Starting phenix.real_space_refine on Wed Jun 18 10:06:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mih_48290/06_2025/9mih_48290.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mih_48290/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9mih_48290/06_2025/9mih_48290.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mih_48290/06_2025/9mih_48290.map" model { file = "/net/cci-nas-00/data/ceres_data/9mih_48290/06_2025/9mih_48290.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mih_48290/06_2025/9mih_48290.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 14.03, per 1000 atoms: 0.67 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: 5.83 Conformation dependent library (CDL) restraints added in 2.9 seconds 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: 3.36 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: 8.22 Time building geometry restraints manager: 6.88 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 503 or resid 601 through 611)) selection = (chain 'C' and (resid 33 through 56 or resid 71 through 185 or resid 189 through \ 503 or resid 601 through 611)) selection = (chain 'E' and (resid 33 through 56 or resid 71 through 457 or resid 463 through \ 503 or resid 601 through 611)) } ncs_group { reference = chain 'B' selection = (chain 'D' and (resid 520 through 545 or resid 569 through 664 or resid 701)) selection = (chain 'F' and (resid 520 through 664 or resid 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: 3.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.890 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 52.530 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.860 ------------------------------------------------------------------------------- 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 : 5.92 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.048 0.002 TRP M 36 HIS 0.021 0.002 HIS E 374 PHE 0.026 0.002 PHE L 98 TYR 0.028 0.002 TYR E 217 ARG 0.031 0.002 ARG B 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00343 ( 51) link_NAG-ASN : angle 2.39503 ( 153) 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_ALPHA1-3 : bond 0.00634 ( 2) link_ALPHA1-3 : angle 2.39474 ( 6) hydrogen bonds : bond 0.12478 ( 727) hydrogen bonds : angle 6.85360 ( 1995) SS BOND : bond 0.14049 ( 41) SS BOND : angle 8.90810 ( 82) covalent geometry : bond 0.00532 (21372) covalent geometry : angle 0.94253 (28993) *********************** 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 : 2.183 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: 0.8315 (m-80) REVERT: L 73 LEU cc_start: 0.9188 (tp) cc_final: 0.8431 (tp) REVERT: L 85 THR cc_start: 0.9186 (m) cc_final: 0.8846 (p) REVERT: A 173 TYR cc_start: 0.7566 (m-80) cc_final: 0.7011 (m-10) REVERT: A 195 ASN cc_start: 0.9167 (p0) cc_final: 0.8490 (t0) REVERT: A 479 TRP cc_start: 0.8745 (m100) cc_final: 0.7897 (m100) 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: 0.7890 (ttp80) REVERT: G 51 ILE cc_start: 0.8895 (tt) cc_final: 0.8692 (tp) REVERT: G 56 LEU cc_start: 0.8714 (tp) cc_final: 0.8481 (tp) REVERT: G 72 ASP cc_start: 0.8813 (t0) cc_final: 0.8430 (t0) 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: 0.8364 (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: 0.8006 (mmm) REVERT: C 368 ASP cc_start: 0.8146 (p0) cc_final: 0.7286 (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: 0.8607 (m-10) REVERT: J 97 MET cc_start: 0.8380 (ttm) cc_final: 0.8056 (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: 0.7838 (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: 0.7915 (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: 0.7968 (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: 0.8634 (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: 0.8972 (m-80) REVERT: N 86 TYR cc_start: 0.7388 (m-10) cc_final: 0.6964 (m-10) REVERT: H 36 TRP cc_start: 0.8815 (m100) cc_final: 0.7510 (m100) outliers start: 3 outliers final: 2 residues processed: 419 average time/residue: 0.3288 time to fit residues: 209.8869 Evaluate side-chains 361 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 359 time to evaluate : 2.420 ------------------------------------------------------------------------------- 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 212 optimal weight: 3.9990 chunk 191 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 chunk 65 optimal weight: 9.9990 chunk 128 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 197 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 120 optimal weight: 0.9980 chunk 147 optimal weight: 5.9990 chunk 228 optimal weight: 10.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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** ** 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 = 0.3392 r_free = 0.3392 target = 0.080458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.066144 restraints weight = 73873.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.068309 restraints weight = 37307.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.069767 restraints weight = 23801.009| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21478 Z= 0.183 Angle : 0.702 9.771 29270 Z= 0.344 Chirality : 0.046 0.281 3434 Planarity : 0.005 0.058 3610 Dihedral : 7.224 75.240 4136 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.51 % Allowed : 20.51 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.17), residues: 2521 helix: 1.38 (0.27), residues: 399 sheet: -0.52 (0.18), residues: 775 loop : -1.24 (0.17), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP K 35 HIS 0.004 0.001 HIS A 249 PHE 0.023 0.002 PHE L 83 TYR 0.025 0.002 TYR E 484 ARG 0.007 0.001 ARG B 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00301 ( 51) link_NAG-ASN : angle 2.41231 ( 153) link_ALPHA1-6 : bond 0.00518 ( 1) link_ALPHA1-6 : angle 1.65951 ( 3) link_BETA1-4 : bond 0.00279 ( 11) link_BETA1-4 : angle 2.35543 ( 33) link_ALPHA1-3 : bond 0.01337 ( 2) link_ALPHA1-3 : angle 1.23622 ( 6) hydrogen bonds : bond 0.04088 ( 727) hydrogen bonds : angle 5.60673 ( 1995) SS BOND : bond 0.00514 ( 41) SS BOND : angle 0.95658 ( 82) covalent geometry : bond 0.00413 (21372) covalent geometry : angle 0.67662 (28993) *********************** 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 429 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 373 time to evaluate : 2.248 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 85 THR cc_start: 0.9066 (m) cc_final: 0.8731 (p) REVERT: L 96 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7627 (pp20) REVERT: A 114 GLN cc_start: 0.8643 (pp30) cc_final: 0.8370 (pp30) REVERT: A 173 TYR cc_start: 0.7572 (m-80) cc_final: 0.7167 (m-80) REVERT: B 535 MET cc_start: 0.8221 (pmm) cc_final: 0.7833 (pmm) REVERT: G 23 ARG cc_start: 0.8277 (ttp80) cc_final: 0.7913 (ttp80) REVERT: G 72 ASP cc_start: 0.8752 (t0) cc_final: 0.8437 (t0) REVERT: G 81 GLN cc_start: 0.8912 (tp40) cc_final: 0.8553 (tp40) REVERT: I 38 GLN cc_start: 0.8241 (pm20) cc_final: 0.7517 (pm20) REVERT: C 271 MET cc_start: 0.8479 (mmm) cc_final: 0.8216 (mmm) REVERT: C 368 ASP cc_start: 0.8170 (OUTLIER) cc_final: 0.7592 (p0) REVERT: C 395 TRP cc_start: 0.7592 (OUTLIER) cc_final: 0.7250 (t60) REVERT: C 396 ILE cc_start: 0.8631 (OUTLIER) cc_final: 0.8382 (mt) REVERT: D 529 THR cc_start: 0.8828 (m) cc_final: 0.8568 (m) REVERT: D 530 MET cc_start: 0.9071 (tpp) cc_final: 0.8688 (mmm) REVERT: D 590 GLN cc_start: 0.8624 (tm-30) cc_final: 0.8406 (tm-30) REVERT: D 626 MET cc_start: 0.8190 (ttm) cc_final: 0.7943 (ttt) REVERT: J 3 GLN cc_start: 0.8287 (tm-30) cc_final: 0.8001 (tm-30) REVERT: J 32 PHE cc_start: 0.8985 (m-10) cc_final: 0.8674 (m-10) REVERT: J 36 TRP cc_start: 0.8598 (m100) cc_final: 0.7009 (m100) REVERT: J 52 ASN cc_start: 0.8664 (p0) cc_final: 0.8165 (p0) REVERT: J 64 LYS cc_start: 0.9291 (tptm) cc_final: 0.8960 (ttmt) REVERT: K 31 ASN cc_start: 0.8265 (t0) cc_final: 0.7955 (t0) REVERT: K 47 MET cc_start: 0.7017 (mmm) cc_final: 0.6593 (mmt) REVERT: E 207 LYS cc_start: 0.8815 (mttt) cc_final: 0.7904 (tptt) REVERT: F 530 MET cc_start: 0.7624 (tpp) cc_final: 0.7357 (tpp) REVERT: F 588 ARG cc_start: 0.8473 (mpt180) cc_final: 0.8191 (mpt180) REVERT: F 634 GLU cc_start: 0.8908 (tm-30) cc_final: 0.8669 (tm-30) REVERT: F 647 GLU cc_start: 0.8639 (tm-30) cc_final: 0.8404 (tm-30) REVERT: F 654 GLU cc_start: 0.8310 (mt-10) cc_final: 0.8103 (mt-10) REVERT: F 664 ASP cc_start: 0.8312 (t70) cc_final: 0.8004 (m-30) REVERT: M 13 GLN cc_start: 0.8382 (pp30) cc_final: 0.8096 (pp30) REVERT: M 34 MET cc_start: 0.8686 (mmm) cc_final: 0.8277 (mmm) REVERT: M 46 GLU cc_start: 0.9148 (tp30) cc_final: 0.8907 (mm-30) REVERT: M 81 GLN cc_start: 0.9173 (tt0) cc_final: 0.8212 (tm-30) REVERT: M 82 MET cc_start: 0.8174 (mpp) cc_final: 0.7880 (mpp) REVERT: M 102 PHE cc_start: 0.9292 (m-80) cc_final: 0.8989 (m-80) REVERT: H 36 TRP cc_start: 0.8710 (m100) cc_final: 0.6843 (m100) REVERT: H 37 MET cc_start: 0.8846 (mmm) cc_final: 0.8546 (mmm) REVERT: H 52 ASN cc_start: 0.8852 (t0) cc_final: 0.8581 (t0) outliers start: 56 outliers final: 34 residues processed: 414 average time/residue: 0.3315 time to fit residues: 211.0872 Evaluate side-chains 386 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 348 time to evaluate : 2.180 ------------------------------------------------------------------------------- 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 48 ILE 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 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 97 optimal weight: 7.9990 chunk 77 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 196 optimal weight: 0.9980 chunk 234 optimal weight: 7.9990 chunk 127 optimal weight: 5.9990 chunk 231 optimal weight: 3.9990 chunk 243 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 202 optimal weight: 2.9990 chunk 164 optimal weight: 0.6980 overall best weight: 2.5386 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.079076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.064799 restraints weight = 73749.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.066915 restraints weight = 37490.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.068349 restraints weight = 24090.560| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 21478 Z= 0.215 Angle : 0.695 12.129 29270 Z= 0.340 Chirality : 0.046 0.294 3434 Planarity : 0.004 0.061 3610 Dihedral : 6.760 59.627 4136 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 4.22 % Allowed : 20.24 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.17), residues: 2521 helix: 1.38 (0.26), residues: 402 sheet: -0.53 (0.18), residues: 797 loop : -1.27 (0.17), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP M 36 HIS 0.005 0.001 HIS K 39 PHE 0.023 0.002 PHE L 83 TYR 0.027 0.002 TYR H 33 ARG 0.012 0.001 ARG A 178 Details of bonding type rmsd link_NAG-ASN : bond 0.00317 ( 51) link_NAG-ASN : angle 2.35743 ( 153) link_ALPHA1-6 : bond 0.00847 ( 1) link_ALPHA1-6 : angle 1.57399 ( 3) link_BETA1-4 : bond 0.00263 ( 11) link_BETA1-4 : angle 2.29823 ( 33) link_ALPHA1-3 : bond 0.01193 ( 2) link_ALPHA1-3 : angle 1.58562 ( 6) hydrogen bonds : bond 0.03833 ( 727) hydrogen bonds : angle 5.36169 ( 1995) SS BOND : bond 0.00536 ( 41) SS BOND : angle 1.56780 ( 82) covalent geometry : bond 0.00483 (21372) covalent geometry : angle 0.66663 (28993) *********************** 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 449 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 355 time to evaluate : 2.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8671 (pp30) cc_final: 0.8365 (pp30) REVERT: A 161 MET cc_start: 0.7801 (mmm) cc_final: 0.7595 (mmm) REVERT: A 173 TYR cc_start: 0.7566 (m-80) cc_final: 0.7153 (m-80) REVERT: A 195 ASN cc_start: 0.9128 (p0) cc_final: 0.8385 (t0) REVERT: A 308 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.7763 (ttm110) REVERT: A 482 GLU cc_start: 0.8133 (mp0) cc_final: 0.7724 (mp0) REVERT: B 535 MET cc_start: 0.8035 (pmm) cc_final: 0.7672 (pmm) REVERT: G 72 ASP cc_start: 0.8695 (t0) cc_final: 0.8376 (t0) REVERT: G 83 ARG cc_start: 0.8241 (tpp80) cc_final: 0.7503 (mmt-90) REVERT: G 92 CYS cc_start: 0.7377 (OUTLIER) cc_final: 0.6760 (m) REVERT: I 35 TRP cc_start: 0.7989 (m-90) cc_final: 0.7539 (m-10) REVERT: I 38 GLN cc_start: 0.8248 (pm20) cc_final: 0.7494 (pm20) REVERT: C 271 MET cc_start: 0.8561 (mmm) cc_final: 0.8333 (mmm) REVERT: C 395 TRP cc_start: 0.7700 (OUTLIER) cc_final: 0.7227 (t60) REVERT: C 396 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8418 (mt) REVERT: C 425 ASN cc_start: 0.8717 (OUTLIER) cc_final: 0.8502 (t0) REVERT: D 529 THR cc_start: 0.8871 (m) cc_final: 0.8622 (m) REVERT: D 584 GLU cc_start: 0.8717 (tt0) cc_final: 0.8311 (tt0) REVERT: D 590 GLN cc_start: 0.8727 (tm-30) cc_final: 0.8517 (tm-30) REVERT: D 626 MET cc_start: 0.8256 (ttm) cc_final: 0.8043 (ttt) REVERT: J 52 ASN cc_start: 0.8685 (p0) cc_final: 0.8335 (p0) REVERT: J 64 LYS cc_start: 0.9302 (tptm) cc_final: 0.8979 (ttmt) REVERT: K 31 ASN cc_start: 0.8227 (t0) cc_final: 0.7929 (t0) REVERT: K 47 MET cc_start: 0.6909 (mmm) cc_final: 0.6495 (mmt) REVERT: E 122 LEU cc_start: 0.9359 (tp) cc_final: 0.9066 (tt) REVERT: E 154 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9111 (mm) REVERT: E 207 LYS cc_start: 0.8837 (mttt) cc_final: 0.7900 (tptt) REVERT: E 256 SER cc_start: 0.9315 (p) cc_final: 0.8864 (t) REVERT: E 259 LEU cc_start: 0.9571 (tp) cc_final: 0.9206 (tp) REVERT: E 475 MET cc_start: 0.8797 (mmm) cc_final: 0.8581 (mmm) REVERT: F 634 GLU cc_start: 0.8934 (tm-30) cc_final: 0.8707 (tm-30) REVERT: F 647 GLU cc_start: 0.8647 (tm-30) cc_final: 0.8416 (tm-30) REVERT: F 654 GLU cc_start: 0.8320 (mt-10) cc_final: 0.8063 (mt-10) REVERT: M 13 GLN cc_start: 0.8459 (pp30) cc_final: 0.7966 (pp30) REVERT: M 23 ARG cc_start: 0.8660 (tmm-80) cc_final: 0.7720 (tmm-80) REVERT: M 34 MET cc_start: 0.8661 (mmm) cc_final: 0.8135 (mmm) REVERT: M 46 GLU cc_start: 0.9161 (tp30) cc_final: 0.8940 (mm-30) REVERT: M 81 GLN cc_start: 0.9195 (tt0) cc_final: 0.8174 (tm-30) REVERT: M 82 MET cc_start: 0.8390 (mpp) cc_final: 0.7957 (mpp) REVERT: N 49 TYR cc_start: 0.8513 (OUTLIER) cc_final: 0.7904 (p90) REVERT: H 36 TRP cc_start: 0.8883 (m100) cc_final: 0.7358 (m100) REVERT: H 47 TRP cc_start: 0.8694 (t60) cc_final: 0.7906 (t60) outliers start: 94 outliers final: 59 residues processed: 417 average time/residue: 0.3287 time to fit residues: 213.6446 Evaluate side-chains 398 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 332 time to evaluate : 2.366 ------------------------------------------------------------------------------- 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 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 73 ASN 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 105 THR 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 C residue 425 ASN 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 4 LEU 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 154 LEU 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 F residue 539 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 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 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 21 SER Chi-restraints excluded: chain H residue 34 MET 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 44 optimal weight: 2.9990 chunk 165 optimal weight: 4.9990 chunk 99 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 233 optimal weight: 0.0370 chunk 246 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 overall best weight: 1.1462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 89 GLN A 203 GLN ** I 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 653 GLN ** J 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.080469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.066186 restraints weight = 74093.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.068366 restraints weight = 37115.