Starting phenix.real_space_refine on Fri Jun 20 20:17:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tcn_25814/06_2025/7tcn_25814_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tcn_25814/06_2025/7tcn_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/cci-nas-00/data/ceres_data/7tcn_25814/06_2025/7tcn_25814.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tcn_25814/06_2025/7tcn_25814.map" model { file = "/net/cci-nas-00/data/ceres_data/7tcn_25814/06_2025/7tcn_25814_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tcn_25814/06_2025/7tcn_25814_neut.cif" } 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. Time to flip 6 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 13.87, per 1000 atoms: 0.58 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA 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: 6.72 Conformation dependent library (CDL) restraints added in 3.2 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: 3.72 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: 9.73 Time building geometry restraints manager: 7.86 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: 0.00 - 1.99: 31687 1.99 - 3.98: 960 3.98 - 5.97: 188 5.97 - 7.96: 41 7.96 - 9.95: 7 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 3.040 nonbonded pdb=" O MET E 84 " pdb=" OG SER E 243 " model vdw 2.088 3.040 nonbonded pdb=" OD2 ASP H 105 " pdb=" OH TYR H 173 " model vdw 2.099 3.040 nonbonded pdb=" OH TYR C 70 " pdb=" OD2 ASP C 81 " model vdw 2.099 3.040 nonbonded pdb=" O6 BMA R 3 " pdb=" O6 MAN C 301 " model vdw 2.105 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 2.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.930 Check model and map are aligned: 0.190 Set scattering table: 0.230 Process input model: 56.710 Find NCS groups from input model: 1.520 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.040 ------------------------------------------------------------------------------- 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 24305 Z= 0.216 Angle : 0.893 20.259 33075 Z= 0.435 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00810 ( 15) link_NAG-ASN : angle 5.16609 ( 45) link_BETA1-4 : bond 0.01626 ( 20) link_BETA1-4 : angle 4.87061 ( 60) link_ALPHA1-3 : bond 0.01068 ( 3) link_ALPHA1-3 : angle 3.02181 ( 9) hydrogen bonds : bond 0.24250 ( 766) hydrogen bonds : angle 8.75122 ( 2151) SS BOND : bond 0.00421 ( 39) SS BOND : angle 1.81059 ( 78) covalent geometry : bond 0.00480 (24228) covalent geometry : angle 0.84426 (32883) *********************** 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 to be fit. rotamer outliers: 3 poor density : 72 time to evaluate : 2.947 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: 0.3701 time to fit residues: 46.8497 Evaluate side-chains 54 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 2.924 ------------------------------------------------------------------------------- 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: 0.8980 chunk 222 optimal weight: 6.9990 chunk 123 optimal weight: 2.9990 chunk 75 optimal weight: 20.0000 chunk 149 optimal weight: 9.9990 chunk 118 optimal weight: 6.9990 chunk 229 optimal weight: 0.9990 chunk 88 optimal weight: 8.9990 chunk 139 optimal weight: 7.9990 chunk 170 optimal weight: 20.0000 chunk 266 optimal weight: 30.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 607 ASN C 164 HIS C 171 GLN D 38 HIS D 137 ASN E 33 ASN E 72 HIS F 577 GLN F 607 ASN H 38 HIS H 155 GLN I 33 ASN K 164 HIS L 137 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.036444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.029483 restraints weight = 287203.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.030238 restraints weight = 151726.