Starting phenix.real_space_refine on Tue Jun 17 09:59:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tq1_41498/06_2025/8tq1_41498.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tq1_41498/06_2025/8tq1_41498.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tq1_41498/06_2025/8tq1_41498.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tq1_41498/06_2025/8tq1_41498.map" model { file = "/net/cci-nas-00/data/ceres_data/8tq1_41498/06_2025/8tq1_41498.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tq1_41498/06_2025/8tq1_41498.cif" } resolution = 3.3 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= -0.001 sd= 0.031 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 132 5.16 5 C 12387 2.51 5 N 3316 2.21 5 O 3953 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 19788 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 3414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3414 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 22, 'TRANS': 409} Chain breaks: 4 Chain: "B" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 981 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "C" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 928 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "D" 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: "J" Number of atoms: 3422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3422 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 22, 'TRANS': 410} Chain breaks: 4 Chain: "K" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "M" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 928 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} 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: "E" Number of atoms: 3421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3421 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 22, 'TRANS': 410} Chain breaks: 4 Chain: "F" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 966 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "G" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 928 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} 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: "H" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 304 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "L" 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: "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: 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: "R" 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: "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: 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: "V" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Y" 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: "A" 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: "B" 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: "J" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "K" 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: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "F" 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 Time building chain proxies: 13.42, per 1000 atoms: 0.68 Number of scatterers: 19788 At special positions: 0 Unit cell: (125.4, 120.175, 164.065, 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 132 16.00 O 3953 8.00 N 3316 7.00 C 12387 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 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=1.48 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 B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS J 54 " - pdb=" SG CYS J 74 " distance=2.06 Simple disulfide: pdb=" SG CYS J 119 " - pdb=" SG CYS J 205 " distance=2.03 Simple disulfide: pdb=" SG CYS J 126 " - pdb=" SG CYS J 196 " distance=2.03 Simple disulfide: pdb=" SG CYS J 131 " - pdb=" SG CYS J 157 " distance=2.03 Simple disulfide: pdb=" SG CYS J 218 " - pdb=" SG CYS J 247 " distance=2.03 Simple disulfide: pdb=" SG CYS J 228 " - pdb=" SG CYS J 239 " distance=2.03 Simple disulfide: pdb=" SG CYS J 296 " - pdb=" SG CYS J 331 " distance=2.03 Simple disulfide: pdb=" SG CYS J 378 " - pdb=" SG CYS J 445 " distance=2.03 Simple disulfide: pdb=" SG CYS J 385 " - pdb=" SG CYS J 418 " distance=2.03 Simple disulfide: pdb=" SG CYS J 501 " - pdb=" SG CYS K 605 " distance=2.20 Simple disulfide: pdb=" SG CYS K 598 " - pdb=" SG CYS K 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=2.04 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 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 G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 109 " - pdb=" SG CYS H 119 " distance=2.03 Simple disulfide: pdb=" SG CYS H 115 " - pdb=" SG CYS H 124 " distance=2.03 Simple disulfide: pdb=" SG CYS H 120 " - pdb=" SG CYS H 131 " distance=2.03 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 Q 3 " - " MAN Q 4 " " BMA U 3 " - " MAN U 4 " " BMA V 3 " - " MAN V 4 " " BMA X 3 " - " MAN X 4 " ALPHA1-6 " BMA Q 3 " - " MAN Q 5 " " BMA U 3 " - " MAN U 5 " BETA1-4 " NAG L 1 " - " NAG L 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " 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 W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 234 " " NAG A 604 " - " ASN A 276 " " NAG A 605 " - " ASN A 295 " " NAG A 606 " - " ASN A 301 " " NAG A 607 " - " ASN A 339 " " NAG A 608 " - " ASN A 355 " " NAG A 609 " - " ASN A 363 " " NAG A 610 " - " ASN A 392 " " NAG A 611 " - " ASN A 386 " " NAG A 612 " - " ASN A 448 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 133 " " 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 339 " " NAG E 608 " - " ASN E 355 " " NAG E 609 " - " ASN E 363 " " NAG E 610 " - " ASN E 392 " " NAG E 611 " - " ASN E 197 " " NAG E 612 " - " ASN E 386 " " NAG E 613 " - " ASN E 448 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 637 " " NAG J 601 " - " ASN J 88 " " NAG J 602 " - " ASN J 133 " " NAG J 603 " - " ASN J 234 " " NAG J 604 " - " ASN J 276 " " NAG J 605 " - " ASN J 295 " " NAG J 606 " - " ASN J 301 " " NAG J 607 " - " ASN J 332 " " NAG J 608 " - " ASN J 339 " " NAG J 609 " - " ASN J 355 " " NAG J 610 " - " ASN J 392 " " NAG J 611 " - " ASN J 197 " " NAG J 612 " - " ASN J 386 " " NAG J 613 " - " ASN J 363 " " NAG J 614 " - " ASN J 448 " " NAG K 701 " - " ASN K 611 " " NAG K 702 " - " ASN K 637 " " NAG L 1 " - " ASN A 160 " " NAG O 1 " - " ASN A 156 " " NAG P 1 " - " ASN A 197 " " NAG Q 1 " - " ASN A 262 " " NAG R 1 " - " ASN A 332 " " NAG S 1 " - " ASN J 160 " " NAG T 1 " - " ASN J 156 " " NAG U 1 " - " ASN J 262 " " NAG V 1 " - " ASN E 160 " " NAG W 1 " - " ASN E 156 " " NAG X 1 " - " ASN E 262 " " NAG Y 1 " - " ASN E 332 " Time building additional restraints: 5.69 Conformation dependent library (CDL) restraints added in 2.6 seconds 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4410 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 45 sheets defined 21.6% alpha, 38.