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.069835 restraints weight = 23598.034| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 21478 Z= 0.134 Angle : 0.644 11.132 29270 Z= 0.314 Chirality : 0.044 0.242 3434 Planarity : 0.004 0.050 3610 Dihedral : 5.898 48.158 4136 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.59 % Allowed : 21.23 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.17), residues: 2521 helix: 1.50 (0.27), residues: 410 sheet: -0.47 (0.18), residues: 795 loop : -1.22 (0.17), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 69 HIS 0.005 0.001 HIS A 249 PHE 0.025 0.001 PHE L 83 TYR 0.026 0.001 TYR H 33 ARG 0.008 0.000 ARG A 480 Details of bonding type rmsd link_NAG-ASN : bond 0.00249 ( 51) link_NAG-ASN : angle 2.12800 ( 153) link_ALPHA1-6 : bond 0.01366 ( 1) link_ALPHA1-6 : angle 1.28711 ( 3) link_BETA1-4 : bond 0.00333 ( 11) link_BETA1-4 : angle 2.10990 ( 33) link_ALPHA1-3 : bond 0.01339 ( 2) link_ALPHA1-3 : angle 1.86788 ( 6) hydrogen bonds : bond 0.03394 ( 727) hydrogen bonds : angle 5.14748 ( 1995) SS BOND : bond 0.00449 ( 41) SS BOND : angle 1.41007 ( 82) covalent geometry : bond 0.00305 (21372) covalent geometry : angle 0.61859 (28993) *********************** 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 462 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 382 time to evaluate : 2.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 85 THR cc_start: 0.9122 (m) cc_final: 0.8827 (p) REVERT: L 96 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7383 (pp20) REVERT: A 114 GLN cc_start: 0.8663 (pp30) cc_final: 0.8454 (pp30) REVERT: A 150 MET cc_start: 0.8555 (ppp) cc_final: 0.8331 (ppp) REVERT: A 161 MET cc_start: 0.7779 (mmm) cc_final: 0.7571 (mmm) REVERT: A 173 TYR cc_start: 0.7575 (m-80) cc_final: 0.7114 (m-10) REVERT: A 195 ASN cc_start: 0.9118 (p0) cc_final: 0.8343 (t0) REVERT: A 308 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.7708 (ttm110) REVERT: A 482 GLU cc_start: 0.8120 (mp0) cc_final: 0.7642 (mp0) REVERT: B 530 MET cc_start: 0.9016 (tpp) cc_final: 0.8482 (tpp) REVERT: B 535 MET cc_start: 0.7892 (pmm) cc_final: 0.7590 (pmm) REVERT: G 34 MET cc_start: 0.8700 (mmt) cc_final: 0.8153 (mmt) REVERT: G 72 ASP cc_start: 0.8704 (t0) cc_final: 0.8382 (t0) REVERT: G 83 ARG cc_start: 0.8224 (tpp80) cc_final: 0.7828 (mmt-90) REVERT: G 92 CYS cc_start: 0.7139 (OUTLIER) cc_final: 0.6613 (m) REVERT: I 35 TRP cc_start: 0.7917 (m-90) cc_final: 0.7438 (m-10) REVERT: I 38 GLN cc_start: 0.8211 (pm20) cc_final: 0.7438 (pm20) REVERT: C 271 MET cc_start: 0.8614 (mmm) cc_final: 0.8224 (mmm) REVERT: C 368 ASP cc_start: 0.8294 (OUTLIER) cc_final: 0.7602 (p0) REVERT: C 395 TRP cc_start: 0.7622 (OUTLIER) cc_final: 0.7050 (t60) REVERT: C 396 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8340 (mt) REVERT: C 425 ASN cc_start: 0.8738 (OUTLIER) cc_final: 0.8523 (t0) REVERT: C 475 MET cc_start: 0.8926 (mmp) cc_final: 0.8374 (mmp) REVERT: D 529 THR cc_start: 0.8885 (m) cc_final: 0.8607 (m) REVERT: D 537 LEU cc_start: 0.8882 (mt) cc_final: 0.8612 (mt) REVERT: D 543 ASN cc_start: 0.9260 (t0) cc_final: 0.8679 (t0) REVERT: D 590 GLN cc_start: 0.8768 (tm-30) cc_final: 0.8545 (tm-30) REVERT: J 32 PHE cc_start: 0.8996 (m-10) cc_final: 0.8702 (m-10) REVERT: J 36 TRP cc_start: 0.8404 (m100) cc_final: 0.6900 (m100) REVERT: J 52 ASN cc_start: 0.8600 (p0) cc_final: 0.8327 (p0) REVERT: J 64 LYS cc_start: 0.9254 (tptm) cc_final: 0.8921 (ttmt) REVERT: J 82 MET cc_start: 0.9211 (pmm) cc_final: 0.8752 (pmm) REVERT: J 109 VAL cc_start: 0.9213 (t) cc_final: 0.9001 (p) REVERT: K 4 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.8061 (mt) REVERT: K 31 ASN cc_start: 0.8165 (t0) cc_final: 0.7857 (t0) REVERT: K 47 MET cc_start: 0.6855 (mmm) cc_final: 0.6546 (mmt) REVERT: E 42 VAL cc_start: 0.9197 (t) cc_final: 0.8846 (p) REVERT: E 122 LEU cc_start: 0.9347 (tp) cc_final: 0.9037 (tt) REVERT: E 207 LYS cc_start: 0.8808 (mttt) cc_final: 0.7870 (tptt) REVERT: E 256 SER cc_start: 0.9327 (p) cc_final: 0.8857 (t) REVERT: E 271 MET cc_start: 0.9286 (mmm) cc_final: 0.8956 (mmm) REVERT: E 421 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8370 (ttpt) REVERT: E 475 MET cc_start: 0.8907 (mmm) cc_final: 0.8667 (mmm) REVERT: F 634 GLU cc_start: 0.8923 (tm-30) cc_final: 0.8681 (tm-30) REVERT: F 647 GLU cc_start: 0.8634 (tm-30) cc_final: 0.8367 (tm-30) REVERT: F 654 GLU cc_start: 0.8304 (mt-10) cc_final: 0.8021 (mt-10) REVERT: M 13 GLN cc_start: 0.8517 (pp30) cc_final: 0.8133 (pp30) REVERT: M 23 ARG cc_start: 0.8682 (tmm-80) cc_final: 0.7729 (tmm-80) REVERT: M 46 GLU cc_start: 0.9132 (tp30) cc_final: 0.8908 (mm-30) REVERT: M 81 GLN cc_start: 0.9142 (tt0) cc_final: 0.8190 (tm-30) REVERT: M 82 MET cc_start: 0.8499 (mpp) cc_final: 0.8123 (mpp) REVERT: N 49 TYR cc_start: 0.8428 (OUTLIER) cc_final: 0.7931 (p90) REVERT: N 81 ASP cc_start: 0.9132 (t0) cc_final: 0.8855 (m-30) REVERT: H 32 PHE cc_start: 0.8461 (m-80) cc_final: 0.7988 (m-80) REVERT: H 36 TRP cc_start: 0.8897 (m100) cc_final: 0.7219 (m100) REVERT: H 37 MET cc_start: 0.9007 (mmm) cc_final: 0.8627 (mmm) REVERT: H 47 TRP cc_start: 0.8645 (t60) cc_final: 0.7925 (t60) REVERT: H 52 ASN cc_start: 0.8703 (t0) cc_final: 0.8477 (t0) outliers start: 80 outliers final: 51 residues processed: 437 average time/residue: 0.3213 time to fit residues: 217.5988 Evaluate side-chains 410 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 349 time to evaluate : 2.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 47 LEU 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 80 ASN Chi-restraints excluded: chain A residue 182 VAL 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 620 SER Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 73 ASN 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 C residue 51 THR Chi-restraints excluded: chain C residue 56 SER 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 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 C residue 425 ASN 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 4 LEU 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 68 THR Chi-restraints excluded: chain M residue 78 LEU 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 34 MET 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 142 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 203 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 225 optimal weight: 4.9990 chunk 221 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 188 ASN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 GLN ** J 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.075862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.061711 restraints weight = 74843.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.063745 restraints weight = 38179.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.065137 restraints weight = 24650.794| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 21478 Z= 0.373 Angle : 0.832 13.108 29270 Z= 0.406 Chirality : 0.048 0.322 3434 Planarity : 0.005 0.080 3610 Dihedral : 6.804 49.548 4136 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.70 % Favored : 92.26 % Rotamer: Outliers : 5.75 % Allowed : 21.45 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.17), residues: 2521 helix: 0.97 (0.26), residues: 396 sheet: -0.62 (0.18), residues: 788 loop : -1.37 (0.17), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 103 HIS 0.009 0.001 HIS K 39 PHE 0.037 0.003 PHE M 102 TYR 0.026 0.002 TYR E 217 ARG 0.007 0.001 ARG A 480 Details of bonding type rmsd link_NAG-ASN : bond 0.00510 ( 51) link_NAG-ASN : angle 2.68589 ( 153) link_ALPHA1-6 : bond 0.00773 ( 1) link_ALPHA1-6 : angle 1.52342 ( 3) link_BETA1-4 : bond 0.00318 ( 11) link_BETA1-4 : angle 2.53753 ( 33) link_ALPHA1-3 : bond 0.01322 ( 2) link_ALPHA1-3 : angle 1.55299 ( 6) hydrogen bonds : bond 0.04397 ( 727) hydrogen bonds : angle 5.65140 ( 1995) SS BOND : bond 0.00620 ( 41) SS BOND : angle 1.38067 ( 82) covalent geometry : bond 0.00832 (21372) covalent geometry : angle 0.80433 (28993) *********************** 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 447 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 319 time to evaluate : 2.