 ARG Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain J residue 105 GLN Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 26 THR Chi-restraints excluded: chain K residue 82 ASP Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 421 LYS Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain F residue 664 ASP Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain N residue 37 GLN Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 108 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 67 optimal weight: 9.9990 chunk 215 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 176 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 170 optimal weight: 1.9990 chunk 231 optimal weight: 5.9990 chunk 29 optimal weight: 0.5980 chunk 244 optimal weight: 0.8980 chunk 143 optimal weight: 8.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 656 ASN I 6 GLN ** I 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 GLN D 653 GLN J 105 GLN E 67 ASN ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 81 GLN H 39 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.079363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.065037 restraints weight = 73507.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.067182 restraints weight = 37104.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.068625 restraints weight = 23730.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.069577 restraints weight = 17447.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.070231 restraints weight = 14125.953| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 21478 Z= 0.162 Angle : 0.676 11.968 29270 Z= 0.325 Chirality : 0.044 0.219 3434 Planarity : 0.004 0.044 3610 Dihedral : 5.794 48.037 4136 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.91 % Favored : 94.05 % Rotamer: Outliers : 4.67 % Allowed : 22.26 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % 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: -0.77 (0.17), residues: 2521 helix: 1.49 (0.26), residues: 404 sheet: -0.39 (0.18), residues: 774 loop : -1.22 (0.17), residues: 1343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 542 TYR 0.031 0.001 TYR H 33 PHE 0.029 0.002 PHE M 102 TRP 0.021 0.001 TRP M 36 HIS 0.006 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00369 (21372) covalent geometry : angle 0.65389 (28993) SS BOND : bond 0.00380 ( 41) SS BOND : angle 1.13281 ( 82) hydrogen bonds : bond 0.03456 ( 727) hydrogen bonds : angle 5.12252 ( 1995) link_ALPHA1-3 : bond 0.01358 ( 2) link_ALPHA1-3 : angle 2.03782 ( 6) link_ALPHA1-6 : bond 0.00898 ( 1) link_ALPHA1-6 : angle 1.32640 ( 3) link_BETA1-4 : bond 0.00270 ( 11) link_BETA1-4 : angle 2.10814 ( 33) link_NAG-ASN : bond 0.00266 ( 51) link_NAG-ASN : angle 2.11052 ( 153) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5042 Ramachandran restraints generated. 2521 Oldfield, 0 Emsley, 2521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5042 Ramachandran restraints generated. 