Starting phenix.real_space_refine on Tue Oct 15 05:33:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tq1_41498/10_2024/8tq1_41498.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tq1_41498/10_2024/8tq1_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tq1_41498/10_2024/8tq1_41498.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tq1_41498/10_2024/8tq1_41498.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tq1_41498/10_2024/8tq1_41498.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tq1_41498/10_2024/8tq1_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-5477/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: 14.28, per 1000 atoms: 0.72 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: 5.61 Conformation dependent library (CDL) restraints added in 2.5 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: 3.21 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: 8.40 Time building geometry restraints manager: 6.40 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: 3.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.800 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 50.400 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.490 ------------------------------------------------------------------------------- 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 : 0.007 0.085 20179 Z= 0.461 Angle : 1.172 11.991 27376 Z= 0.660 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 *********************** 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 fitting. rotamer outliers: 5 poor density : 365 time to evaluate : 2.341 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: 0.3690 time to fit residues: 197.3467 Evaluate side-chains 269 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 267 time to evaluate : 2.281 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 20179 Z= 0.381 Angle : 0.690 12.782 27376 Z= 0.364 Chirality : 0.049 0.283 3289 Planarity : 0.004 0.040 3384 Dihedral : 8.686 82.269 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 *********************** 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 fitting. rotamer outliers: 36 poor density : 292 time to evaluate : 2.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 19 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8661 (tptm) REVERT: C 72 ASP cc_start: 0.8077 (t70) cc_final: 0.7855 (t0) REVERT: J 141 ASP cc_start: 0.7987 (m-30) cc_final: 0.7777 (t0) REVERT: J 320 THR cc_start: 0.9472 (m) cc_final: 0.9003 (p) REVERT: K 636 SER cc_start: 0.9231 (t) cc_final: 0.8883 (p) REVERT: M 3 GLN cc_start: 0.8240 (mm-40) cc_final: 0.7995 (mm110) REVERT: E 173 TYR cc_start: 0.8276 (p90) cc_final: 0.8070 (p90) REVERT: F 648 GLU cc_start: 0.8235 (tp30) cc_final: 0.7797 (tp30) REVERT: G 75 LYS cc_start: 0.9146 (mptt) cc_final: 0.8941 (mmtm) outliers start: 36 outliers final: 24 residues processed: 315 average time/residue: 0.3678 time to fit residues: 170.6347 Evaluate side-chains 282 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 257 time to evaluate : 2.256 ------------------------------------------------------------------------------- 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 118 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 177 optimal weight: 0.9990 chunk 145 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 213 optimal weight: 1.9990 chunk 230 optimal weight: 1.9990 chunk 190 optimal weight: 0.6980 chunk 212 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 171 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 20179 Z= 0.245 Angle : 0.587 10.392 27376 Z= 0.306 Chirality : 0.046 0.299 3289 Planarity : 0.004 0.035 3384 Dihedral : 7.508 70.130 4208 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.68 % Allowed : 8.12 % Favored : 90.19 % 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: 0.63 (0.17), residues: 2344 helix: 1.57 (0.27), residues: 412 sheet: 0.47 (0.19), residues: 735 loop : 0.09 (0.18), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J 479 HIS 0.005 0.001 HIS J 105 PHE 0.018 0.002 PHE A 53 TYR 0.018 0.001 TYR G 27 ARG 0.010 0.001 ARG A 166 *********************** 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 322 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 287 time to