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 96 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7860 (pp20) REVERT: A 195 ASN cc_start: 0.9237 (p0) cc_final: 0.8530 (t0) REVERT: A 282 LYS cc_start: 0.8269 (mmtt) cc_final: 0.8043 (mptt) REVERT: A 308 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.7963 (ttm110) REVERT: G 72 ASP cc_start: 0.8693 (t0) cc_final: 0.8353 (t0) REVERT: G 92 CYS cc_start: 0.7494 (OUTLIER) cc_final: 0.6877 (m) REVERT: I 38 GLN cc_start: 0.8212 (pm20) cc_final: 0.7079 (pm20) REVERT: C 368 ASP cc_start: 0.8467 (OUTLIER) cc_final: 0.8135 (p0) REVERT: C 395 TRP cc_start: 0.7903 (OUTLIER) cc_final: 0.7220 (t60) REVERT: C 396 ILE cc_start: 0.8651 (OUTLIER) cc_final: 0.8440 (mt) REVERT: C 425 ASN cc_start: 0.8626 (OUTLIER) cc_final: 0.8397 (t0) REVERT: D 590 GLN cc_start: 0.8874 (tm-30) cc_final: 0.8667 (tm-30) REVERT: J 52 ASN cc_start: 0.8817 (p0) cc_final: 0.8435 (p0) REVERT: J 82 MET cc_start: 0.9095 (pmm) cc_final: 0.8732 (pmm) REVERT: K 31 ASN cc_start: 0.8312 (t0) cc_final: 0.8074 (t0) REVERT: K 47 MET cc_start: 0.7035 (mmm) cc_final: 0.6718 (mmt) REVERT: E 122 LEU cc_start: 0.9417 (tp) cc_final: 0.9084 (tt) REVERT: E 207 LYS cc_start: 0.8848 (mttt) cc_final: 0.7941 (tptt) REVERT: E 217 TYR cc_start: 0.7580 (m-80) cc_final: 0.7303 (m-80) REVERT: E 271 MET cc_start: 0.9147 (mmm) cc_final: 0.8739 (mmm) REVERT: E 272 ILE cc_start: 0.9136 (OUTLIER) cc_final: 0.8743 (mp) REVERT: E 315 GLN cc_start: 0.8891 (pm20) cc_final: 0.8646 (pm20) REVERT: F 626 MET cc_start: 0.8490 (ttt) cc_final: 0.8225 (ttt) REVERT: F 634 GLU cc_start: 0.9026 (tm-30) cc_final: 0.8769 (tm-30) REVERT: F 647 GLU cc_start: 0.8797 (tm-30) cc_final: 0.8582 (tm-30) REVERT: F 654 GLU cc_start: 0.8359 (mt-10) cc_final: 0.8081 (mt-10) REVERT: M 13 GLN cc_start: 0.8581 (pp30) cc_final: 0.8133 (pp30) REVERT: M 23 ARG cc_start: 0.8777 (tmm-80) cc_final: 0.7942 (tmm-80) REVERT: M 46 GLU cc_start: 0.9105 (tp30) cc_final: 0.8845 (mm-30) REVERT: M 81 GLN cc_start: 0.9320 (tt0) cc_final: 0.8806 (tp-100) REVERT: N 49 TYR cc_start: 0.8755 (OUTLIER) cc_final: 0.8190 (p90) REVERT: N 81 ASP cc_start: 0.9232 (t0) cc_final: 0.8906 (m-30) REVERT: H 36 TRP cc_start: 0.9056 (m100) cc_final: 0.7952 (m100) REVERT: H 39 GLN cc_start: 0.7888 (pp30) cc_final: 0.7454 (tm-30) REVERT: H 52 ASN cc_start: 0.8923 (t0) cc_final: 0.8656 (t0) outliers start: 128 outliers final: 86 residues processed: 421 average time/residue: 0.3153 time to fit residues: 210.4050 Evaluate side-chains 401 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 306 time to evaluate : 2.532 ------------------------------------------------------------------------------- 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 56 SER Chi-restraints excluded: chain A residue 139 THR 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 48 VAL 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 48 ILE Chi-restraints excluded: chain I residue 49 TYR Chi-restraints excluded: chain I residue 74 THR 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 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 359 ILE Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 387 THR 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 C residue 425 ASN Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 651 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 110 THR Chi-restraints excluded: chain K residue 4 LEU 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 215 ILE Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 303 THR 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 449 ILE Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain F residue 641 ILE 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 34 MET Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 70 THR 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 148 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 173 optimal weight: 1.9990 chunk 196 optimal weight: 3.9990 chunk 201 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 chunk 36 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 18 optimal weight: 7.9990 chunk 104 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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** C 287 GLN ** J 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 105 GLN ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 591 GLN ** 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 = 0.3337 r_free = 0.3337 target = 0.077912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.063645 restraints weight = 73651.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.065751 restraints weight = 37171.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.067169 restraints weight = 23840.089| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 21478 Z= 0.195 Angle : 0.718 13.022 29270 Z= 0.346 Chirality : 0.046 0.275 3434 Planarity : 0.004 0.066 3610 Dihedral : 6.301 46.995 4136 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.31 % Favored : 93.61 % Rotamer: Outliers : 4.80 % Allowed : 23.61 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.17), residues: 2521 helix: 1.20 (0.26), residues: 404 sheet: -0.48 (0.19), residues: 770 loop : -1.39 (0.17), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP M 36 HIS 0.007 0.001 HIS K 39 PHE 0.025 0.002 PHE M 102 TYR 0.030 0.002 TYR H 33 ARG 0.007 0.001 ARG G 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00291 ( 51) link_NAG-ASN : angle 2.38964 ( 153) link_ALPHA1-6 : bond 0.01190 ( 1) link_ALPHA1-6 : angle 1.43361 ( 3) link_BETA1-4 : bond 0.00273 ( 11) link_BETA1-4 : angle 2.21417 ( 33) link_ALPHA1-3 : bond 0.01324 ( 2) link_ALPHA1-3 : angle 1.98310 ( 6) hydrogen bonds : bond 0.03723 ( 727) hydrogen bonds : angle 5.34527 ( 1995) SS BOND : bond 0.00434 ( 41) SS BOND : angle 1.19538 ( 82) covalent geometry : bond 0.00440 (21372) covalent geometry : angle 0.69268 (28993) *********************** 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 450 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 343 time to evaluate : 2.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 35 TRP cc_start: 0.7684 (OUTLIER) cc_final: 0.7378 (m-10) REVERT: L 96 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7701 (pp20) REVERT: A 195 ASN cc_start: 0.9183 (p0) cc_final: 0.8476 (t0) REVERT: A 251 ILE cc_start: 0.9047 (mp) cc_final: 0.8557 (pt) REVERT: A 282 LYS cc_start: 0.8181 (mmtt) cc_final: 0.7582 (mmtt) REVERT: A 308 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7919 (ttm110) REVERT: A 426 MET cc_start: 0.8489 (mmm) cc_final: 0.7967 (tpp) REVERT: A 482 GLU cc_start: 0.8128 (mp0) cc_final: 0.7640 (mp0) REVERT: B 656 ASN cc_start: 0.9016 (m-40) cc_final: 0.8608 (m-40) REVERT: G 19 LYS cc_start: 0.9102 (OUTLIER) cc_final: 0.8639 (tptt) REVERT: G 34 MET cc_start: 0.8676 (mmt) cc_final: 0.8295 (mmt) REVERT: G 72 ASP cc_start: 0.8606 (t0) cc_final: 0.8303 (t0) REVERT: G 92 CYS cc_start: 0.7286 (OUTLIER) cc_final: 0.6732 (m) REVERT: I 35 TRP cc_start: 0.8104 (OUTLIER) cc_final: 0.7655 (m-10) REVERT: I 37 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.7776 (pt0) REVERT: I 38 GLN cc_start: 0.8138 (pm20) cc_final: 0.7141 (pm20) REVERT: C 271 MET cc_start: 0.8479 (mmm) cc_final: 0.7958 (mmm) REVERT: C 368 ASP cc_start: 0.8467 (OUTLIER) cc_final: 0.7929 (p0) REVERT: C 395 TRP cc_start: 0.7824 (OUTLIER) cc_final: 0.7107 (t60) REVERT: C 396 ILE cc_start: 0.8638 (OUTLIER) cc_final: 0.8424 (mt) REVERT: C 425 ASN cc_start: 0.8663 (OUTLIER) cc_final: 0.8442 (t0) REVERT: C 475 MET cc_start: 0.9056 (mmp) cc_final: 0.8856 (mmm) REVERT: D 543 ASN cc_start: 0.9307 (t0) cc_final: 0.8993 (t0) REVERT: D 590 GLN cc_start: 0.8869 (tm-30) cc_final: 0.8635 (tm-30) REVERT: J 52 ASN cc_start: 0.8802 (p0) cc_final: 0.8534 (p0) REVERT: J 82 MET cc_start: 0.9152 (pmm) cc_final: 0.8764 (pmm) REVERT: K 4 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7944 (mt) REVERT: K 31 ASN cc_start: 0.8248 (t0) cc_final: 0.7991 (t0) REVERT: K 47 MET cc_start: 0.6923 (mmm) cc_final: 0.6544 (mmt) REVERT: E 122 LEU cc_start: 0.9424 (tp) cc_final: 0.9128 (tt) REVERT: E 207 LYS cc_start: 0.8825 (mttt) cc_final: 0.7901 (tptt) REVERT: E 210 PHE cc_start: 0.8618 (OUTLIER) cc_final: 0.8375 (m-10) REVERT: E 217 TYR cc_start: 0.7280 (m-80) cc_final: 0.7061 (m-10) REVERT: E 256 SER cc_start: 0.9410 (p) cc_final: 0.8963 (t) REVERT: E 315 GLN cc_start: 0.8887 (pm20) cc_final: 0.8683 (pm20) REVERT: E 475 MET cc_start: 0.8949 (mmm) cc_final: 0.8440 (mmm) REVERT: F 634 GLU cc_start: 0.8951 (tm-30) cc_final: 0.8699 (tm-30) REVERT: F 647 GLU cc_start: 0.8743 (tm-30) cc_final: 0.8478 (tm-30) REVERT: F 654 GLU cc_start: 0.8301 (mt-10) cc_final: 0.8028 (mt-10) REVERT: M 13 GLN cc_start: 0.8576 (pp30) cc_final: 0.8171 (pp30) REVERT: M 23 ARG cc_start: 0.8755 (tmm-80) cc_final: 0.7916 (tmm-80) REVERT: M 46 GLU cc_start: 0.9044 (tp30) cc_final: 0.8752 (mm-30) REVERT: M 81 GLN cc_start: 0.9218 (tt0) cc_final: 0.8641 (tm-30) REVERT: N 49 TYR cc_start: 0.8649 (OUTLIER) cc_final: 0.8111 (p90) REVERT: N 81 ASP cc_start: 0.9194 (t0) cc_final: 0.8903 (m-30) REVERT: N 103 ARG cc_start: 0.8701 (mmm160) cc_final: 0.8402 (mmm160) REVERT: H 34 MET cc_start: 0.8710 (OUTLIER) cc_final: 0.8316 (mtt) REVERT: H 36 TRP cc_start: 0.8903 (m100) cc_final: 0.7775 (m100) REVERT: H 37 MET cc_start: 0.8869 (mmm) cc_final: 0.8502 (mmm) REVERT: H 47 TRP cc_start: 0.8696 (t60) cc_final: 0.8246 (t60) REVERT: H 52 ASN cc_start: 0.8798 (t0) cc_final: 0.8196 (t0) outliers start: 107 outliers final: 72 residues processed: 424 average time/residue: 0.3236 time to fit residues: 214.5659 Evaluate side-chains 412 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 325 time to evaluate : 2.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 35 TRP 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 80 ASN 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 574 LYS 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 92 CYS Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 97 MET Chi-restraints excluded: chain I residue 35 TRP Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 135 THR 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 C residue 425 ASN Chi-restraints excluded: chain D residue 537 LEU 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 110 THR Chi-restraints excluded: chain K residue 4 LEU 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 E residue 90 THR Chi-restraints excluded: chain E residue 210 PHE Chi-restraints excluded: chain E residue 215 ILE 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 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 M residue 48 VAL Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 78 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 18 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 34 MET 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 ************** Weight determination summary: number of chunks: 252 random chunks: chunk 220 optimal weight: 10.0000 chunk 228 optimal weight: 9.9990 chunk 201 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 31 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 241 optimal weight: 3.9990 chunk 123 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 247 optimal weight: 5.9990 chunk 222 optimal weight: 0.9980 overall best weight: 1.3382 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.078907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.064693 restraints weight = 73863.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.066867 restraints weight = 37068.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.068307 restraints weight = 23567.312| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21478 Z= 0.149 Angle : 0.695 12.921 29270 Z= 0.335 Chirality : 0.045 0.252 3434 Planarity : 0.004 0.052 3610 Dihedral : 5.897 48.178 4136 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.03 % Favored : 93.89 % Rotamer: Outliers : 4.40 % Allowed : 24.33 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.17), residues: 2521 helix: 1.40 (0.26), residues: 404 sheet: -0.39 (0.19), residues: 762 loop : -1.35 (0.17), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 427 HIS 0.007 0.001 HIS K 39 PHE 0.037 0.002 PHE M 102 TYR 0.015 0.001 TYR I 30 ARG 0.006 0.001 ARG B 585 Details of bonding type rmsd link_NAG-ASN : bond 0.00290 ( 51) link_NAG-ASN : angle 2.15623 ( 153) link_ALPHA1-6 : bond 0.01004 ( 1) link_ALPHA1-6 : angle 1.30874 ( 3) link_BETA1-4 : bond 0.00301 ( 11) link_BETA1-4 : angle 2.08095 ( 33) link_ALPHA1-3 : bond 0.01353 ( 2) link_ALPHA1-3 : angle 2.17411 ( 6) hydrogen bonds : bond 0.03491 ( 727) hydrogen bonds : angle 5.14931 ( 1995) SS BOND : bond 0.00395 ( 41) SS BOND : angle 1.26309 ( 82) covalent geometry : bond 0.00341 (21372) covalent geometry : angle 0.67236 (28993) *********************** REFINEMENT MACRO_CYCLE 7 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 451 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 353 time to evaluate : 2.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 35 TRP cc_start: 0.7529 (OUTLIER) cc_final: 0.7191 (m-10) REVERT: L 96 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7644 (pp20) REVERT: A 195 ASN cc_start: 0.9096 (p0) cc_final: 0.8315 (t0) REVERT: A 251 ILE cc_start: 0.9048 (mp) cc_final: 0.8577 (pt) REVERT: A 308 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.7960 (ttm110) REVERT: A 482 GLU cc_start: 0.8075 (mp0) cc_final: 0.7570 (mp0) REVERT: B 530 MET cc_start: 0.8932 (tpp) cc_final: 0.8470 (tpp) REVERT: B 656 ASN cc_start: 0.8955 (m-40) cc_final: 0.8506 (m-40) REVERT: G 34 MET cc_start: 0.8656 (mmt) cc_final: 0.8342 (mmt) REVERT: G 72 ASP cc_start: 0.8585 (t0) cc_final: 0.8318 (t0) REVERT: I 35 TRP cc_start: 0.8039 (OUTLIER) cc_final: 0.7602 (m-10) REVERT: I 37 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7722 (pt0) REVERT: I 38 GLN cc_start: 0.8141 (pm20) cc_final: 0.7134 (pm20) REVERT: C 125 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.9099 (mt) REVERT: C 271 MET cc_start: 0.8516 (mmm) cc_final: 0.8003 (mmm) REVERT: C 368 ASP cc_start: 0.8443 (OUTLIER) cc_final: 0.7950 (p0) REVERT: C 395 TRP cc_start: 0.7807 (OUTLIER) cc_final: 0.7097 (t60) REVERT: C 396 ILE cc_start: 0.8677 (OUTLIER) cc_final: 0.8365 (mt) REVERT: C 425 ASN cc_start: 0.8711 (OUTLIER) cc_final: 0.8489 (t0) REVERT: D 529 THR cc_start: 0.9027 (m) cc_final: 0.8695 (m) REVERT: D 543 ASN cc_start: 0.9284 (t0) cc_final: 0.8746 (t0) REVERT: D 590 GLN cc_start: 0.8851 (tm-30) cc_final: 0.8632 (tm-30) REVERT: J 52 ASN cc_start: 0.8976 (p0) cc_final: 0.8636 (p0) REVERT: J 82 MET cc_start: 0.9329 (pmm) cc_final: 0.8836 (pmm) REVERT: K 4 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7926 (mt) REVERT: K 31 ASN cc_start: 0.8308 (t0) cc_final: 0.8030 (t0) REVERT: K 47 MET cc_start: 0.6832 (mmm) cc_final: 0.6472 (mmt) REVERT: E 42 VAL cc_start: 0.9217 (t) cc_final: 0.8878 (p) REVERT: E 122 LEU cc_start: 0.9394 (tp) cc_final: 0.9059 (tt) REVERT: E 207 LYS cc_start: 0.8781 (mttt) cc_final: 0.7855 (tptt) REVERT: E 256 SER cc_start: 0.9370 (p) cc_final: 0.8963 (t) REVERT: E 271 MET cc_start: 0.9151 (mmm) cc_final: 0.8806 (mmm) REVERT: E 421 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8424 (ttpp) REVERT: E 475 MET cc_start: 0.8960 (mmm) cc_final: 0.8427 (mmm) REVERT: F 634 GLU cc_start: 0.8912 (tm-30) cc_final: 0.8669 (tm-30) REVERT: F 647 GLU cc_start: 0.8612 (tm-30) cc_final: 0.8340 (tm-30) REVERT: F 654 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7967 (mt-10) REVERT: M 13 GLN cc_start: 0.8561 (pp30) cc_final: 0.8186 (pp30) REVERT: M 23 ARG cc_start: 0.8689 (tmm-80) cc_final: 0.7998 (ttp80) REVERT: M 46 GLU cc_start: 0.8993 (tp30) cc_final: 0.8715 (mm-30) REVERT: M 81 GLN cc_start: 0.9190 (tt0) cc_final: 0.8699 (tp-100) REVERT: N 49 TYR cc_start: 0.8507 (OUTLIER) cc_final: 0.8064 (p90) REVERT: N 81 ASP cc_start: 0.9172 (t0) cc_final: 0.8908 (m-30) REVERT: N 103 ARG cc_start: 0.8641 (mmm160) cc_final: 0.8331 (mmm160) REVERT: H 32 PHE cc_start: 0.8421 (m-80) cc_final: 0.7957 (m-80) REVERT: H 36 TRP cc_start: 0.8860 (m100) cc_final: 0.7852 (m100) REVERT: H 37 MET cc_start: 0.9012 (mmm) cc_final: 0.8499 (mmm) REVERT: H 39 GLN cc_start: 0.7868 (pp30) cc_final: 0.7415 (tm-30) REVERT: H 47 TRP cc_start: 0.8573 (t60) cc_final: 0.8214 (t60) REVERT: H 52 ASN cc_start: 0.8772 (t0) cc_final: 0.8360 (t0) outliers start: 98 outliers final: 66 residues processed: 423 average time/residue: 0.3098 time to fit residues: 205.0107 Evaluate side-chains 415 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 336 time to evaluate : 2.