2521 Oldfield, 0 Emsley, 2521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 361 time to evaluate : 0.858 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: L 96 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7561 (pp20) REVERT: A 114 GLN cc_start: 0.8660 (pp30) cc_final: 0.8446 (pp30) REVERT: A 173 TYR cc_start: 0.7602 (m-80) cc_final: 0.7221 (m-80) REVERT: A 195 ASN cc_start: 0.9160 (p0) cc_final: 0.8490 (t0) REVERT: A 308 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7878 (ttm110) REVERT: A 427 TRP cc_start: 0.8527 (m100) cc_final: 0.8180 (m100) REVERT: A 482 GLU cc_start: 0.8145 (mp0) cc_final: 0.7634 (mp0) REVERT: B 530 MET cc_start: 0.8955 (tpp) cc_final: 0.8347 (tpp) REVERT: B 535 MET cc_start: 0.7831 (pmm) cc_final: 0.7630 (pmm) REVERT: B 656 ASN cc_start: 0.8834 (m-40) cc_final: 0.8574 (m-40) REVERT: G 19 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8706 (tptt) REVERT: G 72 ASP cc_start: 0.8654 (t0) cc_final: 0.8343 (t0) REVERT: G 81 GLN cc_start: 0.9041 (tp40) cc_final: 0.8579 (tp40) REVERT: G 92 CYS cc_start: 0.7101 (OUTLIER) cc_final: 0.6554 (m) REVERT: I 35 TRP cc_start: 0.7988 (OUTLIER) cc_final: 0.7559 (m-10) REVERT: I 37 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.7696 (pt0) REVERT: I 38 GLN cc_start: 0.8135 (pm20) cc_final: 0.7109 (pm20) REVERT: C 271 MET cc_start: 0.8396 (mmm) cc_final: 0.7985 (mmm) REVERT: C 368 ASP cc_start: 0.8384 (OUTLIER) cc_final: 0.7834 (p0) REVERT: C 395 TRP cc_start: 0.7719 (OUTLIER) cc_final: 0.7090 (t60) REVERT: C 396 ILE cc_start: 0.8682 (OUTLIER) cc_final: 0.8381 (mt) REVERT: C 475 MET cc_start: 0.8980 (mmp) cc_final: 0.8593 (mmp) REVERT: D 529 THR cc_start: 0.8999 (m) cc_final: 0.8697 (m) REVERT: D 543 ASN cc_start: 0.9283 (t0) cc_final: 0.8700 (t0) REVERT: D 590 GLN cc_start: 0.8827 (tm-30) cc_final: 0.8594 (tm-30) REVERT: D 650 GLN cc_start: 0.8537 (tm-30) cc_final: 0.8276 (tm-30) REVERT: J 45 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9165 (mt) REVERT: J 52 ASN cc_start: 0.8762 (p0) cc_final: 0.8522 (p0) REVERT: J 64 LYS cc_start: 0.9243 (tptm) cc_final: 0.8941 (ttmt) REVERT: J 82 MET cc_start: 0.9170 (pmm) cc_final: 0.8764 (pmm) REVERT: K 31 ASN cc_start: 0.8183 (t0) cc_final: 0.7888 (t0) REVERT: K 47 MET cc_start: 0.6824 (mmm) cc_final: 0.6416 (mmt) REVERT: E 107 ASP cc_start: 0.9022 (t0) cc_final: 0.8761 (t0) REVERT: E 122 LEU cc_start: 0.9384 (tp) cc_final: 0.9058 (tt) REVERT: E 207 LYS cc_start: 0.8780 (mttt) cc_final: 0.7862 (tptt) REVERT: E 256 SER cc_start: 0.9388 (p) cc_final: 0.8878 (t) REVERT: E 271 MET cc_start: 0.9296 (mmm) cc_final: 0.8967 (mmm) REVERT: E 421 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8488 (ttpt) REVERT: E 475 MET cc_start: 0.8897 (mmm) cc_final: 0.8391 (mmm) REVERT: F 634 GLU cc_start: 0.8887 (tm-30) cc_final: 0.8654 (tm-30) REVERT: F 647 GLU cc_start: 0.8662 (tm-30) cc_final: 0.8379 (tm-30) REVERT: F 654 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7968 (mt-10) REVERT: M 13 GLN cc_start: 0.8570 (pp30) cc_final: 0.8181 (pp30) REVERT: M 23 ARG cc_start: 0.8712 (tmm-80) cc_final: 0.7900 (tmm-80) REVERT: M 46 GLU cc_start: 0.9037 (tp30) cc_final: 0.8731 (mm-30) REVERT: M 81 GLN cc_start: 0.9178 (tt0) cc_final: 0.8572 (tm-30) REVERT: N 49 TYR cc_start: 0.8480 (OUTLIER) cc_final: 0.8033 (p90) REVERT: N 81 ASP cc_start: 0.9121 (t0) cc_final: 0.8842 (m-30) REVERT: H 32 PHE cc_start: 0.8511 (m-80) cc_final: 0.8138 (m-80) REVERT: H 36 TRP cc_start: 0.8828 (m100) cc_final: 0.7602 (m100) REVERT: H 37 MET cc_start: 0.8696 (mmm) cc_final: 0.8332 (mmm) REVERT: H 47 TRP cc_start: 0.8519 (t60) cc_final: 0.8097 (t60) REVERT: H 52 ASN cc_start: 0.8809 (t0) cc_final: 0.8455 (t0) REVERT: H 101 ASP cc_start: 0.8265 (p0) cc_final: 0.7968 (p0) REVERT: H 102 