evaluate : 2.586 Fit side-chains revert: symmetry clash REVERT: A 161 MET cc_start: 0.9354 (tpp) cc_final: 0.8475 (tpt) REVERT: A 381 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7588 (mm-30) REVERT: B 588 ARG cc_start: 0.8622 (mtm110) cc_final: 0.8257 (mtt-85) REVERT: C 19 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8629 (tptm) REVERT: J 78 ASP cc_start: 0.6369 (t0) cc_final: 0.6147 (p0) REVERT: J 114 GLN cc_start: 0.8203 (mm-40) cc_final: 0.7974 (mm-40) REVERT: J 150 MET cc_start: 0.8680 (mmm) cc_final: 0.8299 (tpp) REVERT: K 636 SER cc_start: 0.9222 (t) cc_final: 0.8909 (p) REVERT: N 42 LYS cc_start: 0.8707 (mmmt) cc_final: 0.8488 (tptp) REVERT: E 150 MET cc_start: 0.7410 (mmt) cc_final: 0.7064 (mmt) REVERT: E 217 TYR cc_start: 0.8959 (m-80) cc_final: 0.8215 (m-80) REVERT: F 632 ASP cc_start: 0.8970 (t0) cc_final: 0.8745 (t0) REVERT: G 52 ASN cc_start: 0.8391 (t0) cc_final: 0.8046 (t0) REVERT: G 75 LYS cc_start: 0.9127 (mptt) cc_final: 0.8918 (mmtm) REVERT: H 129 TYR cc_start: 0.7919 (m-80) cc_final: 0.7621 (m-80) outliers start: 35 outliers final: 28 residues processed: 310 average time/residue: 0.3649 time to fit residues: 167.8209 Evaluate side-chains 294 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 265 time to evaluate : 2.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 505 VAL Chi-restraints excluded: chain K residue 599 SER Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 52 THR 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 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 211 optimal weight: 0.6980 chunk 160 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 214 optimal weight: 0.9980 chunk 227 optimal weight: 8.9990 chunk 112 optimal weight: 0.9990 chunk 203 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 81 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20179 Z= 0.207 Angle : 0.546 9.473 27376 Z= 0.283 Chirality : 0.045 0.322 3289 Planarity : 0.004 0.035 3384 Dihedral : 6.679 57.423 4208 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.07 % Allowed : 9.04 % Favored : 88.89 % 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: 0.61 (0.18), residues: 2344 helix: 1.62 (0.27), residues: 414 sheet: 0.53 (0.19), residues: 735 loop : -0.02 (0.18), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 479 HIS 0.004 0.001 HIS J 105 PHE 0.013 0.001 PHE M 102 TYR 0.021 0.001 TYR J 173 ARG 0.009 0.000 ARG K 542 *********************** 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 329 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 286 time to evaluate : 2.461 Fit side-chains revert: symmetry clash REVERT: B 588 ARG cc_start: 0.8632 (mtm110) cc_final: 0.8249 (mtt-85) REVERT: C 19 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8626 (tptm) REVERT: D 45 LYS cc_start: 0.8720 (tttp) cc_final: 0.8285 (tttm) REVERT: D 79 GLN cc_start: 0.7826 (OUTLIER) cc_final: 0.7157 (mp10) REVERT: J 114 GLN cc_start: 0.8234 (mm-40) cc_final: 0.7986 (mm-40) REVERT: J 150 MET cc_start: 0.8669 (mmm) cc_final: 0.8388 (tpp) REVERT: K 581 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8553 (tp) REVERT: K 636 SER cc_start: 0.9220 (t) cc_final: 0.8926 (p) REVERT: K 664 ASP cc_start: 0.7403 (m-30) cc_final: 0.7177 (m-30) REVERT: E 217 TYR cc_start: 0.8969 (m-80) cc_final: 0.8243 (m-80) REVERT: F 648 GLU cc_start: 0.8212 (tp30) cc_final: 0.7852 (tp30) REVERT: G 52 ASN cc_start: 0.8420 (t0) cc_final: 0.8018 (t0) REVERT: G 72 ASP cc_start: 0.8230 (t0) cc_final: 0.7955 (t0) REVERT: G 83 ARG cc_start: 0.7135 (ptp90) cc_final: 0.6682 (ptp90) outliers start: 43 outliers final: 29 residues processed: 314 average time/residue: 0.3610 time to fit residues: 167.3856 Evaluate side-chains 298 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 266 time to evaluate : 2.439 ------------------------------------------------------------------------------- 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 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 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 120 VAL Chi-restraints excluded: chain F residue 581 LEU 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 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 189 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 