Starting phenix.real_space_refine on Tue Mar 19 09:33:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tcn_25814/03_2024/7tcn_25814_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tcn_25814/03_2024/7tcn_25814.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tcn_25814/03_2024/7tcn_25814.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tcn_25814/03_2024/7tcn_25814.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tcn_25814/03_2024/7tcn_25814_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tcn_25814/03_2024/7tcn_25814_neut.pdb" } resolution = 4.1 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= 0.004 sd= 0.127 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 139 5.16 5 C 14898 2.51 5 N 4045 2.21 5 O 4665 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23747 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 3357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3357 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain breaks: 4 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 969 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "C" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1677 Classifications: {'peptide': 220} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 206} Chain breaks: 1 Chain: "D" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1635 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 201} Chain: "E" Number of atoms: 3446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3446 Classifications: {'peptide': 438} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 417} Chain breaks: 4 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 969 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "G" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1677 Classifications: {'peptide': 220} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 206} Chain breaks: 1 Chain: "H" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1635 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 201} Chain: "I" Number of atoms: 3446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3446 Classifications: {'peptide': 438} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 417} Chain breaks: 4 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "J" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 969 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "K" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1677 Classifications: {'peptide': 220} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 206} Chain breaks: 1 Chain: "L" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1635 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 201} Chain: "0" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "4" 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: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" 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: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "h" 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "n" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "v" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} 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: "C" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} 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: "G" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} 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: "K" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 12.26, per 1000 atoms: 0.52 Number of scatterers: 23747 At special positions: 0 Unit cell: (177.12, 183.6, 117.72, 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 139 16.00 O 4665 8.00 N 4045 7.00 C 14898 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 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=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 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=2.04 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 C 140 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 134 " - pdb=" SG CYS D 194 " 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=2.03 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 F 598 " - pdb=" SG CYS F 604 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 140 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 134 " - pdb=" SG CYS H 194 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.02 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.03 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.03 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.04 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.02 Simple disulfide: pdb=" SG CYS K 140 " - pdb=" SG CYS K 196 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 4 3 " - " MAN 4 4 " " BMA R 3 " - " MAN R 4 " " BMA n 3 " - " MAN n 4 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 0 2 " - " BMA 0 3 " " NAG 4 1 " - " NAG 4 2 " " NAG 4 2 " - " BMA 4 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG h 1 " - " NAG h 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG v 1 " - " NAG v 2 " " NAG v 2 " - " BMA v 3 " " NAG y 1 " - " NAG y 2 " NAG-ASN " NAG 0 1 " - " ASN I 262 " " NAG 4 1 " - " ASN I 197 " " NAG A 601 " - " ASN A 339 " " NAG A 605 " - " ASN A 392 " " NAG E 604 " - " ASN E 392 " " NAG I 604 " - " ASN I 392 " " NAG M 1 " - " ASN A 262 " " NAG N 1 " - " ASN A 386 " " NAG R 1 " - " ASN A 197 " " NAG e 1 " - " ASN E 386 " " NAG h 1 " - " ASN E 339 " " NAG j 1 " - " ASN E 262 " " NAG n 1 " - " ASN E 197 " " NAG v 1 " - " ASN I 386 " " NAG y 1 " - " ASN I 339 " Time building additional restraints: 8.89 Conformation dependent library (CDL) restraints added in 3.7 seconds 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5520 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 62 sheets defined 17.6% alpha, 37.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.76 Creating SS restraints... Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 122 through 127 removed outlier: 4.066A pdb=" N VAL A 127 " --> pdb=" O PRO A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 334 through 353 removed outlier: 3.846A pdb=" N GLN A 343 " --> pdb=" O ASN A 339 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N TYR A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 472 through 479 removed outlier: 4.241A pdb=" N ASN A 476 " --> pdb=" O ASN A 472 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TRP A 477 " --> pdb=" O MET A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 482 No H-bonds generated for 'chain 'A' and resid 480 through 482' Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.723A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 575 Processing helix chain 'B' and resid 576 through 596 removed outlier: 4.049A pdb=" N VAL B 580 " --> pdb=" O LEU B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 663 removed outlier: 3.571A pdb=" N TRP B 631 " --> pdb=" O THR B 627 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ASN B 637 " --> pdb=" O LYS B 633 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N TYR B 638 " --> pdb=" O GLU B 634 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N GLN B 640 " --> pdb=" O SER B 636 