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.13 Creating SS restraints... Processing helix chain 'A' and resid 98 through 117 removed outlier: 3.919A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 334 through 354 removed outlier: 3.850A 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 391 Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.559A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.433A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 542 Processing helix chain 'B' and resid 569 through 596 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 661 Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 61 through 64 Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.562A pdb=" N GLU D 83 " --> pdb=" O ALA D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 95B removed outlier: 4.342A pdb=" N THR D 95A" --> pdb=" O ALA D 92 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 117 removed outlier: 4.027A pdb=" N GLU J 102 " --> pdb=" O ASN J 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 126 Processing helix chain 'J' and resid 139 through 151 Processing helix chain 'J' and resid 195 through 198 Processing helix chain 'J' and resid 334 through 354 removed outlier: 3.906A pdb=" N HIS J 352 " --> pdb=" O GLN J 348 " (cutoff:3.500A) Processing helix chain 'J' and resid 368 through 373 Processing helix chain 'J' and resid 387 through 390 Processing helix chain 'J' and resid 475 through 484 Processing helix chain 'K' and resid 523 through 528 removed outlier: 4.383A pdb=" N GLY K 527 " --> pdb=" O GLY K 524 " (cutoff:3.500A) Processing helix chain 'K' and resid 536 through 542 Processing helix chain 'K' and resid 569 through 596 Processing helix chain 'K' and resid 618 through 625 Processing helix chain 'K' and resid 627 through 635 Processing helix chain 'K' and resid 638 through 659 Processing helix chain 'M' and resid 28 through 32 Processing helix chain 'M' and resid 61 through 64 Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.582A pdb=" N GLU N 83 " --> pdb=" O ALA N 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.194A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 139 through 151 Processing helix chain 'E' and resid 195 through 198 Processing helix chain 'E' and resid 335 through 354 removed outlier: 3.903A 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 480 Processing helix chain 'F' and resid 536 through 542 Processing helix chain 'F' and resid 543 through 545 No H-bonds generated for 'chain 'F' and resid 543 through 545' Processing helix chain 'F' and resid 570 through 571 No H-bonds generated for 'chain 'F' and resid 570 through 571' Processing helix chain 'F' and resid 572 through 596 Processing helix chain 'F' and resid 619 through 625 removed outlier: 3.515A pdb=" N ASN F 625 " --> pdb=" O GLU F 621 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 660 Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 61 through 64 Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'I' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.390A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR B 606 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.989A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N THR A 236 " --> pdb=" O GLU A 92 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N GLU A 92 " --> pdb=" O THR A 236 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N THR A 90 " --> pdb=" O PRO A 238 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N ASN A 88 " --> pdb=" O PRO A 240 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA5, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.644A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 259 through 261 removed outlier: 3.602A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 10.272A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 10.879A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 9.771A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.128A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.488A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.239A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 8.982A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 9.964A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.903A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 9.964A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 8.982A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.239A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.488A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.128A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.771A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 10.879A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.272A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.955A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 3 through 8 Processing sheet with id=AB1, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.985A pdb=" N MET C 34 " --> pdb=" O LEU C 50 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N LEU C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.934A pdb=" N CYS C 92 " --> pdb=" O TRP C 103 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N TRP C 103 " --> pdb=" O CYS C 92 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N THR C 94 " --> pdb=" O ASP C 101 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 9 through 13 removed outlier: 6.326A pdb=" N TRP D 35 " --> pdb=" O MET D 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 9 through 13 Processing sheet with id=AB5, first strand: chain 'D' and resid 19 through 24 Processing sheet with id=AB6, first strand: chain 'J' and resid 494 through 499 removed outlier: 5.363A pdb=" N VAL K 608 " --> pdb=" O VAL J 36 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N VAL J 38 " --> pdb=" O THR K 606 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N THR K 606 " --> pdb=" O VAL J 38 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N TYR J 40 " --> pdb=" O CYS K 604 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N CYS K 604 " --> pdb=" O TYR J 40 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 45 through 47 removed outlier: 3.791A pdb=" N ILE J 225 " --> pdb=" O VAL J 245 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N VAL J 242 " --> pdb=" O LEU J 86 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 75 through 76 removed outlier: 6.557A pdb=" N CYS J 54 " --> pdb=" O VAL J 75 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 91 through 94 Processing sheet with id=AC1, first strand: chain 'J' and resid 169 through 177 Processing sheet with id=AC2, first strand: chain 'J' and resid 200 through 203 removed outlier: 6.627A pdb=" N ALA J 200 " --> pdb=" O ALA J 433 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N TYR J 435 " --> pdb=" O ALA J 200 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N THR J 202 " --> pdb=" O TYR J 435 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 259 through 261 removed outlier: 3.623A pdb=" N GLY J 451 " --> pdb=" O LEU J 260 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N GLY J 441 " --> pdb=" O ASN J 300 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N ASN J 300 " --> pdb=" O GLY J 441 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLY J 451 " --> pdb=" O THR J 290 " (cutoff:3.500A) removed outlier: 10.681A pdb=" N THR J 290 " --> pdb=" O GLY J 451 " (cutoff:3.500A) removed outlier: 11.961A pdb=" N ILE J 453 " --> pdb=" O PHE J 288 " (cutoff:3.500A) removed outlier: 11.924A pdb=" N PHE J 288 " --> pdb=" O ILE J 453 " (cutoff:3.500A) removed outlier: 10.857A pdb=" N THR J 455 " --> pdb=" O VAL J 286 " (cutoff:3.500A) removed outlier: 10.521A pdb=" N VAL J 286 " --> pdb=" O THR J 455 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA J 329 " --> pdb=" O CYS J 418 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N PHE J 382 " --> pdb=" O LYS J 421 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 271 through 274 removed outlier: 10.521A pdb=" N VAL J 286 " --> pdb=" O THR J 455 " (cutoff:3.500A) removed outlier: 10.857A pdb=" N THR J 455 " --> pdb=" O VAL J 286 " (cutoff:3.500A) removed outlier: 11.924A pdb=" N PHE J 288 " --> pdb=" O ILE J 453 " (cutoff:3.500A) removed outlier: 11.961A pdb=" N ILE J 453 " --> pdb=" O PHE J 288 " (cutoff:3.500A) removed outlier: 10.681A pdb=" N THR J 290 " --> pdb=" O GLY J 451 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLY J 451 " --> pdb=" O THR J 290 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N ASN J 300 " --> pdb=" O GLY J 441 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N GLY J 441 " --> pdb=" O ASN J 300 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ILE J 358 " --> pdb=" O GLU J 466 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N PHE J 468 " --> pdb=" O ILE J 358 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ARG J 360 " --> pdb=" O