3 optimal weight: 0.2980 chunk 169 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 193 optimal weight: 3.9990 chunk 157 optimal weight: 7.9990 chunk 0 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 203 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- 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** J 246 GLN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 20179 Z= 0.386 Angle : 0.623 9.440 27376 Z= 0.320 Chirality : 0.047 0.321 3289 Planarity : 0.004 0.038 3384 Dihedral : 6.567 57.386 4208 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.31 % Allowed : 9.52 % Favored : 88.17 % 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: 0.39 (0.17), residues: 2344 helix: 1.34 (0.27), residues: 416 sheet: 0.43 (0.20), residues: 702 loop : -0.15 (0.18), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 479 HIS 0.006 0.001 HIS E 105 PHE 0.017 0.002 PHE J 383 TYR 0.019 0.002 TYR D 49 ARG 0.010 0.001 ARG K 542 *********************** 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 311 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 263 time to evaluate : 2.026 Fit side-chains revert: symmetry clash REVERT: B 588 ARG cc_start: 0.8700 (mtm110) cc_final: 0.8291 (mtt-85) REVERT: C 72 ASP cc_start: 0.8044 (t0) cc_final: 0.7543 (t0) REVERT: C 75 LYS cc_start: 0.8899 (mttp) cc_final: 0.8661 (ptpp) REVERT: D 17 GLN cc_start: 0.6505 (OUTLIER) cc_final: 0.6301 (tm-30) REVERT: D 45 LYS cc_start: 0.8829 (tttp) cc_final: 0.8418 (tttm) REVERT: J 150 MET cc_start: 0.8671 (mmm) cc_final: 0.8382 (tpp) REVERT: J 475 MET cc_start: 0.9232 (mmm) cc_final: 0.8804 (mmm) REVERT: K 581 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8619 (tp) REVERT: K 636 SER cc_start: 0.9263 (t) cc_final: 0.8932 (p) REVERT: N 83 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.6826 (mm-30) REVERT: E 351 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8718 (mtmm) REVERT: H 113 GLU cc_start: 0.7856 (tt0) cc_final: 0.7479 (tt0) REVERT: H 133 ASP cc_start: 0.8015 (m-30) cc_final: 0.7699 (m-30) outliers start: 48 outliers final: 40 residues processed: 294 average time/residue: 0.3702 time to fit residues: 161.6846 Evaluate side-chains 287 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 243 time to evaluate : 2.465 ------------------------------------------------------------------------------- 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 138 ILE 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 K residue 639 THR 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 42 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 351 LYS 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 37 VAL Chi-restraints excluded: chain G residue 63 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 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 76 optimal weight: 1.9990 chunk 204 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 133 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 227 optimal weight: 9.9990 chunk 188 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 119 optimal weight: 0.5980 overall best weight: 1.1188 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20179 Z= 0.241 Angle : 0.551 9.447 27376 Z= 0.284 Chirality : 0.045 0.334 3289 Planarity : 0.004 0.051 3384 Dihedral : 6.135 56.975 4208 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.16 % Allowed : 10.34 % 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: 0.44 (0.18), residues: 2344 helix: 1.50 (0.27), residues: 416 sheet: 0.49 (0.20), residues: 692 loop : -0.18 (0.18), residues: 1236 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 0.014 0.001 PHE J 383 TYR 0.018 0.001 TYR G 27 ARG 0.010 0.000 ARG K 542 *********************** 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 311 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 266 time to evaluate : 2.255 Fit side-chains revert: symmetry clash REVERT: B 588 ARG cc_start: 0.8667 (mtm110) cc_final: 0.8277 (mtt-85) REVERT: C 19 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8709 (tptm) REVERT: D 45 LYS cc_start: 0.8813 (tttp) cc_final: 0.8412 (tttm) REVERT: D 79 GLN cc_start: 0.7843 (mp10) cc_final: 0.7270 (mp10) REVERT: J 150 MET cc_start: 0.8650 (mmm) cc_final: 0.8405 (tpp) REVERT: K 581 