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N ILE B 641 " --> pdb=" O ASN B 637 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU B 645 " --> pdb=" O ILE B 641 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU B 663 " --> pdb=" O ASP B 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 64 removed outlier: 4.029A pdb=" N ARG C 64 " --> pdb=" O GLY C 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 61 through 64' Processing helix chain 'C' and resid 73 through 75 No H-bonds generated for 'chain 'C' and resid 73 through 75' Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'C' and resid 187 through 192 Processing helix chain 'D' and resid 121 through 126 removed outlier: 3.568A pdb=" N LYS D 126 " --> pdb=" O ASP D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 189 removed outlier: 3.690A pdb=" N HIS D 189 " --> pdb=" O ASP D 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 117 removed outlier: 3.571A pdb=" N ILE E 109 " --> pdb=" O HIS E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 179 No H-bonds generated for 'chain 'E' and resid 177 through 179' Processing helix chain 'E' and resid 334 through 353 removed outlier: 3.747A pdb=" N ASN E 339 " --> pdb=" O GLU E 335 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N TYR E 352 " --> pdb=" O LYS E 348 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE E 353 " --> pdb=" O LEU E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 473 through 481 removed outlier: 3.920A pdb=" N TRP E 477 " --> pdb=" O MET E 473 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU E 480 " --> pdb=" O ASN E 476 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 543 removed outlier: 3.653A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 575 Processing helix chain 'F' and resid 576 through 596 removed outlier: 4.004A pdb=" N VAL F 580 " --> pdb=" O LEU F 576 " (cutoff:3.500A) Processing helix chain 'F' and resid 621 through 625 removed outlier: 3.724A pdb=" N ASP F 624 " --> pdb=" O GLU F 621 " (cutoff:3.500A) Processing helix chain 'F' and resid 628 through 636 Processing helix chain 'F' and resid 638 through 663 removed outlier: 4.094A pdb=" N GLY F 644 " --> pdb=" O GLN F 640 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU F 645 " --> pdb=" O ILE F 641 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU F 663 " --> pdb=" O ASP F 659 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'G' and resid 187 through 191 Processing helix chain 'G' and resid 212 through 215 Processing helix chain 'H' and resid 121 through 126 Processing helix chain 'H' and resid 182 through 189 removed outlier: 3.696A pdb=" N HIS H 189 " --> pdb=" O ASP H 185 " (cutoff:3.500A) Processing helix chain 'I' and resid 99 through 117 removed outlier: 3.512A pdb=" N GLN I 103 " --> pdb=" O ASP I 99 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 127 removed outlier: 4.117A pdb=" N VAL I 127 " --> pdb=" O PRO I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 179 No H-bonds generated for 'chain 'I' and resid 177 through 179' Processing helix chain 'I' and resid 205 through 209 removed outlier: 3.554A pdb=" N SER I 209 " --> pdb=" O PRO I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 334 through 353 removed outlier: 3.631A pdb=" N ASN I 339 " --> pdb=" O GLU I 335 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN I 343 " --> pdb=" O ASN I 339 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU I 351 " --> pdb=" O LYS I 347 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N TYR I 352 " --> pdb=" O LYS I 348 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE I 353 " --> pdb=" O LEU I 349 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 removed outlier: 3.515A pdb=" N THR I 373 " --> pdb=" O LEU I 369 " (cutoff:3.500A) Processing helix chain 'I' and resid 388 through 392 removed outlier: 3.985A pdb=" N ASN I 392 " --> pdb=" O SER I 389 " (cutoff:3.500A) Processing helix chain 'I' and resid 473 through 479 removed outlier: 4.243A pdb=" N TRP I 477 " --> pdb=" O MET I 473 " (cutoff:3.500A) Processing helix chain 'I' and resid 480 through 482 No H-bonds generated for 'chain 'I' and resid 480 through 482' Processing helix chain 'J' and resid 529 through 535 Processing helix chain 'J' and resid 536 through 542 removed outlier: 3.714A pdb=" N GLN J 540 " --> pdb=" O THR J 536 " (cutoff:3.500A) Processing helix chain 'J' and resid 572 through 575 Processing helix chain 'J' and resid 576 through 596 removed outlier: 3.962A pdb=" N VAL J 580 " --> pdb=" O LEU J 576 " (cutoff:3.500A) Processing helix chain 'J' and resid 618 through 623 removed outlier: 3.736A pdb=" N ILE J 622 " --> pdb=" O ASN J 618 " (cutoff:3.500A) Processing helix chain 'J' and resid 627 through 663 removed outlier: 4.613A pdb=" N ASN J 637 " --> pdb=" O LYS J 633 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N TYR J 638 " --> pdb=" O GLU J 634 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N GLN J 640 " --> pdb=" O SER J 636 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ILE J 641 " --> pdb=" O ASN J 637 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLY J 644 " --> pdb=" O GLN J 640 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU J 645 " --> pdb=" O ILE J 641 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU J 663 " --> pdb=" O ASP J 659 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 64 removed outlier: 4.053A pdb=" N ARG K 64 " --> pdb=" O GLY K 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 61 through 64' Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'K' and resid 186 through 190 removed outlier: 4.090A pdb=" N GLY K 190 " --> pdb=" O SER K 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 186 through 190' Processing helix chain 'L' and resid 121 through 126 Processing helix chain 'L' and resid 182 through 189 removed outlier: 3.754A pdb=" N HIS L 189 " --> pdb=" O ASP L 185 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 493 through 497 removed outlier: 3.575A pdb=" N CYS B 604 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.205A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA4, first strand: chain 'A' and resid 129 through 130 Processing sheet with id=AA5, first strand: chain 'A' and resid 158 through 162 Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.453A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 260 removed outlier: 7.167A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL A 292 " --> pdb=" O ILE A 449 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.519A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.703A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.788A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 10.463A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.823A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.950A pdb=" N ASP A 457 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 12.192A pdb=" N ILE A 284 " --> pdb=" O ASP A 457 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 273 removed outlier: 12.192A pdb=" N ILE A 284 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 10.950A pdb=" N ASP A 457 