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.030694 restraints weight = 100062.027| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 24305 Z= 0.184 Angle : 0.741 13.875 33075 Z= 0.365 Chirality : 0.049 0.473 3846 Planarity : 0.005 0.060 4124 Dihedral : 11.253 68.635 4211 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.45 % Favored : 94.52 % Rotamer: Outliers : 0.12 % Allowed : 2.32 % Favored : 97.56 % 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: -1.07 (0.16), residues: 2901 helix: 1.68 (0.29), residues: 358 sheet: -0.82 (0.16), residues: 944 loop : -1.19 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP F 610 HIS 0.005 0.001 HIS I 417 PHE 0.017 0.002 PHE H 71 TYR 0.021 0.002 TYR E 191 ARG 0.004 0.000 ARG I 169 Details of bonding type rmsd link_NAG-ASN : bond 0.02111 ( 15) link_NAG-ASN : angle 4.32576 ( 45) link_BETA1-4 : bond 0.01008 ( 20) link_BETA1-4 : angle 3.52097 ( 60) link_ALPHA1-3 : bond 0.00256 ( 3) link_ALPHA1-3 : angle 2.48360 ( 9) hydrogen bonds : bond 0.04603 ( 766) hydrogen bonds : angle 6.29724 ( 2151) SS BOND : bond 0.00394 ( 39) SS BOND : angle 1.20533 ( 78) covalent geometry : bond 0.00398 (24228) covalent geometry : angle 0.70617 (32883) *********************** 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 60 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 3.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 626 MET cc_start: 0.5729 (tmm) cc_final: 0.5120 (tmm) REVERT: E 100 MET cc_start: 0.8914 (ptt) cc_final: 0.8461 (pmm) REVERT: F 530 MET cc_start: 0.6899 (mpp) cc_final: 0.6552 (mpp) outliers start: 3 outliers final: 0 residues processed: 60 average time/residue: 0.3662 time to fit residues: 38.5769 Evaluate side-chains 52 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 2.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 45 optimal weight: 0.7980 chunk 274 optimal weight: 30.0000 chunk 164 optimal weight: 20.0000 chunk 91 optimal weight: 20.0000 chunk 225 optimal weight: 9.9990 chunk 211 optimal weight: 10.0000 chunk 110 optimal weight: 10.0000 chunk 265 optimal weight: 8.9990 chunk 80 optimal weight: 5.9990 chunk 257 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 overall best weight: 6.1588 ------------------------------------------------------------------------------- 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** B 577 GLN C 171 GLN ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 147 GLN E 33 ASN E 72 HIS ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 105 HIS J 625 ASN K 6 GLN ** L 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.033217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.026249 restraints weight = 293769.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.026933 restraints weight = 155879.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.027361 restraints weight = 104028.712| |-----------------------------------------------------------------------------| r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 24305 Z= 0.257 Angle : 0.782 13.951 33075 Z= 0.389 Chirality : 0.049 0.494 3846 Planarity : 0.005 0.053 4124 Dihedral : 9.181 59.513 4211 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.83 % Favored : 93.14 % Rotamer: Outliers : 0.12 % Allowed : 5.15 % Favored : 94.73 % 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: -1.33 (0.15), residues: 2901 helix: 1.19 (0.28), residues: 373 sheet: -0.86 (0.16), residues: 912 loop : -1.40 (0.15), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP L 96 HIS 0.007 0.002 HIS A 105 PHE 0.030 0.003 PHE K 69 TYR 0.024 0.002 TYR C 91 ARG 0.006 0.001 ARG K 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00641 ( 15) link_NAG-ASN : angle 4.26298 ( 45) link_BETA1-4 : bond 0.01213 ( 20) link_BETA1-4 : angle 3.16110 ( 60) link_ALPHA1-3 : bond 0.01239 ( 3) link_ALPHA1-3 : angle 1.53162 ( 9) hydrogen bonds : bond 0.05468 ( 766) hydrogen bonds : angle 6.01802 ( 2151) SS BOND : bond 0.00579 ( 39) SS BOND : angle 1.11506 ( 78) covalent geometry : bond 0.00570 (24228) covalent geometry : angle 0.75404 (32883) *********************** 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 60 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 2.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 95 MET cc_start: 0.7538 (ppp) cc_final: 0.7048 (ppp) REVERT: E 100 MET cc_start: 0.8969 (ptt) cc_final: 0.8643 (pmm) REVERT: E 396 MET cc_start: 0.8823 (pmm) cc_final: 0.8580 (pmm) REVERT: F 530 MET cc_start: 0.7327 (mpp) cc_final: 0.6773 (mpp) REVERT: H 96 TRP cc_start: 0.8472 (OUTLIER) cc_final: 0.7551 (m100) REVERT: I 396 MET cc_start: 0.8619 (ptt) cc_final: 0.8377 (mtp) REVERT: J 626 MET cc_start: 0.7873 (tmm) cc_final: 0.7643 (tmm) REVERT: K 89 MET cc_start: 0.8223 (ttp) cc_final: 0.7862 (ttm) REVERT: L 96 TRP cc_start: 0.8512 (OUTLIER) cc_final: 0.7586 (m100) outliers start: 3 outliers final: 0 residues processed: 60 average time/residue: 0.4028 time to fit residues: 41.4965 Evaluate side-chains 52 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 3.