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8623 (tp) REVERT: K 636 SER cc_start: 0.9297 (t) cc_final: 0.8952 (p) REVERT: N 83 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.7022 (mm-30) REVERT: E 217 TYR cc_start: 0.8996 (m-80) cc_final: 0.8205 (m-80) REVERT: F 648 GLU cc_start: 0.8159 (tp30) cc_final: 0.7735 (tp30) REVERT: H 113 GLU cc_start: 0.7781 (tt0) cc_final: 0.7390 (tt0) REVERT: H 133 ASP cc_start: 0.7997 (m-30) cc_final: 0.7640 (m-30) outliers start: 45 outliers final: 35 residues processed: 296 average time/residue: 0.3704 time to fit residues: 161.5713 Evaluate side-chains 291 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 253 time to evaluate : 2.501 ------------------------------------------------------------------------------- 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 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 M residue 70 SER 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 219 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 129 optimal weight: 0.6980 chunk 166 optimal weight: 4.9990 chunk 128 optimal weight: 0.4980 chunk 191 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 226 optimal weight: 3.9990 chunk 141 optimal weight: 6.9990 chunk 138 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20179 Z= 0.183 Angle : 0.534 9.517 27376 Z= 0.273 Chirality : 0.044 0.321 3289 Planarity : 0.004 0.056 3384 Dihedral : 5.803 56.797 4208 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.92 % Allowed : 10.96 % Favored : 87.12 % 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: 0.51 (0.18), residues: 2344 helix: 1.68 (0.27), residues: 416 sheet: 0.53 (0.20), residues: 683 loop : -0.17 (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 0.012 0.001 PHE A 383 TYR 0.018 0.001 TYR G 27 ARG 0.011 0.000 ARG K 542 *********************** 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 308 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 268 time to evaluate : 2.447 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 588 ARG cc_start: 0.8650 (mtm110) cc_final: 0.8307 (mtt-85) REVERT: J 114 GLN cc_start: 0.8203 (mm-40) cc_final: 0.7942 (mm-40) REVERT: K 581 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8616 (tp) REVERT: K 636 SER cc_start: 0.9295 (t) cc_final: 0.8967 (p) REVERT: N 83 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.6767 (mm-30) REVERT: E 217 TYR cc_start: 0.8983 (m-80) cc_final: 0.8205 (m-80) REVERT: F 648 GLU cc_start: 0.8195 (tp30) cc_final: 0.7716 (tp30) REVERT: G 83 ARG cc_start: 0.7625 (ptp90) cc_final: 0.7314 (ptp-170) REVERT: I 95 GLN cc_start: 0.8146 (mm-40) cc_final: 0.7718 (mp10) REVERT: H 113 GLU cc_start: 0.7811 (tt0) cc_final: 0.7550 (tt0) REVERT: H 133 ASP cc_start: 0.7962 (m-30) cc_final: 0.7604 (m-30) outliers start: 40 outliers final: 30 residues processed: 293 average time/residue: 0.3636 time to fit residues: 158.8823 Evaluate side-chains 284 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 252 time to evaluate : 2.553 ------------------------------------------------------------------------------- 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 C residue 7 THR Chi-restraints excluded: chain C residue 28 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 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 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 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 140 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 135 optimal weight: 0.9980 chunk 68 optimal weight: 7.9990 chunk 44 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 chunk 154 optimal weight: 2.9990 chunk 111 optimal weight: 7.9990 chunk 21 optimal weight: 0.0030 chunk 178 optimal weight: 0.8980 overall best weight: 1.1392 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20179 Z= 0.237 Angle : 0.550 9.492 27376 Z= 0.281 Chirality : 0.044 0.300 3289 Planarity : 0.004 0.055 3384 Dihedral : 5.689 56.981 4208 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.97 % Allowed : 11.25 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.18), residues: 2344 helix: 1.69 (0.27), residues: 416 sheet: 0.52 (0.20), residues: 681 loop : -0.16 (0.18), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 479 HIS 0.004 0.001 HIS E 105 