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 10.823A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.463A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.788A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 11.703A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.519A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL A 292 " --> pdb=" O ILE A 449 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N THR A 465 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N THR A 359 " --> pdb=" O PHE A 466 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 301 through 308 removed outlier: 6.979A pdb=" N ASN A 301 " --> pdb=" O VAL A 322 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N VAL A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 4 through 7 removed outlier: 3.589A pdb=" N TYR C 7 " --> pdb=" O SER C 21 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER C 21 " --> pdb=" O TYR C 7 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET C 80 " --> pdb=" O LEU C 20 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR C 70 " --> pdb=" O TYR C 79 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.662A pdb=" N GLY C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ARG C 38 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N LEU C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 10 through 12 removed outlier: 4.348A pdb=" N HIS C 102 " --> pdb=" O ARG C 94 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL C 96 " --> pdb=" O TYR C 100E" (cutoff:3.500A) removed outlier: 6.334A pdb=" N TYR C 100E" --> pdb=" O VAL C 96 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 120 through 124 removed outlier: 5.123A pdb=" N ALA C 137 " --> pdb=" O VAL C 184 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL C 184 " --> pdb=" O ALA C 137 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N GLY C 139 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL C 182 " --> pdb=" O GLY C 139 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N LEU C 141 " --> pdb=" O SER C 180 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N SER C 180 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N LYS C 143 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N LEU C 178 " --> pdb=" O LYS C 143 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 120 through 124 removed outlier: 5.123A pdb=" N ALA C 137 " --> pdb=" O VAL C 184 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL C 184 " --> pdb=" O ALA C 137 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N GLY C 139 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL C 182 " --> pdb=" O GLY C 139 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N LEU C 141 " --> pdb=" O SER C 180 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N SER C 180 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N LYS C 143 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N LEU C 178 " --> pdb=" O LYS C 143 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 151 through 154 removed outlier: 3.633A pdb=" N THR C 205 " --> pdb=" O HIS C 200 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.550A pdb=" N THR D 22 " --> pdb=" O SER D 7 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU D 70 " --> pdb=" O SER D 67 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.170A pdb=" N LEU D 11 " --> pdb=" O ASP D 105 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL D 85 " --> pdb=" O HIS D 38 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N GLN D 37 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N LEU D 46 " --> pdb=" O GLN D 37 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.170A pdb=" N LEU D 11 " --> pdb=" O ASP D 105 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLN D 90 " --> pdb=" O THR D 97 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N THR D 97 " --> pdb=" O GLN D 90 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 114 through 118 removed outlier: 3.606A pdb=" N ASN D 137 " --> pdb=" O SER D 114 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER D 177 " --> pdb=" O CYS D 134 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N TYR D 173 " --> pdb=" O ASN D 138 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 154 through 155 removed outlier: 4.582A pdb=" N TRP D 148 " --> pdb=" O GLN D 155 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 493 through 494 removed outlier: 6.255A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.188A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 91 through 94 removed outlier: 3.533A pdb=" N GLY E 237 " --> pdb=" O PHE E 93 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 129 through 130 Processing sheet with id=AC7, first strand: chain 'E' and resid 158 through 162 Processing sheet with id=AC8, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.326A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.981A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 10.570A pdb=" N THR E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.916A pdb=" N ILE E 294 " --> pdb=" O THR E 444 " (cutoff:3.500A) removed outlier: 10.376A pdb=" N ILE E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.191A pdb=" N VAL E 292 " --> pdb=" O ILE E 446 " (cutoff:3.500A) removed outlier: 9.578A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 9.908A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR E 330 " --> pdb=" O THR E 297 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE E 416 " --> pdb=" O CYS E 331 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE E 376 " --> pdb=" O PHE E 383 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 271 through 273 removed outlier: 6.530A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 9.908A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.578A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 11.191A pdb=" N VAL E 292 " --> pdb=" O ILE E 446 " (cutoff:3.500A) removed outlier: 10.376A pdb=" N ILE E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.916A pdb=" N ILE E 294 " --> pdb=" O THR E 444 " (cutoff:3.500A) removed outlier: 10.570A pdb=" N THR E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 301 through 308 removed outlier: 6.935A pdb=" N ASN E 301 " --> pdb=" O VAL E 322 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N VAL E 322 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 358 through 359 removed outlier: 3.523A pdb=" N ILE E 358 " --> pdb=" O TYR E 395 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 4 through 8 removed outlier: 3.574A pdb=" N TYR G 7 " --> pdb=" O SER G 21 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N SER G 21 " --> pdb=" O TYR G 7 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET G 80 " --> pdb=" O LEU G 20 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR G 70 " --> pdb=" O TYR G 79 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.723A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ARG G 38 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N LEU G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.939A pdb=" N CYS G 92 " --> pdb=" O TRP G 103 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N