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 20 optimal weight: 9.9990 chunk 206 optimal weight: 0.5980 chunk 187 optimal weight: 5.9990 chunk 119 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 chunk 235 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 chunk 204 optimal weight: 0.4980 chunk 283 optimal weight: 0.8980 chunk 185 optimal weight: 20.0000 chunk 273 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS A 334 ASN A 461 ASN D 38 HIS D 210 ASN H 38 HIS L 210 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.040508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.028800 restraints weight = 249950.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.029758 restraints weight = 145742.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.030382 restraints weight = 104589.757| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 24305 Z= 0.110 Angle : 0.639 12.679 33075 Z= 0.318 Chirality : 0.046 0.471 3846 Planarity : 0.004 0.047 4124 Dihedral : 8.287 58.717 4211 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.62 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % 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: -0.93 (0.16), residues: 2901 helix: 1.44 (0.28), residues: 385 sheet: -0.53 (0.17), residues: 910 loop : -1.18 (0.16), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 631 HIS 0.005 0.001 HIS A 374 PHE 0.016 0.001 PHE L 71 TYR 0.019 0.001 TYR L 91 ARG 0.005 0.000 ARG D 108 Details of bonding type rmsd link_NAG-ASN : bond 0.00453 ( 15) link_NAG-ASN : angle 3.82730 ( 45) link_BETA1-4 : bond 0.00833 ( 20) link_BETA1-4 : angle 2.69447 ( 60) link_ALPHA1-3 : bond 0.00404 ( 3) link_ALPHA1-3 : angle 2.35768 ( 9) hydrogen bonds : bond 0.03734 ( 766) hydrogen bonds : angle 5.49159 ( 2151) SS BOND : bond 0.00348 ( 39) SS BOND : angle 1.28627 ( 78) covalent geometry : bond 0.00234 (24228) covalent geometry : angle 0.60995 (32883) *********************** 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 57 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 2.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7739 (ppp) cc_final: 0.7421 (ppp) REVERT: B 530 MET cc_start: 0.7345 (mmm) cc_final: 0.6705 (mmp) REVERT: B 626 MET cc_start: 0.6203 (tmm) cc_final: 0.5683 (tmm) REVERT: C 89 MET cc_start: 0.8335 (ttp) cc_final: 0.7864 (ttm) REVERT: E 100 MET cc_start: 0.8985 (ptt) cc_final: 0.8578 (pmm) REVERT: F 530 MET cc_start: 0.6943 (mpp) cc_final: 0.6386 (mpp) REVERT: I 396 MET cc_start: 0.8759 (ptt) cc_final: 0.8392 (mtp) REVERT: K 89 MET cc_start: 0.8184 (ttp) cc_final: 0.7814 (ttm) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.3368 time to fit residues: 33.8443 Evaluate side-chains 51 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 2.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 197 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 86 optimal weight: 20.0000 chunk 232 optimal weight: 10.0000 chunk 141 optimal weight: 8.9990 chunk 243 optimal weight: 0.0270 chunk 116 optimal weight: 20.0000 chunk 156 optimal weight: 10.0000 chunk 94 optimal weight: 20.0000 chunk 162 optimal weight: 8.9990 chunk 53 optimal weight: 8.9990 overall best weight: 6.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321AGLN E 321AGLN H 210 ASN I 321AGLN I 334 ASN K 102 HIS ** L 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.032509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.025529 restraints weight = 295895.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.026208 restraints weight = 157105.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.026637 restraints weight = 104878.640| |-----------------------------------------------------------------------------| r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 24305 Z= 0.255 Angle : 0.735 12.552 33075 Z= 0.363 Chirality : 0.047 0.487 3846 Planarity : 0.005 0.043 4124 Dihedral : 8.340 56.779 4211 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % 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: 1.40 (0.28), residues: 399 sheet: -0.82 (0.17), residues: 854 loop : -1.53 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 427 HIS 0.005 0.001 HIS H 38 PHE 0.022 0.002 PHE L 71 TYR 0.020 0.002 TYR E 191 ARG 0.005 0.001 ARG A 501 Details of bonding type rmsd link_NAG-ASN : bond 0.00509 ( 15) link_NAG-ASN : angle 3.89046 ( 45) link_BETA1-4 : bond 0.00888 ( 20) link_BETA1-4 : angle 2.85277 ( 60) link_ALPHA1-3 : bond 0.00619 ( 3) link_ALPHA1-3 : angle 2.48278 ( 9) hydrogen bonds : bond 0.04504 ( 766) hydrogen bonds : angle 5.72196 ( 2151) SS BOND : bond 0.00841 ( 39) SS BOND : angle 1.11393 ( 78) covalent geometry : bond 0.00573 (24228) covalent geometry : angle 0.70984 (32883) *********************** 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 50 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 3.