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 35 TRP 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 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 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 48 VAL Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain I residue 35 TRP Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 135 THR 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 C residue 425 ASN 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 12 VAL Chi-restraints excluded: chain K residue 4 LEU 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 E residue 90 THR Chi-restraints excluded: chain E residue 215 ILE 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 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 639 THR Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 78 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 N residue 97 ILE 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 84 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 208 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 109 optimal weight: 7.9990 chunk 108 optimal weight: 7.9990 chunk 227 optimal weight: 1.9990 chunk 151 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 chunk 168 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 154 optimal weight: 5.9990 chunk 115 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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** ** J 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.078766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.064478 restraints weight = 74093.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.066629 restraints weight = 37170.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.068059 restraints weight = 23690.825| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21478 Z= 0.170 Angle : 0.703 13.067 29270 Z= 0.341 Chirality : 0.045 0.249 3434 Planarity : 0.004 0.047 3610 Dihedral : 5.789 48.561 4136 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.35 % Favored : 93.57 % Rotamer: Outliers : 4.44 % Allowed : 24.46 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.17), residues: 2521 helix: 1.33 (0.26), residues: 406 sheet: -0.36 (0.19), residues: 762 loop : -1.32 (0.17), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP M 36 HIS 0.007 0.001 HIS K 39 PHE 0.020 0.002 PHE M 102 TYR 0.030 0.001 TYR L 32 ARG 0.007 0.001 ARG B 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00267 ( 51) link_NAG-ASN : angle 2.12800 ( 153) link_ALPHA1-6 : bond 0.00668 ( 1) link_ALPHA1-6 : angle 1.33201 ( 3) link_BETA1-4 : bond 0.00279 ( 11) link_BETA1-4 : angle 2.06931 ( 33) link_ALPHA1-3 : bond 0.01404 ( 2) link_ALPHA1-3 : angle 2.19992 ( 6) hydrogen bonds : bond 0.03507 ( 727) hydrogen bonds : angle 5.13385 ( 1995) SS BOND : bond 0.00381 ( 41) SS BOND : angle 1.31814 ( 82) covalent geometry : bond 0.00388 (21372) covalent geometry : angle 0.68097 (28993) *********************** REFINEMENT MACRO_CYCLE 8 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 448 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 349 time to evaluate : 2.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 35 TRP cc_start: 0.7536 (OUTLIER) cc_final: 0.7207 (m-10) REVERT: L 96 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7653 (pp20) REVERT: A 161 MET cc_start: 0.7740 (mmm) cc_final: 0.7526 (mmm) REVERT: A 195 ASN cc_start: 0.9115 (p0) cc_final: 0.8320 (t0) REVERT: A 251 ILE cc_start: 0.8969 (mp) cc_final: 0.8512 (pt) REVERT: A 308 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.7876 (ttm110) REVERT: A 482 GLU cc_start: 0.8090 (mp0) cc_final: 0.7575 (mp0) REVERT: B 530 MET cc_start: 0.8992 (tpp) cc_final: 0.8522 (tpp) REVERT: B 656 ASN cc_start: 0.8959 (m-40) cc_final: 0.8512 (m-40) REVERT: G 19 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8570 (tptt) REVERT: G 34 MET cc_start: 0.8669 (mmt) cc_final: 0.8324 (mmt) REVERT: G 72 ASP cc_start: 0.8668 (t0) cc_final: 0.8385 (t0) REVERT: I 35 TRP cc_start: 0.8079 (OUTLIER) cc_final: 0.7620 (m-10) REVERT: I 37 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.7840 (pt0) REVERT: I 38 GLN cc_start: 0.8161 (pm20) cc_final: 0.7126 (pm20) REVERT: C 271 MET cc_start: 0.8573 (mmm) cc_final: 0.8065 (mmm) REVERT: C 395 TRP cc_start: 0.7788 (OUTLIER) cc_final: 0.6994 (t60) REVERT: C 396 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8376 (mt) REVERT: C 425 ASN cc_start: 0.8738 (OUTLIER) cc_final: 0.8505 (t0) REVERT: C 475 MET cc_start: 0.8972 (mmp) cc_final: 0.8545 (mmp) REVERT: D 529 THR cc_start: 0.9078 (m) cc_final: 0.8763 (m) REVERT: D 543 ASN cc_start: 0.9304 (t0) cc_final: 0.8760 (t0) REVERT: D 590 GLN cc_start: 0.8878 (tm-30) cc_final: 0.8658 (tm-30) REVERT: J 52 ASN cc_start: 0.8963 (p0) cc_final: 0.8617 (p0) REVERT: J 64 LYS cc_start: 0.9303 (tptm) cc_final: 0.9000 (ttmt) REVERT: J 82 MET cc_start: 0.9239 (pmm) cc_final: 0.8830 (pmm) REVERT: K 4 LEU cc_start: 0.8170 (mp) cc_final: 0.7937 (mt) REVERT: K 31 ASN cc_start: 0.8333 (t0) cc_final: 0.8051 (t0) REVERT: K 47 MET cc_start: 0.6870 (mmm) cc_final: 0.6511 (mmt) REVERT: E 42 VAL cc_start: 0.9302 (t) cc_final: 0.8936 (p) REVERT: E 122 LEU cc_start: 0.9353 (tp) cc_final: 0.9043 (tt) REVERT: E 207 LYS cc_start: 0.8789 (mttt) cc_final: 0.7862 (tptt) REVERT: E 256 SER cc_start: 0.9384 (p) cc_final: 0.9007 (t) REVERT: E 271 MET cc_start: 0.9148 (mmm) cc_final: 0.8793 (mmm) REVERT: E 421 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8539 (ttpt) REVERT: E 475 MET cc_start: 0.9013 (mmm) cc_final: 0.8444 (mmm) REVERT: F 616 ASN cc_start: 0.7666 (t0) cc_final: 0.7459 (t0) REVERT: F 626 MET cc_start: 0.8427 (ttt) cc_final: 0.8224 (ttt) REVERT: F 634 GLU cc_start: 0.8919 (tm-30) cc_final: 0.8662 (tm-30) REVERT: F 647 GLU cc_start: 0.8642 (tm-30) cc_final: 0.8366 (tm-30) REVERT: F 654 GLU cc_start: 0.8272 (mt-10) cc_final: 0.7987 (mt-10) REVERT: M 13 GLN cc_start: 0.8506 (pp30) cc_final: 0.8135 (pp30) REVERT: M 23 ARG cc_start: 0.8690 (tmm-80) cc_final: 0.7965 (ttp80) REVERT: M 46 GLU cc_start: 0.9022 (tp30) cc_final: 0.8747 (mm-30) REVERT: N 49 TYR cc_start: 0.8540 (OUTLIER) cc_final: 0.7994 (p90) REVERT: N 81 ASP cc_start: 0.9172 (t0) cc_final: 0.8875 (m-30) REVERT: N 103 ARG cc_start: 0.8664 (mmm160) cc_final: 0.8341 (mmm160) REVERT: H 36 TRP cc_start: 0.8849 (m100) cc_final: 0.7806 (m100) REVERT: H 37 MET cc_start: 0.9055 (mmm) cc_final: 0.8627 (mmm) REVERT: H 39 GLN cc_start: 0.7836 (pp30) cc_final: 0.7391 (tm-30) REVERT: H 47 TRP cc_start: 0.8571 (t60) cc_final: 0.8226 (t60) outliers start: 99 outliers final: 76 residues processed: 423 average time/residue: 0.3090 time to fit residues: 205.0882 Evaluate side-chains 425 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 338 time to evaluate : 2.