TRP G 103 " --> pdb=" O CYS G 92 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ARG G 94 " --> pdb=" O ASP G 101 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP G 101 " --> pdb=" O ARG G 94 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N HIS G 100D" --> pdb=" O VAL G 96 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 120 through 124 removed outlier: 5.264A pdb=" N ALA G 137 " --> pdb=" O VAL G 184 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL G 184 " --> pdb=" O ALA G 137 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N GLY G 139 " --> pdb=" O VAL G 182 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N VAL G 182 " --> pdb=" O GLY G 139 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N LEU G 141 " --> pdb=" O SER G 180 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N SER G 180 " --> pdb=" O LEU G 141 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N LYS G 143 " --> pdb=" O LEU G 178 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N LEU G 178 " --> pdb=" O LYS G 143 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 120 through 124 removed outlier: 5.264A pdb=" N ALA G 137 " --> pdb=" O VAL G 184 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL G 184 " --> pdb=" O ALA G 137 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N GLY G 139 " --> pdb=" O VAL G 182 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N VAL G 182 " --> pdb=" O GLY G 139 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N LEU G 141 " --> pdb=" O SER G 180 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N SER G 180 " --> pdb=" O LEU G 141 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N LYS G 143 " --> pdb=" O LEU G 178 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N LEU G 178 " --> pdb=" O LYS G 143 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 151 through 154 Processing sheet with id=AE1, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.503A pdb=" N THR H 22 " --> pdb=" O SER H 7 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLU H 17 " --> pdb=" O LEU H 78 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N VAL H 19 " --> pdb=" O SER H 76 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N SER H 76 " --> pdb=" O VAL H 19 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LEU H 21 " --> pdb=" O ALA H 74 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ALA H 74 " --> pdb=" O LEU H 21 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N CYS H 23 " --> pdb=" O THR H 72 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N THR H 72 " --> pdb=" O CYS H 23 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ALA H 25 " --> pdb=" O GLU H 70 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLU H 70 " --> pdb=" O ALA H 25 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.134A pdb=" N LEU H 11 " --> pdb=" O ASP H 105 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL H 85 " --> pdb=" O HIS H 38 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N GLN H 37 " --> pdb=" O LEU H 46 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N LEU H 46 " --> pdb=" O GLN H 37 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.134A pdb=" N LEU H 11 " --> pdb=" O ASP H 105 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLN H 90 " --> pdb=" O THR H 97 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR H 97 " --> pdb=" O GLN H 90 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 114 through 118 removed outlier: 3.666A pdb=" N ASN H 137 " --> pdb=" O SER H 114 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER H 177 " --> pdb=" O CYS H 134 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N TYR H 173 " --> pdb=" O ASN H 138 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 153 through 154 removed outlier: 3.513A pdb=" N VAL H 150 " --> pdb=" O ALA H 153 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 493 through 497 removed outlier: 3.617A pdb=" N CYS J 604 " --> pdb=" O VAL I 38 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 45 through 47 removed outlier: 4.133A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 91 through 94 removed outlier: 3.579A pdb=" N GLY I 237 " --> pdb=" O PHE I 93 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 129 through 130 Processing sheet with id=AF1, first strand: chain 'I' and resid 158 through 161 Processing sheet with id=AF2, first strand: chain 'I' and resid 201 through 203 removed outlier: 6.403A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 259 through 260 removed outlier: 7.005A pdb=" N LEU I 260 " --> pdb=" O THR I 450 " (cutoff:3.500A) removed outlier: 10.548A pdb=" N THR I 444 " --> pdb=" O ILE I 294 " (cutoff:3.500A) removed outlier: 11.881A pdb=" N ILE I 294 " --> pdb=" O THR I 444 " (cutoff:3.500A) removed outlier: 10.316A pdb=" N ILE I 446 " --> pdb=" O VAL I 292 " (cutoff:3.500A) removed outlier: 11.143A pdb=" N VAL I 292 " --> pdb=" O ILE I 446 " (cutoff:3.500A) removed outlier: 9.605A pdb=" N ASN I 448 " --> pdb=" O GLU I 290 " (cutoff:3.500A) removed outlier: 9.733A pdb=" N GLU I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N THR I 450 " --> pdb=" O LEU I 288 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 271 through 273 removed outlier: 6.483A pdb=" N THR I 450 " --> pdb=" O LEU I 288 " (cutoff:3.500A) removed outlier: 9.733A pdb=" N GLU I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 9.605A pdb=" N ASN I 448 " --> pdb=" O GLU I 290 " (cutoff:3.500A) removed outlier: 11.143A pdb=" N VAL I 292 " --> pdb=" O ILE I 446 " (cutoff:3.500A) removed outlier: 10.316A pdb=" N ILE I 446 " --> pdb=" O VAL I 292 " (cutoff:3.500A) removed outlier: 11.881A pdb=" N ILE I 294 " --> pdb=" O THR I 444 " (cutoff:3.500A) removed outlier: 10.548A pdb=" N THR I 444 " --> pdb=" O ILE I 294 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 301 through 308 removed outlier: 6.893A pdb=" N ASN I 301 " --> pdb=" O VAL I 322 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N VAL I 322 " --> pdb=" O ASN I 301 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N THR I 303 " --> pdb=" O GLY I 321 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 358 through 359 removed outlier: 3.616A pdb=" N ILE I 358 " --> pdb=" O TYR I 395 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 4 through 7 removed outlier: 4.198A pdb=" N SER K 21 " --> pdb=" O TYR K 7 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR K 70 " --> pdb=" O TYR K 79 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.642A pdb=" N GLY K 49 " --> pdb=" O TRP K 36 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ARG K 38 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N LEU K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.995A pdb=" N CYS K 92 " --> pdb=" O TRP K 103 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N TRP K 103 " --> pdb=" O CYS K 92 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ARG K 94 " --> pdb=" O ASP K 101 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N HIS K 100D" --> pdb=" O VAL K 96 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 120 through 124 removed outlier: 5.247A pdb=" N ALA K 137 " --> pdb=" O