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 396 MET cc_start: 0.8202 (pmm) cc_final: 0.7524 (pmm) REVERT: B 530 MET cc_start: 0.7691 (mmm) cc_final: 0.7423 (mmp) REVERT: E 100 MET cc_start: 0.9070 (ptt) cc_final: 0.8671 (pmm) REVERT: F 530 MET cc_start: 0.7451 (mpp) cc_final: 0.7019 (mpp) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.4099 time to fit residues: 37.2439 Evaluate side-chains 50 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 3.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 96 optimal weight: 7.9990 chunk 234 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 chunk 125 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 134 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 217 optimal weight: 4.9990 chunk 154 optimal weight: 6.9990 chunk 277 optimal weight: 9.9990 chunk 219 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 164 HIS I 374 HIS L 38 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.032252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.025318 restraints weight = 297835.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.025995 restraints weight = 157209.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.026422 restraints weight = 104276.299| |-----------------------------------------------------------------------------| r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.4742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 24305 Z= 0.214 Angle : 0.676 13.010 33075 Z= 0.337 Chirality : 0.046 0.479 3846 Planarity : 0.004 0.052 4124 Dihedral : 8.097 56.409 4211 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % 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: 1.50 (0.28), residues: 400 sheet: -0.83 (0.17), residues: 852 loop : -1.55 (0.15), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 623 HIS 0.005 0.001 HIS C 102 PHE 0.019 0.002 PHE L 71 TYR 0.017 0.002 TYR G 50 ARG 0.004 0.000 ARG G 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00429 ( 15) link_NAG-ASN : angle 3.82562 ( 45) link_BETA1-4 : bond 0.00834 ( 20) link_BETA1-4 : angle 2.63727 ( 60) link_ALPHA1-3 : bond 0.00558 ( 3) link_ALPHA1-3 : angle 2.49151 ( 9) hydrogen bonds : bond 0.04129 ( 766) hydrogen bonds : angle 5.58287 ( 2151) SS BOND : bond 0.00437 ( 39) SS BOND : angle 0.98365 ( 78) covalent geometry : bond 0.00479 (24228) covalent geometry : angle 0.64984 (32883) *********************** 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 52 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 3.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8349 (ppp) cc_final: 0.8135 (ppp) REVERT: A 396 MET cc_start: 0.8261 (pmm) cc_final: 0.7649 (pmm) REVERT: B 530 MET cc_start: 0.7949 (mmm) cc_final: 0.7480 (mmp) REVERT: E 396 MET cc_start: 0.8881 (pmm) cc_final: 0.7747 (mtt) REVERT: F 530 MET cc_start: 0.7557 (mpp) cc_final: 0.6936 (mpp) REVERT: I 145 MET cc_start: 0.6423 (mtp) cc_final: 0.6138 (mtp) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.4574 time to fit residues: 42.6245 Evaluate side-chains 50 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 3.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 13 optimal weight: 0.9990 chunk 238 optimal weight: 10.0000 chunk 114 optimal weight: 7.9990 chunk 188 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 55 optimal weight: 8.9990 chunk 60 optimal weight: 9.9990 chunk 285 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 29 optimal weight: 0.0050 overall best weight: 2.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.032580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.025669 restraints weight = 297985.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.026377 restraints weight = 153684.