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 35 TRP 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 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 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 94 THR Chi-restraints excluded: chain G residue 97 MET Chi-restraints excluded: chain I residue 35 TRP Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 228 CYS 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 378 CYS Chi-restraints excluded: chain C residue 387 THR 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 C residue 425 ASN Chi-restraints excluded: chain D residue 580 VAL 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 12 VAL 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 E residue 90 THR Chi-restraints excluded: chain E residue 215 ILE 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 539 VAL Chi-restraints excluded: chain F residue 545 LEU 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 639 THR Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 78 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 N residue 97 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 47 optimal weight: 6.9990 chunk 211 optimal weight: 5.9990 chunk 141 optimal weight: 0.0060 chunk 174 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 246 optimal weight: 3.9990 chunk 195 optimal weight: 5.9990 chunk 187 optimal weight: 6.9990 chunk 172 optimal weight: 0.8980 chunk 235 optimal weight: 8.9990 chunk 75 optimal weight: 10.0000 overall best weight: 3.3802 ------------------------------------------------------------------------------- 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** ** J 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.077054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.062914 restraints weight = 74853.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.065003 restraints weight = 37998.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.066397 restraints weight = 24395.268| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 21478 Z= 0.272 Angle : 0.778 13.716 29270 Z= 0.379 Chirality : 0.046 0.279 3434 Planarity : 0.004 0.048 3610 Dihedral : 6.228 47.186 4136 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.42 % Favored : 92.50 % Rotamer: Outliers : 4.44 % Allowed : 24.55 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.17), residues: 2521 helix: 1.00 (0.26), residues: 406 sheet: -0.44 (0.19), residues: 762 loop : -1.38 (0.17), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP M 36 HIS 0.007 0.001 HIS K 39 PHE 0.021 0.002 PHE M 102 TYR 0.035 0.002 TYR L 32 ARG 0.007 0.001 ARG D 585 Details of bonding type rmsd link_NAG-ASN : bond 0.00362 ( 51) link_NAG-ASN : angle 2.35644 ( 153) link_ALPHA1-6 : bond 0.00632 ( 1) link_ALPHA1-6 : angle 1.50415 ( 3) link_BETA1-4 : bond 0.00254 ( 11) link_BETA1-4 : angle 2.23610 ( 33) link_ALPHA1-3 : bond 0.01156 ( 2) link_ALPHA1-3 : angle 1.97745 ( 6) hydrogen bonds : bond 0.03863 ( 727) hydrogen bonds : angle 5.35219 ( 1995) SS BOND : bond 0.00519 ( 41) SS BOND : angle 1.45877 ( 82) covalent geometry : bond 0.00609 (21372) covalent geometry : angle 0.75404 (28993) *********************** REFINEMENT MACRO_CYCLE 9 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 430 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 331 time to evaluate : 2.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 35 TRP cc_start: 0.7515 (OUTLIER) cc_final: 0.7134 (m-10) REVERT: L 96 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7790 (pp20) REVERT: A 195 ASN cc_start: 0.9161 (p0) cc_final: 0.8435 (t0) REVERT: A 251 ILE cc_start: 0.8988 (mp) cc_final: 0.8540 (pt) REVERT: A 308 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.7998 (ttm110) REVERT: A 482 GLU cc_start: 0.8153 (mp0) cc_final: 0.7578 (mp0) REVERT: B 656 ASN cc_start: 0.8961 (m-40) cc_final: 0.8522 (m-40) REVERT: G 19 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8613 (tptt) REVERT: G 34 MET cc_start: 0.8665 (mmt) cc_final: 0.8309 (mmt) REVERT: G 72 ASP cc_start: 0.8585 (t0) cc_final: 0.8264 (t0) REVERT: I 35 TRP cc_start: 0.8116 (OUTLIER) cc_final: 0.7665 (m-10) REVERT: I 37 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.7796 (pt0) REVERT: I 38 GLN cc_start: 0.8158 (pm20) cc_final: 0.7039 (pm20) REVERT: C 271 MET cc_start: 0.8669 (mmm) cc_final: 0.8173 (mmm) REVERT: C 395 TRP cc_start: 0.7792 (OUTLIER) cc_final: 0.6951 (t60) REVERT: C 396 ILE cc_start: 0.8714 (OUTLIER) cc_final: 0.8411 (mt) REVERT: C 425 ASN cc_start: 0.8710 (OUTLIER) cc_final: 0.8474 (t0) REVERT: C 475 MET cc_start: 0.9032 (mmp) cc_final: 0.8637 (mmp) REVERT: D 543 ASN cc_start: 0.9321 (t0) cc_final: 0.9006 (t0) REVERT: D 590 GLN cc_start: 0.8901 (tm-30) cc_final: 0.8679 (tm-30) REVERT: J 52 ASN cc_start: 0.9005 (p0) cc_final: 0.8608 (p0) REVERT: J 82 MET cc_start: 0.9142 (pmm) cc_final: 0.8814 (pmm) REVERT: K 31 ASN cc_start: 0.8375 (t0) cc_final: 0.8117 (t0) REVERT: K 47 MET cc_start: 0.6941 (mmm) cc_final: 0.6557 (mmt) REVERT: E 122 LEU cc_start: 0.9352 (tp) cc_final: 0.9063 (tt) REVERT: E 207 LYS cc_start: 0.8812 (mttt) cc_final: 0.7893 (tptt) REVERT: E 225 ILE cc_start: 0.9022 (mp) cc_final: 0.8548 (mm) REVERT: E 271 MET cc_start: 0.9098 (mmm) cc_final: 0.8824 (mmm) REVERT: E 421 LYS cc_start: 0.9146 (OUTLIER) cc_final: 0.8507 (ttpp) REVERT: F 616 ASN cc_start: 0.7637 (t0) cc_final: 0.7416 (t0) REVERT: F 634 GLU cc_start: 0.8938 (tm-30) cc_final: 0.8686 (tm-30) REVERT: F 647 GLU cc_start: 0.8705 (tm-30) cc_final: 0.8445 (tm-30) REVERT: F 654 GLU cc_start: 0.8303 (mt-10) cc_final: 0.8012 (mt-10) REVERT: M 23 ARG cc_start: 0.8745 (tmm-80) cc_final: 0.7950 (tmm-80) REVERT: M 46 GLU cc_start: 0.9021 (tp30) cc_final: 0.8735 (mm-30) REVERT: N 49 TYR cc_start: 0.8671 (OUTLIER) cc_final: 0.8153 (p90) REVERT: N 81 ASP cc_start: 0.9190 (t0) cc_final: 0.8891 (m-30) REVERT: H 36 TRP cc_start: 0.9021 (m100) cc_final: 0.8143 (m100) REVERT: H 37 MET cc_start: 0.9083 (mmm) cc_final: 0.8693 (mmm) REVERT: H 39 GLN cc_start: 0.7828 (pp30) cc_final: 0.7364 (tm-30) REVERT: H 47 TRP cc_start: 0.8686 (t60) cc_final: 0.8328 (t60) outliers start: 99 outliers final: 81 residues processed: 405 average time/residue: 0.3192 time to fit residues: 203.8145 Evaluate side-chains 412 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 320 time to evaluate : 2.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 35 TRP 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 56 SER 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 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 94 THR Chi-restraints excluded: chain G residue 97 MET 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 134 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 228 CYS 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 378 CYS Chi-restraints excluded: chain C residue 387 THR 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 C residue 425 ASN Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 606 THR 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 12 VAL 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 E residue 90 THR Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 215 ILE 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 539 VAL Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 56 LEU 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 N residue 97 ILE Chi-restraints excluded: chain N residue 105 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 65 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 169 optimal weight: 0.9990 chunk 142 optimal weight: 8.9990 chunk 232 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 159 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.078806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.064490 restraints weight = 73963.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.066619 restraints weight = 37499.