VAL K 184 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL K 184 " --> pdb=" O ALA K 137 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N GLY K 139 " --> pdb=" O VAL K 182 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N VAL K 182 " --> pdb=" O GLY K 139 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N LEU K 141 " --> pdb=" O SER K 180 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N SER K 180 " --> pdb=" O LEU K 141 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N LYS K 143 " --> pdb=" O LEU K 178 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N LEU K 178 " --> pdb=" O LYS K 143 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 120 through 124 removed outlier: 5.247A pdb=" N ALA K 137 " --> pdb=" O VAL K 184 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL K 184 " --> pdb=" O ALA K 137 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N GLY K 139 " --> pdb=" O VAL K 182 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N VAL K 182 " --> pdb=" O GLY K 139 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N LEU K 141 " --> pdb=" O SER K 180 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N SER K 180 " --> pdb=" O LEU K 141 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N LYS K 143 " --> pdb=" O LEU K 178 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N LEU K 178 " --> pdb=" O LYS K 143 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'K' and resid 151 through 154 Processing sheet with id=AG4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AG5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.236A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL L 85 " --> pdb=" O HIS L 38 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.236A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLN L 90 " --> pdb=" O THR L 97 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.942A pdb=" N SER L 177 " --> pdb=" O CYS L 134 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'L' and resid 153 through 155 removed outlier: 4.455A pdb=" N TRP L 148 " --> pdb=" O GLN L 155 " (cutoff:3.500A) 832 hydrogen bonds defined for protein. 2151 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: 9.65 Time building geometry restraints manager: 9.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7513 1.34 - 1.46: 5708 1.46 - 1.58: 10821 1.58 - 1.71: 0 1.71 - 1.83: 186 Bond restraints: 24228 Sorted by residual: bond pdb=" C ALA E 495 " pdb=" N PRO E 496 " ideal model delta sigma weight residual 1.334 1.380 -0.046 1.11e-02 8.12e+03 1.71e+01 bond pdb=" C1 NAG y 1 " pdb=" O5 NAG y 1 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.46e+00 bond pdb=" C1 NAG h 1 " pdb=" O5 NAG h 1 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.75e+00 bond pdb=" C GLU C 212 " pdb=" N PRO C 213 " ideal model delta sigma weight residual 1.333 1.363 -0.030 1.44e-02 4.82e+03 4.32e+00 bond pdb=" C1 NAG M 2 " pdb=" O5 NAG M 2 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 3.91e+00 ... (remaining 24223 not shown) Histogram of bond angle deviations from ideal: 97.89 - 105.19: 468 105.19 - 112.48: 12689 112.48 - 119.78: 8192 119.78 - 127.07: 11207 127.07 - 134.37: 327 Bond angle restraints: 32883 Sorted by residual: angle pdb=" N PRO E 496 " pdb=" CA PRO E 496 " pdb=" C PRO E 496 " ideal model delta sigma weight residual 110.55 120.50 -9.95 1.63e+00 3.76e-01 3.73e+01 angle pdb=" C ASN F 607 " pdb=" N VAL F 608 " pdb=" CA VAL F 608 " ideal model delta sigma weight residual 122.13 131.24 -9.11 1.85e+00 2.92e-01 2.42e+01 angle pdb=" N GLU C 212 " pdb=" CA GLU C 212 " pdb=" C GLU C 212 " ideal model delta sigma weight residual 109.81 118.69 -8.88 2.21e+00 2.05e-01 1.62e+01 angle pdb=" N THR K 28 " pdb=" CA THR K 28 " pdb=" C THR K 28 " ideal model delta sigma weight residual 110.80 103.24 7.56 2.13e+00 2.20e-01 1.26e+01 angle pdb=" CA VAL J 608 " pdb=" CB VAL J 608 " pdb=" CG2 VAL J 608 " ideal model delta sigma weight residual 110.40 116.35 -5.95 1.70e+00 3.46e-01 1.22e+01 ... (remaining 32878 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.47: 14402 22.47 - 44.94: 601 44.94 - 67.40: 112 67.40 - 89.87: 78 89.87 - 112.34: 36 Dihedral angle restraints: 15229 sinusoidal: 6656 harmonic: 8573 Sorted by residual: dihedral pdb=" CB CYS J 598 " pdb=" SG CYS J 598 " pdb=" SG CYS J 604 " pdb=" CB CYS J 604 " ideal model delta sinusoidal sigma weight residual -86.00 -143.72 57.72 1 1.00e+01 1.00e-02 4.47e+01 dihedral pdb=" CB CYS B 598 " pdb=" SG CYS B 598 " pdb=" SG CYS B 604 " pdb=" CB CYS B 604 " ideal model delta sinusoidal sigma weight residual -86.00 -141.23 55.23 1 1.00e+01 1.00e-02 4.13e+01 dihedral pdb=" CB CYS I 126 " pdb=" SG CYS I 126 " pdb=" SG CYS I 196 " pdb=" CB CYS I 196 " ideal model delta sinusoidal sigma weight residual -86.00 -139.95 53.95 1 1.00e+01 1.00e-02 3.95e+01 ... (remaining 15226 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.153: 3814 0.153 - 0.305: 25 0.305 - 0.458: 5 0.458 - 0.611: 1 0.611 - 0.763: 1 Chirality restraints: 3846 Sorted by residual: chirality pdb=" C1 NAG j 1 " pdb=" ND2 ASN E 262 " pdb=" C2 NAG j 1 " pdb=" O5 NAG j 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.64 -0.76 2.00e-01 2.50e+01 1.46e+01 chirality pdb=" C1 NAG 0 1 " pdb=" ND2 ASN I 262 " pdb=" C2 NAG 0 1 " pdb=" O5 NAG 0 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.22e+00 chirality pdb=" CA THR E 198 " pdb=" N THR E 198 " pdb=" C THR E 198 " pdb=" CB THR E 198 " both_signs ideal model delta sigma weight residual False 2.53 2.14 0.39 2.00e-01 2.50e+01 3.79e+00 ... (remaining 3843 not shown) Planarity restraints: 4139 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 610 " 0.026 2.00e-02 2.50e+03 4.09e-02 4.18e+01 pdb=" CG TRP F 610 " -0.100 2.00e-02 2.50e+03 pdb=" CD1 TRP F 610 " 0.064 2.00e-02 2.50e+03 pdb=" CD2 TRP F 610 " -0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP F 610 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP F 610 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP F 610 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 610 " -0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 610 " 0.040 2.00e-02 2.50e+03 pdb=" CH2 TRP F 610 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL F 608 " 0.069 5.00e-02 4.00e+02 1.06e-01 1.79e+01 pdb=" N PRO F 609 " -0.183 5.00e-02 4.00e+02 pdb=" CA PRO F 609 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO F 609 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN I 339 " 0.029 2.00e-02 2.50e+03 2.83e-02 1.00e+01 pdb=" CG ASN I 339 " -0.037 2.00e-02 2.50e+03 pdb=" OD1 ASN I 339 " 0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN I 339 " -0.030 2.00e-02 2.50e+03 pdb=" C1 NAG y 1 " 0.029 2.00e-02 2.50e+03 ... (remaining 4136 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 306 2.61 - 3.18: 21252 3.18 - 3.75: 35537 3.75 - 4.33: 49244 4.33 - 4.90: 81012 Nonbonded interactions: 187351 Sorted by model distance: nonbonded pdb=" O6 BMA 4 3 " pdb=" O3 MAN K 301 " model vdw 2.037 2.440 nonbonded pdb=" O MET E 84 " pdb=" OG SER E 243 " model vdw 2.088 2.440 nonbonded pdb=" OD2 ASP H 105 " pdb=" OH TYR H 173 " model vdw 2.099 2.440 nonbonded pdb=" OH TYR C 70 " pdb=" OD2 ASP C 81 " model vdw 2.099 2.440 nonbonded pdb=" O6 BMA R 3 " pdb=" O6 MAN C 301 " model vdw 2.105 2.440 ... (remaining 187346 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '0' selection = chain 'M' selection = chain 'N' selection = chain 'e' selection = chain 'j' selection = chain 'v' } ncs_group { reference = chain '4' selection = chain 'R' selection = chain 'n' } ncs_group { reference = (chain 'A' and (resid 32 through 503 or resid 601 through 604)) selection = (chain 'E' and (resid 32 through 56 or resid 75 through 144 or resid 157 through \ 396 or resid 398 through 503 or resid 601 through 604)) selection = (chain 'I' and (resid 32 through 56 or resid 75 through 144 or resid 157 through \ 396 or resid 409 through 503 or resid 601 through 604)) } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'h' selection = chain 'y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.990 Check model and map are aligned: 0.300 Set scattering table: 0.200 Process input model: 60.700 Find NCS groups from input model: 1.570 Set up NCS constraints: 0.300 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:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 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 : 0.005 0.063 24228 Z= 0.315 Angle : 0.844 9.954 32883 Z= 0.423 Chirality : 0.054 0.763 3846 Planarity : 0.005 0.106 4124 Dihedral : 15.297 112.338 9592 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.10 % Favored : 93.86 % Rotamer: Outliers : 0.12 % Allowed : 0.23 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.15), residues: 2901 helix: 0.93 (0.28), residues: 391 sheet: -0.98 (0.16), residues: 879 loop : -1.30 (0.15), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.100 0.003 TRP F 610 HIS 0.006 0.002 HIS C 35 PHE 0.018 0.002 PHE H 71 TYR 0.033 0.002 TYR H 91 ARG 0.007 0.001 ARG E 432 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 2584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 72 time to evaluate : 2.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 626 MET cc_start: 0.7053 (tpp) cc_final: 0.6522 (tpp) REVERT: J 626 MET cc_start: 0.6552 (ptm) cc_final: 0.5996 (tmm) outliers start: 3 outliers final: 1 residues processed: 75 average time/residue: 0.3568 time to fit residues: 44.9277 Evaluate side-chains 54 residues out of total 2584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 53 time to evaluate : 2.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 247 optimal weight: 0.0070 chunk 222 optimal weight: 10.0000 chunk 123 optimal weight: 5.9990 chunk 75 optimal weight: 20.0000 chunk 149 optimal weight: 0.0020 chunk 118 optimal weight: 3.9990 chunk 229 optimal weight: 5.9990 chunk 88 optimal weight: 9.9990 chunk 139 optimal weight: 7.9990 chunk 170 optimal weight: 20.0000 chunk 266 optimal weight: 30.0000 overall best weight: 3.2012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 461 ASN C 164 HIS C 171 GLN C 192 GLN D 38 HIS D 137 ASN E 72 HIS F 577 GLN G 6 GLN H 38 HIS H 155 GLN K 6 GLN K 164 HIS L 137 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24228 Z= 0.225 Angle : 0.675 9.271 32883 Z= 0.342 Chirality : 0.049 0.691 3846 Planarity : 0.005 0.059 4124 Dihedral : 10.831 67.067 4211 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.48 % Favored : 94.48 % Rotamer: Outliers : 0.08 % Allowed : 2.40 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.15), residues: 2901 helix: 1.71 (0.29), residues: 359 sheet: -0.74 (0.16), residues: 937 loop : -1.21 (0.15), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP F 610 HIS 0.004 0.001 HIS I 417 PHE 0.016 0.002 PHE H 71 TYR 0.021 0.002 TYR E 191 ARG 0.004 0.000 ARG F 585 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 2584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 57 time to evaluate : 2.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.7755 (mpp) cc_final: 0.7378 (mpp) REVERT: B 626 MET cc_start: 0.5790 (tmm) cc_final: 0.5141 (tmm) REVERT: E 100 MET cc_start: 0.9035 (ptt) cc_final: 0.8466 (pmm) REVERT: F 530 MET cc_start: 0.6816 (mpp) cc_final: 0.6433 (mpp) REVERT: K 89 MET cc_start: 0.8969 (ttm) cc_final: 0.8661 (ttp) outliers start: 2 outliers final: 0 residues processed: 59 average time/residue: 0.3466 time to fit residues: 35.7641 Evaluate side-chains 51 residues out of total 2584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 2.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 147 optimal weight: 20.0000 chunk 82 optimal weight: 20.0000 chunk 221 optimal weight: 10.0000 chunk 181 optimal weight: 20.0000 chunk 73 optimal weight: 50.0000 chunk 266 optimal weight: 30.0000 chunk 287 optimal weight: 20.0000 chunk 237 optimal weight: 9.9990 chunk 264 optimal weight: 40.0000 chunk 90 optimal weight: 7.9990 chunk 213 optimal weight: 1.9990 overall best weight: 9.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 ASN A 461 ASN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 577 GLN B 607 ASN ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 147 GLN E 72 HIS ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 607 ASN F 625 ASN G 171 GLN ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 105 HIS ** I 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 334 ASN J 625 ASN K 102 HIS K 171 GLN ** L 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.093 24228 Z= 0.555 Angle : 0.900 13.238 32883 Z= 0.455 Chirality : 0.052 0.608 3846 Planarity : 0.006 0.058 4124 Dihedral : 10.535 59.916 4211 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.48 % Favored : 91.49 % Rotamer: Outliers : 0.12 % Allowed : 5.04 % Favored : 94.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.15), residues: 2901 helix: 0.91 (0.28), residues: 388 sheet: -1.21 (0.16), residues: 913 loop : -1.69 (0.15), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP B 610 HIS 0.008 0.002 HIS G 100D PHE 0.041 0.003 PHE K 69 TYR 0.026 0.003 TYR E 191 ARG 0.012 0.001 ARG D 108 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 2584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 54 time to evaluate : 2.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 626 MET cc_start: 0.7034 (ttp) cc_final: 0.6640 (tmm) REVERT: E 95 MET cc_start: 0.7461 (ppp) cc_final: 0.7019 (ppp) REVERT: E 100 MET cc_start: 0.9191 (ptt) cc_final: 0.8633 (pmm) REVERT: E 145 MET cc_start: 0.6693 (mtp) cc_final: 0.6386 (mtp) REVERT: F 530 MET cc_start: 0.7514 (mpp) cc_final: 0.6789 (mpp) REVERT: H 96 TRP cc_start: 0.8423 (OUTLIER) cc_final: 0.7498 (m100) REVERT: I 396 MET cc_start: 0.8820 (ptt) cc_final: 0.8466 (mtp) REVERT: I 426 MET cc_start: 0.9134 (tmm) cc_final: 0.8508 (tmm) outliers start: 3 outliers final: 0 residues processed: 57 average time/residue: 0.3498 time to fit residues: 34.5727 Evaluate side-chains 51 residues out of total 2584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 50 time to evaluate : 2.