PHE 0.014 0.001 PHE M 102 TYR 0.017 0.001 TYR G 27 ARG 0.013 0.001 ARG K 542 *********************** 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 298 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 257 time to evaluate : 2.388 Fit side-chains revert: symmetry clash REVERT: B 588 ARG cc_start: 0.8664 (mtm110) cc_final: 0.8319 (mtt-85) REVERT: D 79 GLN cc_start: 0.7773 (mp10) cc_final: 0.7236 (mp10) REVERT: K 581 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8626 (tp) REVERT: K 636 SER cc_start: 0.9302 (t) cc_final: 0.8976 (p) REVERT: N 83 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.7038 (mm-30) REVERT: E 217 TYR cc_start: 0.8995 (m-80) cc_final: 0.8157 (m-80) REVERT: G 83 ARG cc_start: 0.7675 (ptp90) cc_final: 0.7319 (ptp90) REVERT: H 113 GLU cc_start: 0.7786 (tt0) cc_final: 0.7362 (tt0) REVERT: H 133 ASP cc_start: 0.7960 (m-30) cc_final: 0.7580 (m-30) outliers start: 41 outliers final: 36 residues processed: 281 average time/residue: 0.3551 time to fit residues: 149.1517 Evaluate side-chains 285 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 247 time to evaluate : 2.333 ------------------------------------------------------------------------------- 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 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 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 206 optimal weight: 0.6980 chunk 216 optimal weight: 0.9990 chunk 197 optimal weight: 1.9990 chunk 211 optimal weight: 0.7980 chunk 127 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 165 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 190 optimal weight: 0.0060 chunk 199 optimal weight: 2.9990 chunk 210 optimal weight: 0.1980 overall best weight: 0.5398 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 20179 Z= 0.157 Angle : 0.531 9.784 27376 Z= 0.270 Chirality : 0.043 0.292 3289 Planarity : 0.004 0.058 3384 Dihedral : 5.392 56.642 4208 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.63 % Allowed : 11.44 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.83 (0.27), residues: 417 sheet: 0.54 (0.20), residues: 686 loop : -0.16 (0.18), residues: 1241 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 0.012 0.001 PHE M 102 TYR 0.017 0.001 TYR G 27 ARG 0.015 0.001 ARG K 542 *********************** 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 305 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 271 time to evaluate : 2.361 Fit side-chains revert: symmetry clash REVERT: A 110 SER cc_start: 0.8869 (m) cc_final: 0.8555 (p) REVERT: B 588 ARG cc_start: 0.8638 (mtm110) cc_final: 0.8298 (mtt-85) REVERT: D 79 GLN cc_start: 0.7786 (mp10) cc_final: 0.7583 (mp10) REVERT: J 114 GLN cc_start: 0.8171 (mm-40) cc_final: 0.7928 (mm-40) REVERT: J 150 MET cc_start: 0.7913 (tpp) cc_final: 0.7604 (tpp) REVERT: K 581 LEU cc_start: 0.8948 (tp) cc_final: 0.8609 (tp) REVERT: K 636 SER cc_start: 0.9288 (t) cc_final: 0.8966 (p) REVERT: M 68 THR cc_start: 0.9383 (m) cc_final: 0.9013 (p) REVERT: N 83 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6946 (mm-30) REVERT: N 94 ARG cc_start: 0.7849 (ttm110) cc_final: 0.7489 (mtp180) REVERT: E 217 TYR cc_start: 0.8972 (m-80) cc_final: 0.8208 (m-80) REVERT: G 66 ARG cc_start: 0.7910 (mtm180) cc_final: 0.7113 (mtm180) REVERT: G 83 ARG cc_start: 0.7596 (ptp90) cc_final: 0.7064 (ptp90) REVERT: I 95 GLN cc_start: 0.8130 (mm-40) cc_final: 0.7744 (mp10) REVERT: H 113 GLU cc_start: 0.7792 (tt0) cc_final: 0.7368 (tt0) REVERT: H 133 ASP cc_start: 0.7907 (m-30) cc_final: 0.7519 (m-30) outliers start: 34 outliers final: 31 residues processed: 291 average time/residue: 0.3767 time to fit residues: 162.8691 Evaluate side-chains 286 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 254 time to evaluate : 2.372 ------------------------------------------------------------------------------- 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 C residue 7 THR Chi-restraints excluded: chain C residue 28 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 434 MET Chi-restraints excluded: chain J residue 505 VAL 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 120 VAL Chi-restraints excluded: chain E residue 351 LYS 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 G residue 12 VAL 