PHE J 468 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 304 through 312 removed outlier: 6.344A pdb=" N GLN J 315 " --> pdb=" O ILE J 309 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 3 through 8 Processing sheet with id=AC7, first strand: chain 'M' and resid 57 through 59 removed outlier: 6.723A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N LEU M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N MET M 34 " --> pdb=" O LEU M 50 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N CYS M 92 " --> pdb=" O TRP M 103 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N TRP M 103 " --> pdb=" O CYS M 92 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N THR M 94 " --> pdb=" O ASP M 101 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 57 through 59 removed outlier: 6.723A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N LEU M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N MET M 34 " --> pdb=" O LEU M 50 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 9 through 13 removed outlier: 6.583A pdb=" N VAL N 11 " --> pdb=" O THR N 105 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N TRP N 35 " --> pdb=" O MET N 47 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 9 through 13 removed outlier: 6.583A pdb=" N VAL N 11 " --> pdb=" O THR N 105 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 19 through 24 Processing sheet with id=AD3, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.205A pdb=" N VAL E 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.870A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 75 through 76 removed outlier: 6.913A pdb=" N CYS E 54 " --> pdb=" O VAL E 75 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AD7, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AD8, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.573A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 259 through 261 removed outlier: 10.433A pdb=" N VAL E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 11.112A pdb=" N CYS E 296 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 9.978A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.490A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.861A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.447A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 8.952A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 9.927A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N THR E 450 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 271 through 274 removed outlier: 6.684A pdb=" N THR E 450 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 9.927A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 8.952A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.447A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.861A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.490A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.978A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.112A pdb=" N CYS E 296 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 10.433A pdb=" N VAL E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 307 through 312 removed outlier: 6.410A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AE4, first strand: chain 'G' and resid 57 through 59 removed outlier: 6.578A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N LEU G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N MET G 34 " --> pdb=" O LEU G 50 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N CYS G 92 " --> pdb=" O TRP G 103 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N TRP G 103 " --> pdb=" O CYS G 92 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N THR G 94 " --> pdb=" O ASP G 101 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 57 through 59 removed outlier: 6.578A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N LEU G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N MET G 34 " --> pdb=" O LEU G 50 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 9 through 13 removed outlier: 6.330A pdb=" N TRP I 35 " --> pdb=" O MET I 47 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 9 through 13 removed outlier: 5.279A pdb=" N PHE I 95B" --> pdb=" O ALA I 92 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 19 through 24 Processing sheet with id=AE9, first strand: chain 'H' and resid 113 through 115 808 hydrogen bonds defined for protein. 2082 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: 8.01 Time building geometry restraints manager: 6.70 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: 3613 1.33 - 1.46: 6925 1.46 - 1.59: 9461 1.59 - 1.72: 0 1.72 - 1.85: 180 Bond restraints: 20179 Sorted by residual: bond pdb=" C LYS E 502 " pdb=" O LYS E 502 " ideal model delta sigma weight residual 1.235 1.195 0.039 1.18e-02 7.18e+03 1.11e+01 bond pdb=" C3 BMA U 3 " pdb=" O3 BMA U 3 " ideal model delta sigma weight residual 1.406 1.464 -0.058 2.00e-02 2.50e+03 8.55e+00 bond pdb=" N CYS J 74 " pdb=" CA CYS J 74 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.31e-02 5.83e+03 7.84e+00 bond pdb=" N CYS A 74 " pdb=" CA CYS A 74 " ideal model delta sigma weight residual 1.456 1.488 -0.033 1.22e-02 6.72e+03 7.11e+00 bond pdb=" N LYS J 502 " pdb=" CA LYS J 502 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.21e-02 6.83e+03 6.83e+00 ... (remaining 20174 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 25942 2.40 - 4.80: 1251 4.80 - 7.19: 160 7.19 - 9.59: 18 9.59 - 11.99: 5 Bond angle restraints: 27376 Sorted by residual: angle pdb=" N GLY G 8 " pdb=" CA GLY G 8 " pdb=" C GLY G 8 " ideal model delta sigma weight residual 112.73 120.42 -7.69 1.20e+00 6.94e-01 4.11e+01 angle pdb=" CA PRO E 206 " pdb=" N PRO E 206 " pdb=" CD PRO E 206 " ideal model delta sigma weight residual 112.00 103.90 8.10 1.40e+00 5.10e-01 3.35e+01 angle pdb=" CA PHE A 53 " pdb=" CB PHE A 53 " pdb=" CG PHE A 53 " ideal model delta sigma weight residual 113.80 119.36 -5.56 1.00e+00 1.00e+00 3.09e+01 angle pdb=" C LEU A 52 " pdb=" N PHE A 53 " pdb=" CA PHE A 53 " ideal model delta sigma weight residual 122.73 113.52 9.21 1.92e+00 2.71e-01 2.30e+01 angle pdb=" CA THR J 499 " pdb=" C THR J 499 " pdb=" O THR J 499 " ideal model delta sigma weight residual 121.33 116.25 5.08 1.08e+00 8.57e-01 2.21e+01 ... (remaining 27371 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.58: 12453 21.58 - 43.16: 431 43.16 - 64.74: 116 64.74 - 86.32: 45 86.32 - 107.91: 26 Dihedral angle restraints: 13071 sinusoidal: 6199 harmonic: 6872 Sorted by residual: dihedral pdb=" CB CYS J 126 " pdb=" SG CYS J 126 " pdb=" SG CYS J 196 " pdb=" CB CYS J 196 " ideal model delta sinusoidal sigma weight residual 93.00 160.31 -67.31 1 1.00e+01 1.00e-02 5.90e+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 93.00 153.76 -60.76 1 1.00e+01 1.00e-02 4.91e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 149.48 -56.48 1 1.00e+01 1.00e-02 4.30e+01 ... (remaining 13068 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2525 0.071 - 0.141: 639 0.141 - 0.212: 109 0.212 - 0.282: 8 0.282 - 0.353: 8 Chirality restraints: 3289 Sorted by residual: chirality pdb=" C1 NAG E 613 " pdb=" ND2 ASN E 448 " pdb=" C2 NAG E 613 " pdb=" O5 NAG E 613 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.12e+00 chirality pdb=" C5 BMA V 3 " pdb=" C4 BMA V 3 " pdb=" C6 BMA V 3 " pdb=" O5 BMA V 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.61 0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" CB ILE H 117 " pdb=" CA ILE H 117 " pdb=" CG1 ILE H 117 " pdb=" CG2 ILE H 117 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.67e+00 ... (remaining 3286 not shown) Planarity restraints: 3441 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG J 504 " 0.597 9.50e-02 1.11e+02 2.68e-01 4.37e+01 pdb=" NE ARG J 504 " -0.035 2.00e-02 2.50e+03 pdb=" CZ ARG J 504 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG J 504 