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 263 optimal weight: 0.3980 chunk 200 optimal weight: 8.9990 chunk 138 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 127 optimal weight: 5.9990 chunk 178 optimal weight: 6.9990 chunk 267 optimal weight: 8.9990 chunk 283 optimal weight: 20.0000 chunk 139 optimal weight: 6.9990 chunk 253 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 HIS D 210 ASN E 229 ASN E 343 GLN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 HIS L 210 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 24228 Z= 0.256 Angle : 0.644 9.279 32883 Z= 0.331 Chirality : 0.046 0.519 3846 Planarity : 0.004 0.051 4124 Dihedral : 9.271 59.774 4211 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.86 % Favored : 94.11 % Rotamer: Outliers : 0.08 % Allowed : 2.21 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.15), residues: 2901 helix: 1.43 (0.29), residues: 388 sheet: -1.01 (0.16), residues: 905 loop : -1.44 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP E 427 HIS 0.008 0.001 HIS A 374 PHE 0.020 0.002 PHE L 71 TYR 0.020 0.002 TYR E 191 ARG 0.003 0.000 ARG C 94 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 2584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 59 time to evaluate : 3.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8109 (ppp) cc_final: 0.7785 (ppp) REVERT: B 626 MET cc_start: 0.7079 (ttp) cc_final: 0.6651 (tmm) REVERT: E 100 MET cc_start: 0.9095 (ptt) cc_final: 0.8553 (pmm) REVERT: F 530 MET cc_start: 0.7513 (mpp) cc_final: 0.7100 (mpp) REVERT: I 396 MET cc_start: 0.8718 (ptt) cc_final: 0.8496 (mtp) REVERT: I 426 MET cc_start: 0.9082 (tmm) cc_final: 0.8499 (tmm) REVERT: K 89 MET cc_start: 0.9198 (ttm) cc_final: 0.8807 (ttp) outliers start: 2 outliers final: 0 residues processed: 61 average time/residue: 0.3668 time to fit residues: 38.3964 Evaluate side-chains 51 residues out of total 2584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 2.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 235 optimal weight: 0.2980 chunk 160 optimal weight: 5.9990 chunk 4 optimal weight: 20.0000 chunk 210 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 chunk 241 optimal weight: 5.9990 chunk 195 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 144 optimal weight: 10.0000 chunk 254 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 overall best weight: 4.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 GLN A 461 ASN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 607 ASN ** F 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 24228 Z= 0.248 Angle : 0.621 9.412 32883 Z= 0.316 Chirality : 0.046 0.485 3846 Planarity : 0.004 0.050 4124 Dihedral : 8.890 59.726 4211 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.15), residues: 2901 helix: 1.60 (0.29), residues: 388 sheet: -1.01 (0.17), residues: 880 loop : -1.44 (0.15), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 427 HIS 0.004 0.001 HIS A 105 PHE 0.019 0.002 PHE L 71 TYR 0.017 0.002 TYR E 191 ARG 0.003 0.000 ARG C 71 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 2584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 2.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8017 (ppp) cc_final: 0.7630 (ppp) REVERT: A 396 MET cc_start: 0.8155 (pmm) cc_final: 0.7806 (pmm) REVERT: B 626 MET cc_start: 0.7285 (ttp) cc_final: 0.6899 (tmm) REVERT: E 100 MET cc_start: 0.9092 (ptt) cc_final: 0.8677 (pmm) REVERT: F 530 MET cc_start: 0.7570 (mpp) cc_final: 0.6969 (mpp) REVERT: I 426 MET cc_start: 0.9105 (tmm) cc_final: 0.8532 (tmm) REVERT: K 89 MET cc_start: 0.9218 (ttm) cc_final: 0.8848 (ttp) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.3547 time to fit residues: 32.3901 Evaluate side-chains 50 residues out of total 2584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 2.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 95 optimal weight: 5.9990 chunk 255 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 166 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 283 optimal weight: 30.0000 chunk 235 optimal weight: 9.9990 chunk 131 optimal weight: 20.0000 chunk 23 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 chunk 148 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS A 133 ASN ** A 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 GLN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 334 ASN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 210 ASN ** J 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.4825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 24228 Z= 0.348 Angle : 0.685 9.954 32883 Z= 0.347 Chirality : 0.047 0.479 3846 Planarity : 0.004 0.052 4124 Dihedral : 8.830 58.243 4211 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.15), residues: 2901 helix: 1.51 (0.29), residues: 399 sheet: -1.07 (0.17), residues: 864 loop : -1.65 (0.15), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP L 96 HIS 0.006 0.001 HIS E 374 PHE 0.021 0.002 PHE L 71 TYR 0.019 0.002 TYR H 91 ARG 0.006 0.000 ARG D 108 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 2584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 2.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8143 (ppp) cc_final: 0.7716 (ppp) REVERT: A 396 MET cc_start: 0.8274 (pmm) cc_final: 0.7910 (pmm) REVERT: E 100 MET cc_start: 0.9187 (ptt) cc_final: 0.8590 (pmm) REVERT: I 426 MET cc_start: 0.9099 (tmm) cc_final: 0.8149 (tmm) REVERT: J 626 MET cc_start: 0.7934 (tmm) cc_final: 0.7725 (tmm) REVERT: K 89 MET cc_start: 0.9234 (ttm) cc_final: 0.8882 (ttp) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.3383 time to fit residues: 30.7444 Evaluate side-chains 49 residues out of total 2584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 2.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 273 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 207 optimal weight: 6.9990 chunk 160 optimal weight: 2.9990 chunk 238 optimal weight: 7.9990 chunk 158 optimal weight: 5.9990 chunk 282 optimal weight: 7.9990 chunk 176 optimal weight: 20.0000 chunk 172 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 GLN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 164 HIS ** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.5000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24228 Z= 0.204 Angle : 0.594 9.473 32883 Z= 0.304 Chirality : 0.045 0.465 3846 Planarity : 0.004 0.056 4124 Dihedral : 8.452 59.384 4211 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.15), residues: 2901 helix: 1.60 (0.29), residues: 399 sheet: -0.90 (0.17), residues: 839 loop : -1.53 (0.15), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K 36 HIS 0.008 0.001 HIS I 374 PHE 0.019 0.001 PHE L 71 TYR 0.036 0.001 TYR L 91 ARG 0.003 0.000 ARG D 108 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 2584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 2.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8134 (ppp) cc_final: 0.7729 (ppp) REVERT: A 396 MET cc_start: 0.8107 (pmm) cc_final: 0.7813 (pmm) REVERT: E 396 MET cc_start: 0.8812 (pmm) cc_final: 0.7701 (mtt) REVERT: F 530 MET cc_start: 0.7651 (mpp) cc_final: 0.6297 (mmp) REVERT: I 426 MET cc_start: 0.9017 (tmm) cc_final: 0.8276 (tmm) REVERT: K 89 MET cc_start: 0.9226 (ttm) cc_final: 0.8868 (ttp) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.3417 time to fit residues: 31.9591 Evaluate side-chains 50 residues out of total 2584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 2.