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.068061 restraints weight = 24049.643| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21478 Z= 0.174 Angle : 0.734 13.356 29270 Z= 0.354 Chirality : 0.045 0.244 3434 Planarity : 0.004 0.047 3610 Dihedral : 5.921 47.969 4136 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.11 % Favored : 93.81 % Rotamer: Outliers : 4.40 % Allowed : 24.91 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.17), residues: 2521 helix: 1.17 (0.26), residues: 406 sheet: -0.38 (0.19), residues: 761 loop : -1.38 (0.17), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP M 36 HIS 0.007 0.001 HIS K 39 PHE 0.025 0.002 PHE M 102 TYR 0.038 0.002 TYR H 33 ARG 0.009 0.001 ARG B 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00275 ( 51) link_NAG-ASN : angle 2.20210 ( 153) link_ALPHA1-6 : bond 0.00672 ( 1) link_ALPHA1-6 : angle 1.35215 ( 3) link_BETA1-4 : bond 0.00269 ( 11) link_BETA1-4 : angle 2.01273 ( 33) link_ALPHA1-3 : bond 0.01157 ( 2) link_ALPHA1-3 : angle 2.25518 ( 6) hydrogen bonds : bond 0.03503 ( 727) hydrogen bonds : angle 5.19000 ( 1995) SS BOND : bond 0.00391 ( 41) SS BOND : angle 1.41593 ( 82) covalent geometry : bond 0.00398 (21372) covalent geometry : angle 0.71211 (28993) ********************** REFINEMENT MACRO_CYCLE 10 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 444 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 346 time to evaluate : 2.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 35 TRP cc_start: 0.7573 (OUTLIER) cc_final: 0.7192 (m-10) REVERT: L 96 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7270 (pp20) REVERT: A 195 ASN cc_start: 0.9131 (p0) cc_final: 0.8344 (t0) REVERT: A 251 ILE cc_start: 0.8963 (mp) cc_final: 0.8523 (pt) REVERT: A 308 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.7902 (ttm110) REVERT: A 482 GLU cc_start: 0.8135 (mp0) cc_final: 0.7594 (mp0) REVERT: B 530 MET cc_start: 0.9046 (tpp) cc_final: 0.8563 (tpp) REVERT: B 656 ASN cc_start: 0.8908 (m-40) cc_final: 0.8465 (m-40) REVERT: G 19 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8560 (tptt) REVERT: G 34 MET cc_start: 0.8629 (mmt) cc_final: 0.8360 (mmt) REVERT: G 72 ASP cc_start: 0.8656 (t0) cc_final: 0.8352 (t0) REVERT: I 35 TRP cc_start: 0.8113 (OUTLIER) cc_final: 0.7645 (m-10) REVERT: I 37 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7634 (pt0) REVERT: I 38 GLN cc_start: 0.8147 (pm20) cc_final: 0.7138 (pm20) REVERT: C 69 TRP cc_start: 0.7370 (m-90) cc_final: 0.7036 (m-90) REVERT: C 271 MET cc_start: 0.8623 (mmm) cc_final: 0.8094 (mmm) REVERT: C 395 TRP cc_start: 0.7786 (OUTLIER) cc_final: 0.7031 (t60) REVERT: C 396 ILE cc_start: 0.8817 (OUTLIER) cc_final: 0.8416 (mt) REVERT: C 425 ASN cc_start: 0.8755 (OUTLIER) cc_final: 0.8499 (t0) REVERT: C 475 MET cc_start: 0.8991 (mmp) cc_final: 0.8604 (mmp) REVERT: D 543 ASN cc_start: 0.9315 (t0) cc_final: 0.8787 (t0) REVERT: D 590 GLN cc_start: 0.8916 (tm-30) cc_final: 0.8695 (tm-30) REVERT: J 52 ASN cc_start: 0.8974 (p0) cc_final: 0.8609 (p0) REVERT: J 64 LYS cc_start: 0.9327 (tptm) cc_final: 0.9018 (ttmt) REVERT: J 82 MET cc_start: 0.9087 (pmm) cc_final: 0.8824 (pmm) REVERT: K 31 ASN cc_start: 0.8328 (t0) cc_final: 0.8058 (t0) REVERT: K 47 MET cc_start: 0.6852 (mmm) cc_final: 0.6508 (mmt) REVERT: E 122 LEU cc_start: 0.9301 (tp) cc_final: 0.8995 (tt) REVERT: E 207 LYS cc_start: 0.8803 (mttt) cc_final: 0.7873 (tptt) REVERT: E 225 ILE cc_start: 0.8960 (mp) cc_final: 0.8539 (mm) REVERT: E 256 SER cc_start: 0.9408 (p) cc_final: 0.8984 (t) REVERT: E 271 MET cc_start: 0.9084 (mmm) cc_final: 0.8802 (mmm) REVERT: E 475 MET cc_start: 0.9039 (mmm) cc_final: 0.8270 (mmm) REVERT: F 616 ASN cc_start: 0.7593 (t0) cc_final: 0.7378 (t0) REVERT: F 634 GLU cc_start: 0.8907 (tm-30) cc_final: 0.8660 (tm-30) REVERT: F 647 GLU cc_start: 0.8646 (tm-30) cc_final: 0.8367 (tm-30) REVERT: F 654 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7984 (mt-10) REVERT: M 13 GLN cc_start: 0.8474 (pp30) cc_final: 0.8149 (pp30) REVERT: M 23 ARG cc_start: 0.8696 (tmm-80) cc_final: 0.7868 (tmm-80) REVERT: M 46 GLU cc_start: 0.9001 (tp30) cc_final: 0.8749 (mm-30) REVERT: M 81 GLN cc_start: 0.9211 (tt0) cc_final: 0.8677 (tp-100) REVERT: N 49 TYR cc_start: 0.8585 (OUTLIER) cc_final: 0.8092 (p90) REVERT: N 53 GLN cc_start: 0.8867 (mm-40) cc_final: 0.8418 (mm-40) REVERT: N 54 ARG cc_start: 0.9078 (OUTLIER) cc_final: 0.8407 (ttm170) REVERT: N 81 ASP cc_start: 0.9161 (t0) cc_final: 0.8907 (m-30) REVERT: H 32 PHE cc_start: 0.8216 (m-80) cc_final: 0.7993 (m-80) REVERT: H 36 TRP cc_start: 0.8904 (m100) cc_final: 0.7835 (m100) REVERT: H 37 MET cc_start: 0.9040 (mmm) cc_final: 0.8623 (mmm) REVERT: H 39 GLN cc_start: 0.7822 (pp30) cc_final: 0.7371 (tm-30) REVERT: H 47 TRP cc_start: 0.8509 (t60) cc_final: 0.8015 (t60) outliers start: 98 outliers final: 80 residues processed: 416 average time/residue: 0.3145 time to fit residues: 202.8218 Evaluate side-chains 424 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 333 time to evaluate : 2.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 35 TRP 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 56 SER 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 265 LEU 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 94 THR Chi-restraints excluded: chain G residue 97 MET Chi-restraints excluded: chain I residue 35 TRP Chi-restraints excluded: chain I residue 37 GLN 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 122 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 228 CYS 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 378 CYS Chi-restraints excluded: chain C residue 387 THR 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 C residue 425 ASN Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 606 THR 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 12 VAL 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 E residue 90 THR Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 215 ILE 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 539 VAL Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 56 LEU 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 54 ARG Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 97 ILE 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 73 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 108 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 139 optimal weight: 0.9980 chunk 171 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 239 optimal weight: 4.9990 chunk 103 optimal weight: 0.0060 chunk 20 optimal weight: 2.9990 chunk 152 optimal weight: 0.1980 chunk 73 optimal weight: 0.0470 chunk 221 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 188 optimal weight: 2.9990 overall best weight: 0.8496 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.079895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.065562 restraints weight = 73765.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.067733 restraints weight = 37041.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.069176 restraints weight = 23563.150| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21478 Z= 0.130 Angle : 0.712 12.592 29270 Z= 0.344 Chirality : 0.045 0.217 3434 Planarity : 0.004 0.045 3610 Dihedral : 5.489 49.900 4136 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.67 % Favored : 94.25 % Rotamer: Outliers : 3.86 % Allowed : 25.49 % Favored : 70.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.17), residues: 2521 helix: 1.36 (0.27), residues: 406 sheet: -0.27 (0.19), residues: 749 loop : -1.29 (0.17), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP M 36 HIS 0.007 0.001 HIS K 39 PHE 0.020 0.001 PHE J 102 TYR 0.033 0.001 TYR H 33 ARG 0.007 0.001 ARG D 585 Details of bonding type rmsd link_NAG-ASN : bond 0.00276 ( 51) link_NAG-ASN : angle 1.93683 ( 153) link_ALPHA1-6 : bond 0.00655 ( 1) link_ALPHA1-6 : angle 1.33943 ( 3) link_BETA1-4 : bond 0.00336 ( 11) link_BETA1-4 : angle 1.88323 ( 33) link_ALPHA1-3 : bond 0.01151 ( 2) link_ALPHA1-3 : angle 2.30214 ( 6) hydrogen bonds : bond 0.03300 ( 727) hydrogen bonds : angle 5.03736 ( 1995) SS BOND : bond 0.00355 ( 41) SS BOND : angle 1.22939 ( 82) covalent geometry : bond 0.00301 (21372) covalent geometry : angle 0.69418 (28993) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6783.00 seconds wall clock time: 118 minutes 58.02 seconds (7138.02 seconds total)