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG J 504 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS E 205 " -0.087 5.00e-02 4.00e+02 1.26e-01 2.55e+01 pdb=" N PRO E 206 " 0.218 5.00e-02 4.00e+02 pdb=" CA PRO E 206 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO E 206 " -0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA F 582 " -0.022 2.00e-02 2.50e+03 4.36e-02 1.90e+01 pdb=" C ALA F 582 " 0.075 2.00e-02 2.50e+03 pdb=" O ALA F 582 " -0.028 2.00e-02 2.50e+03 pdb=" N VAL F 583 " -0.025 2.00e-02 2.50e+03 ... (remaining 3438 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 363 2.67 - 3.22: 17872 3.22 - 3.78: 29998 3.78 - 4.34: 42522 4.34 - 4.90: 69363 Nonbonded interactions: 160118 Sorted by model distance: nonbonded pdb=" O GLY C 96 " pdb=" OH TYR D 96 " model vdw 2.108 3.040 nonbonded pdb=" NE2 GLN D 17 " pdb=" O SER D 18 " model vdw 2.139 3.120 nonbonded pdb=" NH1 ARG A 178 " pdb=" O VAL A 181 " model vdw 2.244 3.120 nonbonded pdb=" O PHE C 29 " pdb=" NH2 ARG C 71 " model vdw 2.256 3.120 nonbonded pdb=" O PHE G 29 " pdb=" NH2 ARG G 71 " model vdw 2.279 3.120 ... (remaining 160113 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 185 or resid 189 through 503 or resid 601 throu \ gh 612)) selection = (chain 'E' and (resid 33 through 457 or resid 464 through 503 or resid 602 throu \ gh 613)) selection = (chain 'J' and (resid 33 through 503 or resid 603 through 614)) } ncs_group { reference = (chain 'B' and (resid 520 through 545 or resid 570 through 664 or resid 701 thro \ ugh 702)) selection = chain 'F' selection = (chain 'K' and (resid 520 through 545 or resid 570 through 664 or resid 701 thro \ ugh 702)) } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'M' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'N' } ncs_group { reference = chain 'L' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'W' selection = chain 'Y' } ncs_group { reference = chain 'Q' selection = chain 'U' } ncs_group { reference = chain 'V' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.330 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: 0.030 Extract box with map and model: 0.820 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 50.940 Find NCS groups from input model: 1.330 Set up NCS constraints: 0.240 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: 0.020 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 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 0.547 20299 Z= 0.390 Angle : 1.220 30.833 27695 Z= 0.673 Chirality : 0.065 0.353 3289 Planarity : 0.009 0.268 3384 Dihedral : 13.271 107.905 8538 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 1.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.24 % Allowed : 4.95 % Favored : 94.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.17), residues: 2344 helix: 0.66 (0.25), residues: 386 sheet: 0.72 (0.19), residues: 677 loop : 0.65 (0.17), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP A 479 HIS 0.009 0.002 HIS E 374 PHE 0.031 0.003 PHE A 53 TYR 0.027 0.003 TYR I 49 ARG 0.025 0.002 ARG A 500 Details of bonding type rmsd link_NAG-ASN : bond 0.00359 ( 57) link_NAG-ASN : angle 2.77283 ( 171) link_ALPHA1-6 : bond 0.00944 ( 2) link_ALPHA1-6 : angle 0.84569 ( 6) link_BETA1-4 : bond 0.00678 ( 16) link_BETA1-4 : angle 3.66502 ( 48) link_ALPHA1-3 : bond 0.00642 ( 4) link_ALPHA1-3 : angle 2.71976 ( 12) hydrogen bonds : bond 0.14654 ( 750) hydrogen bonds : angle 7.53961 ( 2082) SS BOND : bond 0.08953 ( 41) SS BOND : angle 4.38661 ( 82) covalent geometry : bond 0.00716 (20179) covalent geometry : angle 1.17210 (27376) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 365 time to evaluate : 2.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 TYR cc_start: 0.8317 (m-80) cc_final: 0.8032 (m-80) REVERT: B 588 ARG cc_start: 0.8563 (mtm110) cc_final: 0.8357 (mtt-85) REVERT: J 114 GLN cc_start: 0.8270 (mm-40) cc_final: 0.7988 (mm-40) REVERT: J 320 THR cc_start: 0.9422 (m) cc_final: 0.9032 (p) REVERT: J 426 MET cc_start: 0.8512 (tpp) cc_final: 0.8212 (mmm) REVERT: K 581 LEU cc_start: 0.8980 (tp) cc_final: 0.8727 (tp) REVERT: K 601 LYS cc_start: 0.9040 (mtmm) cc_final: 0.8650 (mtpt) REVERT: K 636 SER cc_start: 0.9126 (t) cc_final: 0.8808 (p) REVERT: E 217 TYR cc_start: 0.8743 (m-80) cc_final: 0.8364 (m-80) REVERT: E 371 VAL cc_start: 0.9345 (t) cc_final: 0.9107 (p) REVERT: F 601 LYS cc_start: 0.8988 (mttp) cc_final: 0.8784 (mtmm) REVERT: G 68 THR cc_start: 0.9139 (m) cc_final: 0.8895 (p) REVERT: I 30 TYR cc_start: 0.8959 (m-80) cc_final: 0.8748 (m-80) REVERT: I 45 LYS cc_start: 0.8720 (tttt) cc_final: 0.8501 (tttt) outliers start: 5 outliers final: 2 residues processed: 367 average time/residue: 0.3475 time to fit residues: 186.6360 Evaluate side-chains 269 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 267 time to evaluate : 2.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 83 GLU Chi-restraints excluded: chain E residue 502 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 198 optimal weight: 2.9990 chunk 178 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 184 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 213 optimal weight: 0.8980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82AHIS D 69 ASN J 302 ASN K 607 ASN K 630 GLN ** M 82AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 ASN F 625 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.095829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.074839 restraints weight = 39574.798| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.43 r_work: 0.2893 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 20299 Z= 0.255 Angle : 0.722 12.769 27695 Z= 0.370 Chirality : 0.049 0.283 3289 Planarity : 0.004 0.040 3384 Dihedral : 8.686 82.278 4215 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.73 % Allowed : 7.07 % Favored : 91.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.17), residues: 2344 helix: 1.39 (0.26), residues: 405 sheet: 0.49 (0.19), residues: 741 loop : 0.27 (0.18), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 479 HIS 0.006 0.001 HIS E 105 PHE 0.016 0.002 PHE M 29 TYR 0.018 0.002 TYR N 96 ARG 0.008 0.001 ARG E 500 Details of bonding type rmsd link_NAG-ASN : bond 0.00285 ( 57) link_NAG-ASN : angle 2.10449 ( 171) link_ALPHA1-6 : bond 0.00995 ( 2) link_ALPHA1-6 : angle 1.70092 ( 6) link_BETA1-4 : bond 0.00577 ( 16) link_BETA1-4 : angle 2.48824 ( 48) link_ALPHA1-3 : bond 0.00543 ( 4) link_ALPHA1-3 : angle 4.00421 ( 12) hydrogen bonds : bond 0.05052 ( 750) hydrogen bonds : angle 5.70790 ( 2082) SS BOND : bond 0.00512 ( 41) SS BOND : angle 1.22485 ( 82) covalent geometry : bond 0.00591 (20179) covalent geometry : angle 0.69011 (27376) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 292 time to evaluate : 2.148 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 19 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8619 (tptm) REVERT: C 72 ASP cc_start: 0.8297 (t70) cc_final: 0.8054 (t0) REVERT: C 75 LYS cc_start: 0.9116 (mttp) cc_final: 0.8915 (mttp) REVERT: J 141 ASP cc_start: 0.8097 (m-30) cc_final: 0.7855 (t0) REVERT: J 320 THR cc_start: 0.9469 (m) cc_final: 0.9002 (p) REVERT: K 636 SER cc_start: 0.9238 (t) cc_final: 0.8883 (p) REVERT: M 3 GLN cc_start: 0.8325 (mm-40) cc_final: 0.8093 (mm110) REVERT: F 648 GLU cc_start: 0.8398 (tp30) cc_final: 0.7961 (tp30) REVERT: G 75 LYS cc_start: 0.9203 (mptt) cc_final: 0.8969 (mmtm) outliers start: 36 outliers final: 24 residues processed: 315 average time/residue: 0.3686 time to fit residues: 170.3730 Evaluate side-chains 282 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 257 time to evaluate : 2.