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 174 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 chunk 168 optimal weight: 6.9990 chunk 85 optimal weight: 7.9990 chunk 55 optimal weight: 9.9990 chunk 54 optimal weight: 4.9990 chunk 179 optimal weight: 20.0000 chunk 192 optimal weight: 8.9990 chunk 139 optimal weight: 9.9990 chunk 26 optimal weight: 7.9990 chunk 221 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321AGLN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.5391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 24228 Z= 0.344 Angle : 0.671 9.428 32883 Z= 0.340 Chirality : 0.046 0.477 3846 Planarity : 0.004 0.059 4124 Dihedral : 8.374 58.407 4211 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.15), residues: 2901 helix: 1.60 (0.29), residues: 399 sheet: -1.03 (0.17), residues: 870 loop : -1.69 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP L 96 HIS 0.005 0.001 HIS H 38 PHE 0.022 0.002 PHE L 71 TYR 0.016 0.002 TYR G 50 ARG 0.005 0.000 ARG I 501 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 2584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 2.776 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8264 (ppp) cc_final: 0.7819 (ppp) REVERT: A 396 MET cc_start: 0.8177 (pmm) cc_final: 0.7867 (pmm) REVERT: C 89 MET cc_start: 0.9201 (ttp) cc_final: 0.8841 (ttm) REVERT: E 396 MET cc_start: 0.8839 (pmm) cc_final: 0.7746 (mtt) REVERT: F 530 MET cc_start: 0.7791 (mpp) cc_final: 0.6474 (mmp) REVERT: I 426 MET cc_start: 0.9088 (tmm) cc_final: 0.8565 (tmm) REVERT: K 89 MET cc_start: 0.9250 (ttm) cc_final: 0.8884 (ttp) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.3633 time to fit residues: 32.3259 Evaluate side-chains 49 residues out of total 2584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 2.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 256 optimal weight: 6.9990 chunk 270 optimal weight: 7.9990 chunk 246 optimal weight: 5.9990 chunk 263 optimal weight: 7.9990 chunk 158 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 chunk 206 optimal weight: 0.8980 chunk 80 optimal weight: 8.9990 chunk 237 optimal weight: 8.9990 chunk 248 optimal weight: 5.9990 chunk 262 optimal weight: 9.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 321AGLN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.5569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 24228 Z= 0.285 Angle : 0.637 9.391 32883 Z= 0.325 Chirality : 0.046 0.459 3846 Planarity : 0.004 0.059 4124 Dihedral : 8.143 58.252 4211 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.15), residues: 2901 helix: 1.58 (0.29), residues: 400 sheet: -1.00 (0.17), residues: 868 loop : -1.72 (0.15), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP L 96 HIS 0.004 0.001 HIS C 102 PHE 0.019 0.002 PHE L 71 TYR 0.024 0.002 TYR H 91 ARG 0.003 0.000 ARG A 501 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 2584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 2.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8243 (ppp) cc_final: 0.7819 (ppp) REVERT: A 396 MET cc_start: 0.8214 (pmm) cc_final: 0.7913 (pmm) REVERT: E 100 MET cc_start: 0.9148 (ptt) cc_final: 0.8456 (pmm) REVERT: E 396 MET cc_start: 0.8896 (pmm) cc_final: 0.7871 (mtt) REVERT: F 530 MET cc_start: 0.7775 (mpp) cc_final: 0.6430 (mmp) REVERT: I 145 MET cc_start: 0.6164 (mtp) cc_final: 0.5962 (mtp) REVERT: I 426 MET cc_start: 0.9035 (tmm) cc_final: 0.8648 (tmm) REVERT: K 89 MET cc_start: 0.9249 (ttm) cc_final: 0.8905 (ttp) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.3387 time to fit residues: 32.2354 Evaluate side-chains 51 residues out of total 2584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 2.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 172 optimal weight: 9.9990 chunk 278 optimal weight: 20.0000 chunk 169 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 193 optimal weight: 50.0000 chunk 291 optimal weight: 30.0000 chunk 268 optimal weight: 6.9990 chunk 232 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 179 optimal weight: 20.0000 chunk 142 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 321AGLN ** J 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.5930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 24228 Z= 0.369 Angle : 0.701 9.921 32883 Z= 0.355 Chirality : 0.047 0.461 3846 Planarity : 0.004 0.059 4124 Dihedral : 8.277 59.491 4211 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.15), residues: 2901 helix: 1.48 (0.29), residues: 401 sheet: -1.19 (0.17), residues: 878 loop : -1.83 (0.15), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 96 HIS 0.005 0.002 HIS H 38 PHE 0.021 0.002 PHE L 71 TYR 0.017 0.002 TYR C 50 ARG 0.004 0.000 ARG I 501 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 2584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 2.876 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8355 (ppp) cc_final: 0.7920 (ppp) REVERT: A 396 MET cc_start: 0.8351 (pmm) cc_final: 0.8058 (pmm) REVERT: E 95 MET cc_start: 0.8485 (ppp) cc_final: 0.8244 (ppp) REVERT: E 145 MET cc_start: 0.6434 (mtp) cc_final: 0.5984 (mtp) REVERT: E 396 MET cc_start: 0.8889 (pmm) cc_final: 0.7925 (mtt) REVERT: E 473 MET cc_start: 0.8540 (mmp) cc_final: 0.8338 (tpp) REVERT: F 530 MET cc_start: 0.7850 (mpp) cc_final: 0.6476 (mmp) REVERT: I 145 MET cc_start: 0.6332 (mtp) cc_final: 0.5868 (mtm) REVERT: I 426 MET cc_start: 0.9121 (tmm) cc_final: 0.8491 (tmm) REVERT: K 89 MET cc_start: 0.9262 (ttm) cc_final: 0.8883 (ttp) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.3377 time to fit residues: 31.0625 Evaluate side-chains 49 residues out of total 2584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 2.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 184 optimal weight: 9.9990 chunk 247 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 214 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 232 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 239 optimal weight: 20.0000 chunk 29 optimal weight: 6.9990 chunk 42 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 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 = 0.3391 r_free = 0.3391 target = 0.038733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.027585 restraints weight = 248781.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.027706 restraints weight = 142032.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.027545 restraints weight = 133300.994| |-----------------------------------------------------------------------------| r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.6058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 24228 Z= 0.325 Angle : 0.658 9.704 32883 Z= 0.336 Chirality : 0.046 0.444 3846 Planarity : 0.004 0.057 4124 Dihedral : 8.151 59.077 4211 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.15), residues: 2901 helix: 1.51 (0.29), residues: 401 sheet: -1.10 (0.17), residues: 871 loop : -1.88 (0.15), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 96 HIS 0.004 0.001 HIS H 38 PHE 0.020 0.002 PHE L 71 TYR 0.019 0.002 TYR H 91 ARG 0.003 0.000 ARG I 501 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2964.71 seconds wall clock time: 57 minutes 3.93 seconds (3423.93 seconds total)