TYR cc_start: 0.8791 (m-80) cc_final: 0.8030 (m-80) outliers start: 104 outliers final: 76 residues processed: 440 average time/residue: 0.1572 time to fit residues: 107.7332 Evaluate side-chains 429 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 341 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 96 GLU Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain G residue 19 LYS Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 35 TRP Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 395 TRP Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 419 ARG Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain J residue 105 GLN Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 26 THR Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 82 ASP Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 421 LYS Chi-restraints excluded: chain E residue 445 CYS Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain F residue 664 ASP Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain N residue 37 GLN Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 84 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.7643 > 50: distance: 20 - 83: 20.515 distance: 23 - 80: 23.654 distance: 64 - 68: 22.526 distance: 68 - 69: 14.061 distance: 69 - 70: 19.960 distance: 69 - 72: 26.712 distance: 70 - 71: 8.717 distance: 70 - 80: 42.341 distance: 72 - 73: 32.169 distance: 73 - 74: 5.612 distance: 73 - 75: 10.124 distance: 74 - 76: 7.704 distance: 75 - 77: 6.586 distance: 76 - 78: 4.544 distance: 77 - 78: 5.055 distance: 78 - 79: 7.157 distance: 80 - 81: 5.140 distance: 81 - 82: 27.783 distance: 81 - 84: 23.320 distance: 82 - 83: 11.427 distance: 82 - 86: 29.069 distance: 84 - 85: 10.435 distance: 85 - 169: 13.936 distance: 86 - 87: 29.129 distance: 87 - 88: 22.799 distance: 87 - 90: 43.403 distance: 88 - 89: 28.380 distance: 88 - 91: 18.293 distance: 91 - 92: 21.652 distance: 91 - 97: 16.599 distance: 92 - 93: 22.542 distance: 92 - 95: 25.906 distance: 93 - 94: 16.464 distance: 93 - 98: 30.463 distance: 95 - 96: 31.942 distance: 96 - 97: 15.586 distance: 98 - 99: 17.658 distance: 99 - 100: 22.795 distance: 99 - 102: 20.898 distance: 100 - 101: 11.732 distance: 100 - 103: 14.614 distance: 103 - 104: 28.086 distance: 104 - 105: 14.166 distance: 105 - 106: 17.082 distance: 105 - 107: 41.822 distance: 107 - 108: 10.784 distance: 108 - 109: 7.238 distance: 108 - 111: 9.581 distance: 109 - 110: 9.604 distance: 109 - 118: 24.640 distance: 111 - 112: 14.873 distance: 112 - 113: 13.540 distance: 112 - 114: 7.791 distance: 113 - 115: 7.075 distance: 114 - 116: 7.336 distance: 115 - 117: 4.934 distance: 116 - 117: 5.266 distance: 118 - 119: 13.946 distance: 118 - 203: 13.845 distance: 119 - 120: 9.107 distance: 119 - 122: 18.772 distance: 120 - 121: 12.892 distance: 120 - 123: 33.175 distance: 121 - 200: 24.036 distance: 123 - 124: 14.149 distance: 124 - 125: 9.681 distance: 124 - 127: 26.365 distance: 125 - 126: 9.835 distance: 125 - 131: 14.198 distance: 126 - 156: 14.202 distance: 127 - 128: 19.797 distance: 127 - 129: 14.369 distance: 128 - 130: 5.811 distance: 131 - 132: 5.828 distance: 131 - 191: 5.905 distance: 132 - 133: 5.542 distance: 132 - 135: 6.626 distance: 133 - 134: 3.537 distance: 133 - 139: 5.822 distance: 134 - 188: 6.387 distance: 135 - 136: 5.466 distance: 136 - 137: 3.146 distance: 136 - 138: 3.536