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain B residue 607 ASN Chi-restraints excluded: chain C residue 19 LYS Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain J residue 72 HIS Chi-restraints excluded: chain J residue 505 VAL Chi-restraints excluded: chain K residue 599 SER Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 52 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 337 THR Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 664 ASP Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain I residue 5 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 195 optimal weight: 0.7980 chunk 190 optimal weight: 0.7980 chunk 157 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 146 optimal weight: 7.9990 chunk 63 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 ASN J 130 GLN H 122 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.097192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.076180 restraints weight = 39260.034| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.49 r_work: 0.2907 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 20299 Z= 0.139 Angle : 0.601 10.185 27695 Z= 0.304 Chirality : 0.045 0.302 3289 Planarity : 0.004 0.035 3384 Dihedral : 7.454 70.245 4208 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.30 % Allowed : 8.22 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.69 (0.17), residues: 2344 helix: 1.62 (0.27), residues: 412 sheet: 0.53 (0.19), residues: 739 loop : 0.10 (0.18), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 479 HIS 0.004 0.001 HIS J 105 PHE 0.016 0.002 PHE A 53 TYR 0.019 0.001 TYR G 27 ARG 0.012 0.001 ARG A 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00215 ( 57) link_NAG-ASN : angle 1.85185 ( 171) link_ALPHA1-6 : bond 0.01438 ( 2) link_ALPHA1-6 : angle 1.20548 ( 6) link_BETA1-4 : bond 0.00539 ( 16) link_BETA1-4 : angle 2.18605 ( 48) link_ALPHA1-3 : bond 0.00608 ( 4) link_ALPHA1-3 : angle 3.69210 ( 12) hydrogen bonds : bond 0.04047 ( 750) hydrogen bonds : angle 5.23354 ( 2082) SS BOND : bond 0.00450 ( 41) SS BOND : angle 1.15101 ( 82) covalent geometry : bond 0.00313 (20179) covalent geometry : angle 0.57069 (27376) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 292 time to evaluate : 2.350 Fit side-chains revert: symmetry clash REVERT: A 161 MET cc_start: 0.9244 (tpp) cc_final: 0.8338 (tpt) REVERT: A 381 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7797 (mm-30) REVERT: B 588 ARG cc_start: 0.8822 (mtm110) cc_final: 0.8312 (mtt-85) REVERT: C 72 ASP cc_start: 0.8269 (t70) cc_final: 0.8066 (t0) REVERT: J 78 ASP cc_start: 0.6801 (t0) cc_final: 0.6358 (p0) REVERT: J 114 GLN cc_start: 0.8287 (mm-40) cc_final: 0.8078 (mm-40) REVERT: J 141 ASP cc_start: 0.8054 (m-30) cc_final: 0.7814 (t0) REVERT: J 150 MET cc_start: 0.8725 (mmm) cc_final: 0.8301 (tpp) REVERT: K 636 SER cc_start: 0.9211 (t) cc_final: 0.8889 (p) REVERT: M 83 ARG cc_start: 0.8160 (ttm110) cc_final: 0.7847 (mtm180) REVERT: N 42 LYS cc_start: 0.8845 (mmmt) cc_final: 0.8574 (tptp) REVERT: E 95 MET cc_start: 0.9384 (ptm) cc_final: 0.9081 (ptm) REVERT: E 150 MET cc_start: 0.7458 (mmt) cc_final: 0.7107 (mmt) REVERT: E 217 TYR cc_start: 0.8972 (m-80) cc_final: 0.8280 (m-80) REVERT: G 75 LYS cc_start: 0.9194 (mptt) cc_final: 0.8987 (mmtm) REVERT: H 129 TYR cc_start: 0.7957 (m-80) cc_final: 0.7685 (m-80) outliers start: 27 outliers final: 21 residues processed: 311 average time/residue: 0.3505 time to fit residues: 163.3121 Evaluate side-chains 284 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 263 time to evaluate : 2.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain J residue 72 HIS Chi-restraints excluded: chain J residue 505 VAL Chi-restraints excluded: chain K residue 599 SER Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 664 ASP Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain I residue 26 THR Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain I residue 105 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 105 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 177 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 174 optimal weight: 0.9980 chunk 215 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS C 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.096457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.075443 restraints weight = 39612.307| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.50 r_work: 0.2902 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20299 Z= 0.145 Angle : 0.579 9.465 27695 Z= 0.290 Chirality : 0.045 0.318 3289 Planarity : 0.004 0.035 3384 Dihedral : 6.772 59.271 4208 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.88 % Allowed : 9.33 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.18), residues: 2344 helix: 1.66 (0.27), residues: 412 sheet: 0.55 (0.19), residues: 733 loop : 0.03 (0.18), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 479 HIS 0.004 0.001 HIS E 105 PHE 0.013 0.001 PHE M 102 TYR 0.018 0.001 TYR J 173 ARG 0.010 0.000 ARG K 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00202 ( 57) link_NAG-ASN : angle 1.74801 ( 171) link_ALPHA1-6 : bond 0.01507 ( 2) link_ALPHA1-6 : angle 1.21718 ( 6) link_BETA1-4 : bond 0.00452 ( 16) link_BETA1-4 : angle 2.10095 ( 48) link_ALPHA1-3 : bond 0.00637 ( 4) link_ALPHA1-3 : angle 3.83182 ( 12) hydrogen bonds : bond 0.03795 ( 750) hydrogen bonds : angle 5.01595 ( 2082) SS BOND : bond 0.00351 ( 41) SS BOND : angle 1.10109 ( 82) covalent geometry : bond 0.00335 (20179) covalent geometry : angle 0.54911 (27376) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 282 time to evaluate : 2.265 Fit side-chains revert: symmetry clash REVERT: A 161 MET cc_start: 0.9282 (tpp) cc_final: 0.8280 (tpt) REVERT: A 381 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7852 (mm-30) REVERT: B 588 ARG cc_start: 0.8905 (mtm110) cc_final: 0.8345 (mtt-85) REVERT: J 78 ASP cc_start: 0.6765 (t0) cc_final: 0.6543 (p0) REVERT: J 114 GLN cc_start: 0.8333 (mm-40) cc_final: 0.8101 (mm-40) REVERT: J 141 ASP cc_start: 0.8039 (m-30) cc_final: 0.7794 (t0) REVERT: J 150 MET cc_start: 0.8707 (mmm) cc_final: 0.8273 (tpp) REVERT: J 475 MET cc_start: 0.9167 (mmm) cc_final: 0.8858 (mmm) REVERT: K 581 LEU cc_start: 0.8968 (tp) cc_final: 0.8576 (tp) REVERT: K 621 GLU cc_start: 0.8243 (tt0) cc_final: 0.7874 (mt-10) REVERT: K 636 SER cc_start: 0.9256 (t) cc_final: 0.8926 (p) REVERT: N 32 TYR cc_start: 0.9130 (m-80) cc_final: 0.8714 (m-80) REVERT: N 42 LYS cc_start: 0.8890 (mmmt) cc_final: 0.8627 (tptp) REVERT: E 217 TYR cc_start: 0.9006 (m-80) cc_final: 0.8267 (m-80) REVERT: F 648 GLU cc_start: 0.8414 (tp30) cc_final: 0.7998 (tp30) REVERT: G 52 ASN cc_start: 0.8280 (t0) cc_final: 0.7944 (t0) REVERT: G 72 ASP cc_start: 0.8347 (t0) cc_final: 0.8071 (t0) outliers start: 39 outliers final: 29 residues processed: 308 average time/residue: 0.3482 time to fit residues: 159.8911 Evaluate side-chains 296 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 267 time to evaluate : 2.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 19 LYS Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain J residue 72 HIS Chi-restraints excluded: chain J residue 320 THR Chi-restraints excluded: chain J residue 505 VAL Chi-restraints excluded: chain K residue 599 SER Chi-restraints excluded: chain N residue 52 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 581 LEU Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 664 ASP Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 26 THR Chi-restraints excluded: chain I residue 105 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 25 optimal weight: 7.9990 chunk 14 optimal weight: 0.0670 chunk 108 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 187 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 224 optimal weight: 0.9990 chunk 194 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 203 optimal weight: 2.9990 chunk 211 optimal weight: 0.9990 overall best weight: 1.