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 138 optimal weight: 2.9990 chunk 223 optimal weight: 0.3980 chunk 136 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 155 optimal weight: 0.9980 chunk 234 optimal weight: 0.0570 chunk 215 optimal weight: 2.9990 chunk 186 optimal weight: 3.9990 chunk 19 optimal weight: 0.0670 chunk 144 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 82AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 20179 Z= 0.153 Angle : 0.528 10.153 27376 Z= 0.268 Chirality : 0.043 0.282 3289 Planarity : 0.004 0.061 3384 Dihedral : 5.217 56.408 4208 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.44 % Allowed : 11.92 % Favored : 86.63 % 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: 0.62 (0.18), residues: 2344 helix: 2.00 (0.27), residues: 411 sheet: 0.61 (0.20), residues: 682 loop : -0.19 (0.18), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 479 HIS 0.003 0.000 HIS E 105 PHE 0.013 0.001 PHE J 53 TYR 0.017 0.001 TYR G 27 ARG 0.014 0.001 ARG K 542 ********************** 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 292 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 262 time to evaluate : 2.498 Fit side-chains REVERT: A 110 SER cc_start: 0.8867 (m) cc_final: 0.8550 (p) REVERT: B 588 ARG cc_start: 0.8631 (mtm110) cc_final: 0.8295 (mtt-85) REVERT: C 101 ASP cc_start: 0.8775 (m-30) cc_final: 0.8573 (m-30) REVERT: J 114 GLN cc_start: 0.8180 (mm-40) cc_final: 0.7937 (mm-40) REVERT: J 150 MET cc_start: 0.7896 (tpp) cc_final: 0.7540 (tpp) REVERT: K 581 LEU cc_start: 0.8922 (tp) cc_final: 0.8587 (tp) REVERT: K 636 SER cc_start: 0.9285 (t) cc_final: 0.8965 (p) REVERT: M 68 THR cc_start: 0.9376 (m) cc_final: 0.9007 (p) REVERT: N 47 MET cc_start: 0.8820 (mmm) cc_final: 0.8461 (mmp) REVERT: N 94 ARG cc_start: 0.7830 (ttm110) cc_final: 0.7547 (mtp180) REVERT: E 217 TYR cc_start: 0.8975 (m-80) cc_final: 0.8216 (m-80) REVERT: G 66 ARG cc_start: 0.7907 (mtm180) cc_final: 0.7450 (mtm110) REVERT: G 83 ARG cc_start: 0.7568 (ptp90) cc_final: 0.7242 (ptp90) REVERT: I 95 GLN cc_start: 0.8144 (mm-40) cc_final: 0.7771 (mp10) REVERT: H 113 GLU cc_start: 0.7860 (tt0) cc_final: 0.7402 (tt0) REVERT: H 133 ASP cc_start: 0.7893 (m-30) cc_final: 0.7512 (m-30) outliers start: 30 outliers final: 28 residues processed: 280 average time/residue: 0.3552 time to fit residues: 149.2093 Evaluate side-chains 279 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 251 time to evaluate : 2.312 ------------------------------------------------------------------------------- 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 28 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 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 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 351 LYS Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 636 SER 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 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 148 optimal weight: 0.0570 chunk 198 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 186 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 191 optimal weight: 0.0270 chunk 23 optimal weight: 0.0010 chunk 34 optimal weight: 7.9990 overall best weight: 0.7564 ------------------------------------------------------------------------------- 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 = 0.3385 r_free = 0.3385 target = 0.095226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.074235 restraints weight = 39106.203| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.51 r_work: 0.2884 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20179 Z= 0.181 Angle : 0.535 9.650 27376 Z= 0.272 Chirality : 0.044 0.279 3289 Planarity : 0.004 0.063 3384 Dihedral : 5.164 56.581 4208 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.68 % Allowed : 11.73 % 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: 0.63 (0.18), residues: 2344 helix: 2.02 (0.27), residues: 410 sheet: 0.61 (0.20), residues: 694 loop : -0.19 (0.18), residues: 1240 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 0.017 0.001 PHE E 53 TYR 0.029 0.001 TYR N 49 ARG 0.015 0.001 ARG K 542 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4642.51 seconds wall clock time: 85 minutes 56.30 seconds (5156.30 seconds total)