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 540 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 = 0.3343 r_free = 0.3343 target = 0.092772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.072004 restraints weight = 39812.885| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 2.39 r_work: 0.2826 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20299 Z= 0.166 Angle : 0.584 9.474 27695 Z= 0.292 Chirality : 0.045 0.327 3289 Planarity : 0.004 0.036 3384 Dihedral : 6.277 56.580 4208 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.12 % Allowed : 9.66 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.17), residues: 2344 helix: 1.60 (0.27), residues: 416 sheet: 0.55 (0.20), residues: 698 loop : -0.05 (0.18), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 479 HIS 0.005 0.001 HIS E 105 PHE 0.012 0.002 PHE J 383 TYR 0.018 0.001 TYR J 484 ARG 0.011 0.001 ARG G 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00200 ( 57) link_NAG-ASN : angle 1.69145 ( 171) link_ALPHA1-6 : bond 0.01578 ( 2) link_ALPHA1-6 : angle 1.60200 ( 6) link_BETA1-4 : bond 0.00427 ( 16) link_BETA1-4 : angle 2.05370 ( 48) link_ALPHA1-3 : bond 0.00614 ( 4) link_ALPHA1-3 : angle 3.76353 ( 12) hydrogen bonds : bond 0.03834 ( 750) hydrogen bonds : angle 4.92643 ( 2082) SS BOND : bond 0.00353 ( 41) SS BOND : angle 1.01359 ( 82) covalent geometry : bond 0.00386 (20179) covalent geometry : angle 0.55618 (27376) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 276 time to evaluate : 2.393 Fit side-chains revert: symmetry clash REVERT: A 161 MET cc_start: 0.9239 (tpp) cc_final: 0.8805 (tpt) REVERT: B 588 ARG cc_start: 0.8838 (mtm110) cc_final: 0.8371 (mtt-85) REVERT: D 17 GLN cc_start: 0.6567 (OUTLIER) cc_final: 0.6367 (tm-30) REVERT: J 114 GLN cc_start: 0.8324 (mm-40) cc_final: 0.8085 (mm-40) REVERT: J 150 MET cc_start: 0.8723 (mmm) cc_final: 0.8306 (tpp) REVERT: J 475 MET cc_start: 0.9117 (mmm) cc_final: 0.8744 (mmm) REVERT: K 581 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8649 (tp) REVERT: K 621 GLU cc_start: 0.8277 (tt0) cc_final: 0.7943 (mt-10) REVERT: K 636 SER cc_start: 0.9230 (t) cc_final: 0.8917 (p) REVERT: N 32 TYR cc_start: 0.9145 (m-80) cc_final: 0.8750 (m-80) REVERT: N 42 LYS cc_start: 0.8917 (mmmt) cc_final: 0.8697 (tptp) REVERT: N 83 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7071 (mm-30) REVERT: E 217 TYR cc_start: 0.9008 (m-80) cc_final: 0.8352 (m-80) REVERT: H 113 GLU cc_start: 0.7749 (tt0) cc_final: 0.7359 (tt0) outliers start: 44 outliers final: 37 residues processed: 305 average time/residue: 0.3516 time to fit residues: 159.4831 Evaluate side-chains 296 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 256 time to evaluate : 2.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 19 LYS Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 17 GLN Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain J residue 72 HIS Chi-restraints excluded: chain J residue 320 THR Chi-restraints excluded: chain J residue 505 VAL Chi-restraints excluded: chain K residue 581 LEU Chi-restraints excluded: chain K residue 599 SER Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 52 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 83 GLU Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 581 LEU Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 664 ASP Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 26 THR Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain H residue 115 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 220 optimal weight: 0.9990 chunk 194 optimal weight: 0.7980 chunk 168 optimal weight: 3.9990 chunk 172 optimal weight: 0.7980 chunk 221 optimal weight: 5.9990 chunk 195 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 246 GLN ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 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 = 0.3334 r_free = 0.3334 target = 0.092119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.070938 restraints weight = 39926.359| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.48 r_work: 0.2811 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20299 Z= 0.155 Angle : 0.570 9.444 27695 Z= 0.285 Chirality : 0.045 0.329 3289 Planarity : 0.004 0.044 3384 Dihedral : 5.870 56.834 4208 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.07 % Allowed : 10.38 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.18), residues: 2344 helix: 1.66 (0.27), residues: 416 sheet: 0.55 (0.20), residues: 692 loop : -0.09 (0.18), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 479 HIS 0.004 0.001 HIS J 105 PHE 0.014 0.001 PHE M 102 TYR 0.017 0.001 TYR G 27 ARG 0.012 0.000 ARG K 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00186 ( 57) link_NAG-ASN : angle 1.65596 ( 171) link_ALPHA1-6 : bond 0.01543 ( 2) link_ALPHA1-6 : angle 1.99610 ( 6) link_BETA1-4 : bond 0.00414 ( 16) link_BETA1-4 : angle 1.98338 ( 48) link_ALPHA1-3 : bond 0.00618 ( 4) link_ALPHA1-3 : angle 3.65727 ( 12) hydrogen bonds : bond 0.03691 ( 750) hydrogen bonds : angle 4.84371 ( 2082) SS BOND : bond 0.00372 ( 41) SS BOND : angle 0.92578 ( 82) covalent geometry : bond 0.00359 (20179) covalent geometry : angle 0.54297 (27376) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 267 time to evaluate : 2.107 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.9287 (tpp) cc_final: 0.8364 (tpt) REVERT: B 588 ARG cc_start: 0.8856 (mtm110) cc_final: 0.8358 (mtt-85) REVERT: J 475 MET cc_start: 0.9120 (mmm) cc_final: 0.8695 (mmm) REVERT: K 581 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8606 (tp) REVERT: K 636 SER cc_start: 0.9258 (t) cc_final: 0.8914 (p) REVERT: N 32 TYR cc_start: 0.9167 (m-80) cc_final: 0.8777 (m-80) REVERT: N 42 LYS cc_start: 0.8895 (mmmt) cc_final: 0.8670 (tptp) REVERT: N 83 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7263 (mm-30) REVERT: E 217 TYR cc_start: 0.9076 (m-80) cc_final: 0.8299 (m-80) REVERT: F 648 GLU cc_start: 0.8294 (tp30) cc_final: 0.7897 (tp30) REVERT: H 113 GLU cc_start: 0.7864 (tt0) cc_final: 0.7414 (tt0) outliers start: 43 outliers final: 33 residues processed: 292 average time/residue: 0.3494 time to fit residues: 152.0844 Evaluate side-chains 286 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 251 time to evaluate : 2.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain J residue 72 HIS Chi-restraints excluded: chain J residue 320 THR Chi-restraints excluded: chain J residue 505 VAL Chi-restraints excluded: chain K residue 581 LEU Chi-restraints excluded: chain K residue 599 SER Chi-restraints excluded: chain N residue 52 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 83 GLU Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 581 LEU Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 664 ASP Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 26 THR Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain H residue 115 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 212 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 139 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 157 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 543 ASN ** J 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 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 = 0.3302 r_free = 0.3302 target = 0.090341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.069311 restraints weight = 39983.182| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 2.39 r_work: 0.2782 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 20299 Z= 0.223 Angle : 0.616 9.423 27695 Z= 0.307 Chirality : 0.046 0.307 3289 Planarity : 0.004 0.052 3384 Dihedral : 5.938 57.264 4208 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.31 % Allowed : 10.19 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.18), residues: 2344 helix: 1.50 (0.27), residues: 416 sheet: 0.48 (0.20), residues: 681 loop : -0.20 (0.18), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 479 HIS 0.006 0.001 HIS E 105 PHE 0.016 0.002 PHE J 383 TYR 0.018 0.002 TYR D 49 ARG 0.011 0.001 ARG K 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00239 ( 57) link_NAG-ASN : angle 1.72571 ( 171) link_ALPHA1-6 : bond 0.01306 ( 2) link_ALPHA1-6 : angle 1.90757 ( 6) link_BETA1-4 : bond 0.00364 ( 16) link_BETA1-4 : angle 2.01407 ( 48) link_ALPHA1-3 : bond 0.00582 ( 4) link_ALPHA1-3 : angle 3.52736 ( 12) hydrogen bonds : bond 0.04050 ( 750) hydrogen bonds : angle 4.93881 ( 2082) SS BOND : bond 0.00421 ( 41) SS BOND : angle 1.02119 ( 82) covalent geometry : bond 0.00525 (20179) covalent geometry : angle 0.59086 (27376) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 256 time to evaluate : 2.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.9268 (tpp) cc_final: 0.9051 (tpt) REVERT: B 588 ARG cc_start: 0.8884 (mtm110) cc_final: 0.8399 (mtt-85) REVERT: K 581 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8684 (tp) REVERT: K 636 SER cc_start: 0.9299 (t) cc_final: 0.8938 (p) REVERT: N 32 TYR cc_start: 0.9194 (m-80) cc_final: 0.8794 (m-80) REVERT: N 42 LYS cc_start: 0.8906 (mmmt) cc_final: 0.8652 (tptp) REVERT: N 83 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7287 (mm-30) REVERT: G 83 ARG cc_start: 0.7832 (ptp90) cc_final: 0.7527 (ptp90) REVERT: H 107 LYS cc_start: 0.8068 (tptp) cc_final: 0.7748 (tptp) REVERT: H 113 GLU cc_start: 0.7837 (tt0) cc_final: 0.7384 (tt0) outliers start: 48 outliers final: 37 residues processed: 286 average time/residue: 0.3490 time to fit residues: 150.7544 Evaluate side-chains 284 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 245 time to evaluate : 2.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 19 LYS Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain J residue 72 HIS Chi-restraints excluded: chain J residue 320 THR Chi-restraints excluded: chain J residue 505 VAL Chi-restraints excluded: chain K residue 581 LEU Chi-restraints excluded: chain K residue 599 SER Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 97 MET Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 52 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 83 GLU Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 664 ASP Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 26 THR Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain H residue 115 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 4 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 229 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 176 optimal weight: 4.9990 chunk 208 optimal weight: 0.5980 chunk 142 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 422 GLN ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 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 = 0.3323 r_free = 0.3323 target = 0.091548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.070323 restraints weight = 40026.033| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 2.48 r_work: 0.2797 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2655 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20299 Z= 0.147 Angle : 0.570 9.454 27695 Z= 0.284 Chirality : 0.044 0.302 3289 Planarity : 0.004 0.054 3384 Dihedral : 5.680 56.979 4208 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.02 % Allowed : 10.82 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.18), residues: 2344 helix: 1.68 (0.27), residues: 416 sheet: 0.53 (0.20), residues: 681 loop : -0.21 (0.18), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 479 HIS 0.004 0.001 HIS E 105 PHE 0.012 0.001 PHE J 383 TYR 0.017 0.001 TYR G 27 ARG 0.013 0.001 ARG K 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00182 ( 57) link_NAG-ASN : angle 1.66919 ( 171) link_ALPHA1-6 : bond 0.01554 ( 2) link_ALPHA1-6 : angle 1.84132 ( 6) link_BETA1-4 : bond 0.00390 ( 16) link_BETA1-4 : angle 1.92882 ( 48) link_ALPHA1-3 : bond 0.00666 ( 4) link_ALPHA1-3 : angle 3.47030 ( 12) hydrogen bonds : bond 0.03676 ( 750) hydrogen bonds : angle 4.79633 ( 2082) SS BOND : bond 0.00339 ( 41) SS BOND : angle 0.89785 ( 82) covalent geometry : bond 0.00339 (20179) covalent geometry : angle 0.54460 (27376) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 259 time to evaluate : 2.187 Fit side-chains revert: symmetry clash REVERT: A 110 SER cc_start: 0.8954 (m) cc_final: 0.8603 (p) REVERT: A 426 MET cc_start: 0.9073 (mmm) cc_final: 0.8837 (mmm) REVERT: B 588 ARG cc_start: 0.8872 (mtm110) cc_final: 0.8388 (mtt-85) REVERT: C 101 ASP cc_start: 0.8727 (m-30) cc_final: 0.8456 (m-30) REVERT: D 79 GLN cc_start: 0.7770 (mp10) cc_final: 0.7193 (mp10) REVERT: J 114 GLN cc_start: 0.8210 (mm-40) cc_final: 0.7951 (mm-40) REVERT: J 150 MET cc_start: 0.8568 (mmm) cc_final: 0.8315 (tpp) REVERT: J 475 MET cc_start: 0.9100 (mmm) cc_final: 0.8721 (mmm) REVERT: K 581 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8641 (tp) REVERT: K 636 SER cc_start: 0.9320 (t) cc_final: 0.8959 (p) REVERT: N 32 TYR cc_start: 0.9171 (m-80) cc_final: 0.8736 (m-80) REVERT: N 42 LYS cc_start: 0.8904 (mmmt) cc_final: 0.8668 (tptp) REVERT: N 83 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7287 (mm-30) REVERT: N 94 ARG cc_start: 0.7862 (ttm110) cc_final: 0.7557 (mtp180) REVERT: G 83 ARG cc_start: 0.7753 (ptp90) cc_final: 0.7225 (ptp90) REVERT: H 113 GLU cc_start: 0.7789 (tt0) cc_final: 0.7335 (tt0) outliers start: 42 outliers final: 35 residues processed: 286 average time/residue: 0.3382 time to fit residues: 145.2520 Evaluate side-chains 287 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 250 time to evaluate : 2.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 19 LYS Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain J residue 72 HIS Chi-restraints excluded: chain J residue 320 THR Chi-restraints excluded: chain J residue 505 VAL Chi-restraints excluded: chain K residue 581 LEU Chi-restraints excluded: chain K residue 599 SER Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 97 MET Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 52 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 83 GLU Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 581 LEU Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 664 ASP Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 26 THR Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain H residue 115 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 74 optimal weight: 0.5980 chunk 52 optimal weight: 0.5980 chunk 8 optimal weight: 0.0040 chunk 24 optimal weight: 2.9990 chunk 178 optimal weight: 0.8980 chunk 194 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 174 optimal weight: 0.9990 chunk 172 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 128 optimal weight: 3.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 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 = 0.3384 r_free = 0.3384 target = 0.095180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.074464 restraints weight = 39332.181| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.44 r_work: 0.2877 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20299 Z= 0.115 Angle : 0.557 10.047 27695 Z= 0.277 Chirality : 0.044 0.294 3289 Planarity : 0.004 0.061 3384 Dihedral : 5.436 56.679 4208 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.78 % Allowed : 11.25 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.18), residues: 2344 helix: 1.85 (0.27), residues: 416 sheet: 0.56 (0.20), residues: 683 loop : -0.21 (0.18), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 479 HIS 0.003 0.001 HIS E 105 PHE 0.011 0.001 PHE A 383 TYR 0.017 0.001 TYR G 27 ARG 0.016 0.000 ARG K 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00184 ( 57) link_NAG-ASN : angle 1.59058 ( 171) link_ALPHA1-6 : bond 0.01478 ( 2) link_ALPHA1-6 : angle 1.75024 ( 6) link_BETA1-4 : bond 0.00403 ( 16) link_BETA1-4 : angle 1.86392 ( 48) link_ALPHA1-3 : bond 0.00755 ( 4) link_ALPHA1-3 : angle 3.36707 ( 12) hydrogen bonds : bond 0.03439 ( 750) hydrogen bonds : angle 4.68019 ( 2082) SS BOND : bond 0.00329 ( 41) SS BOND : angle 0.85998 ( 82) covalent geometry : bond 0.00262 (20179) covalent geometry : angle 0.53320 (27376) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 277 time to evaluate : 2.121 Fit side-chains revert: symmetry clash REVERT: A 110 SER cc_start: 0.8890 (m) cc_final: 0.8550 (p) REVERT: A 426 MET cc_start: 0.9010 (mmm) cc_final: 0.8786 (mmm) REVERT: B 588 ARG cc_start: 0.8905 (mtm110) cc_final: 0.8379 (mtt-85) REVERT: D 17 GLN cc_start: 0.7743 (mp10) cc_final: 0.7481 (pp30) REVERT: D 79 GLN cc_start: 0.7749 (OUTLIER) cc_final: 0.7480 (mp10) REVERT: J 114 GLN cc_start: 0.8219 (mm-40) cc_final: 0.7683 (mm-40) REVERT: J 150 MET cc_start: 0.8549 (mmm) cc_final: 0.8334 (tpp) REVERT: J 475 MET cc_start: 0.9051 (mmm) cc_final: 0.8680 (mmm) REVERT: K 581 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8665 (tp) REVERT: K 636 SER cc_start: 0.9310 (t) cc_final: 0.8963 (p) REVERT: M 68 THR cc_start: 0.9400 (m) cc_final: 0.9001 (p) REVERT: N 32 TYR cc_start: 0.9180 (m-80) cc_final: 0.8742 (m-80) REVERT: N 42 LYS cc_start: 0.8809 (mmmt) cc_final: 0.8591 (tptp) REVERT: N 83 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.7147 (mm-30) REVERT: N 94 ARG cc_start: 0.7802 (ttm110) cc_final: 0.7538 (mtp180) REVERT: E 217 TYR cc_start: 0.9055 (m-80) cc_final: 0.8278 (m-80) REVERT: G 83 ARG cc_start: 0.7615 (ptp90) cc_final: 0.7264 (ptp90) REVERT: I 95 GLN cc_start: 0.8222 (mm-40) cc_final: 0.7830 (mp10) REVERT: H 113 GLU cc_start: 0.7767 (tt0) cc_final: 0.7295 (tt0) outliers start: 37 outliers final: 34 residues processed: 300 average time/residue: 0.3316 time to fit residues: 148.9219 Evaluate side-chains 291 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 254 time to evaluate : 2.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 19 LYS Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain J residue 72 HIS Chi-restraints excluded: chain J residue 320 THR Chi-restraints excluded: chain J residue 505 VAL Chi-restraints excluded: chain K residue 581 LEU Chi-restraints excluded: chain K residue 599 SER Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 97 MET Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 83 GLU Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 581 LEU Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 664 ASP Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain I residue 26 THR Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain H residue 115 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 72 optimal weight: 4.9990 chunk 109 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 201 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 198 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 216 optimal weight: 3.9990 chunk 150 optimal weight: 10.0000 chunk 71 optimal weight: 0.3980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS C 76 ASN ** J 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.093637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.072633 restraints weight = 39450.759| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 2.45 r_work: 0.2843 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20299 Z= 0.189 Angle : 0.603 10.083 27695 Z= 0.301 Chirality : 0.045 0.293 3289 Planarity : 0.004 0.063 3384 Dihedral : 5.563 57.108 4208 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.88 % Allowed : 11.73 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.18), residues: 2344 helix: 1.75 (0.27), residues: 412 sheet: 0.58 (0.21), residues: 683 loop : -0.28 (0.18), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 479 HIS 0.004 0.001 HIS E 105 PHE 0.017 0.002 PHE E 53 TYR 0.017 0.001 TYR G 27 ARG 0.015 0.001 ARG K 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00214 ( 57) link_NAG-ASN : angle 1.64586 ( 171) link_ALPHA1-6 : bond 0.01333 ( 2) link_ALPHA1-6 : angle 1.79137 ( 6) link_BETA1-4 : bond 0.00373 ( 16) link_BETA1-4 : angle 1.91365 ( 48) link_ALPHA1-3 : bond 0.00682 ( 4) link_ALPHA1-3 : angle 3.28807 ( 12) hydrogen bonds : bond 0.03849 ( 750) hydrogen bonds : angle 4.79646 ( 2082) SS BOND : bond 0.00391 ( 41) SS BOND : angle 0.94203 ( 82) covalent geometry : bond 0.00442 (20179) covalent geometry : angle 0.58036 (27376) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 249 time to evaluate : 2.375 Fit side-chains revert: symmetry clash REVERT: A 110 SER cc_start: 0.8938 (m) cc_final: 0.8593 (p) REVERT: A 426 MET cc_start: 0.9011 (mmm) cc_final: 0.8804 (mmm) REVERT: B 588 ARG cc_start: 0.8930 (mtm110) cc_final: 0.8411 (mtt-85) REVERT: D 79 GLN cc_start: 0.7848 (OUTLIER) cc_final: 0.7271 (mp10) REVERT: J 114 GLN cc_start: 0.8278 (mm-40) cc_final: 0.7737 (mm-40) REVERT: J 150 MET cc_start: 0.8580 (mmm) cc_final: 0.8356 (tpp) REVERT: J 320 THR cc_start: 0.9452 (OUTLIER) cc_final: 0.8977 (p) REVERT: J 475 MET cc_start: 0.9080 (mmm) cc_final: 0.8693 (mmm) REVERT: K 581 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8703 (tp) REVERT: K 636 SER cc_start: 0.9265 (t) cc_final: 0.8891 (p) REVERT: N 32 TYR cc_start: 0.9224 (m-80) cc_final: 0.8822 (m-80) REVERT: N 42 LYS cc_start: 0.8817 (mmmt) cc_final: 0.8604 (tptp) REVERT: G 83 ARG cc_start: 0.7554 (ptp90) cc_final: 0.7299 (ptp90) REVERT: I 95 GLN cc_start: 0.8269 (mm-40) cc_final: 0.7873 (mp10) REVERT: H 113 GLU cc_start: 0.7776 (tt0) cc_final: 0.7335 (tt0) outliers start: 39 outliers final: 34 residues processed: 274 average time/residue: 0.3295 time to fit residues: 137.1457 Evaluate side-chains 284 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 247 time to evaluate : 2.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 19 LYS Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain J residue 72 HIS Chi-restraints excluded: chain J residue 320 THR Chi-restraints excluded: chain J residue 505 VAL Chi-restraints excluded: chain K residue 581 LEU Chi-restraints excluded: chain K residue 599 SER Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 97 MET Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 52 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 581 LEU Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 664 ASP Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 26 THR Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain H residue 115 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 92 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 164 optimal weight: 5.9990 chunk 217 optimal weight: 0.7980 chunk 216 optimal weight: 3.9990 chunk 167 optimal weight: 0.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 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 = 0.3346 r_free = 0.3346 target = 0.092963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.071733 restraints weight = 39744.945| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 2.53 r_work: 0.2823 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20299 Z= 0.190 Angle : 0.604 9.845 27695 Z= 0.300 Chirality : 0.045 0.294 3289 Planarity : 0.004 0.065 3384 Dihedral : 5.589 57.175 4208 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.97 % Allowed : 11.44 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.18), residues: 2344 helix: 1.65 (0.27), residues: 418 sheet: 0.54 (0.21), residues: 683 loop : -0.29 (0.18), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 479 HIS 0.005 0.001 HIS J 105 PHE 0.014 0.002 PHE J 383 TYR 0.018 0.001 TYR A 173 ARG 0.015 0.001 ARG K 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00203 ( 57) link_NAG-ASN : angle 1.66992 ( 171) link_ALPHA1-6 : bond 0.01439 ( 2) link_ALPHA1-6 : angle 1.77347 ( 6) link_BETA1-4 : bond 0.00361 ( 16) link_BETA1-4 : angle 1.90315 ( 48) link_ALPHA1-3 : bond 0.00688 ( 4) link_ALPHA1-3 : angle 3.27006 ( 12) hydrogen bonds : bond 0.03828 ( 750) hydrogen bonds : angle 4.81504 ( 2082) SS BOND : bond 0.00386 ( 41) SS BOND : angle 0.95498 ( 82) covalent geometry : bond 0.00445 (20179) covalent geometry : angle 0.58069 (27376) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12322.50 seconds wall clock time: 214 minutes 21.29 seconds (12861.29 seconds total)