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.026811 restraints weight = 100810.791| |-----------------------------------------------------------------------------| r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.4887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24305 Z= 0.123 Angle : 0.619 12.305 33075 Z= 0.307 Chirality : 0.045 0.462 3846 Planarity : 0.004 0.053 4124 Dihedral : 7.638 57.969 4211 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % 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: -1.11 (0.16), residues: 2901 helix: 1.72 (0.28), residues: 390 sheet: -0.65 (0.18), residues: 819 loop : -1.41 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP I 427 HIS 0.005 0.001 HIS C 100D PHE 0.017 0.001 PHE L 71 TYR 0.016 0.001 TYR G 91 ARG 0.004 0.000 ARG H 108 Details of bonding type rmsd link_NAG-ASN : bond 0.00377 ( 15) link_NAG-ASN : angle 4.21513 ( 45) link_BETA1-4 : bond 0.00810 ( 20) link_BETA1-4 : angle 2.44788 ( 60) link_ALPHA1-3 : bond 0.00628 ( 3) link_ALPHA1-3 : angle 2.20133 ( 9) hydrogen bonds : bond 0.03661 ( 766) hydrogen bonds : angle 5.33856 ( 2151) SS BOND : bond 0.00268 ( 39) SS BOND : angle 0.91034 ( 78) covalent geometry : bond 0.00270 (24228) covalent geometry : angle 0.58874 (32883) *********************** 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 54 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 3.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8262 (ppp) cc_final: 0.7987 (ppp) REVERT: A 396 MET cc_start: 0.8233 (pmm) cc_final: 0.7603 (pmm) REVERT: B 530 MET cc_start: 0.7939 (mmm) cc_final: 0.7389 (mmp) REVERT: E 100 MET cc_start: 0.9021 (ptt) cc_final: 0.8679 (pmm) REVERT: E 396 MET cc_start: 0.8816 (pmm) cc_final: 0.7659 (mtt) REVERT: F 530 MET cc_start: 0.7405 (mpp) cc_final: 0.6744 (mpp) REVERT: I 145 MET cc_start: 0.6394 (mtp) cc_final: 0.6159 (mtp) REVERT: J 626 MET cc_start: 0.7675 (tmm) cc_final: 0.7422 (tmm) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.3587 time to fit residues: 34.6123 Evaluate side-chains 50 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 3.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 115 optimal weight: 8.9990 chunk 240 optimal weight: 20.0000 chunk 229 optimal weight: 20.0000 chunk 174 optimal weight: 8.9990 chunk 233 optimal weight: 3.9990 chunk 187 optimal weight: 7.9990 chunk 46 optimal weight: 9.9990 chunk 199 optimal weight: 7.9990 chunk 4 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 251 optimal weight: 10.0000 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 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.031899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.024985 restraints weight = 304993.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.025653 restraints weight = 157406.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.026089 restraints weight = 104167.442| |-----------------------------------------------------------------------------| r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.5303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 24305 Z= 0.245 Angle : 0.714 12.655 33075 Z= 0.354 Chirality : 0.046 0.472 3846 Planarity : 0.004 0.055 4124 Dihedral : 7.822 57.873 4211 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % 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: 1.54 (0.29), residues: 399 sheet: -0.77 (0.17), residues: 854 loop : -1.65 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP D 96 HIS 0.005 0.001 HIS D 38 PHE 0.020 0.002 PHE L 71 TYR 0.019 0.002 TYR G 50 ARG 0.005 0.001 ARG I 501 Details of bonding type rmsd link_NAG-ASN : bond 0.00472 ( 15) link_NAG-ASN : angle 4.18625 ( 45) link_BETA1-4 : bond 0.00885 ( 20) link_BETA1-4 : angle 2.61753 ( 60) link_ALPHA1-3 : bond 0.00575 ( 3) link_ALPHA1-3 : angle 2.30763 ( 9) hydrogen bonds : bond 0.04262 ( 766) hydrogen bonds : angle 5.59255 ( 2151) SS BOND : bond 0.00446 ( 39) SS BOND : angle 0.92797 ( 78) covalent geometry : bond 0.00550 (24228) covalent geometry : angle 0.68750 (32883) *********************** 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 50 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 2.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8501 (ppp) cc_final: 0.8214 (ppp) REVERT: A 396 MET cc_start: 0.8307 (pmm) cc_final: 0.7736 (pmm) REVERT: B 530 MET cc_start: 0.7984 (mmm) cc_final: 0.7622 (mmp) REVERT: E 396 MET cc_start: 0.8801 (pmm) cc_final: 0.7715 (mtt) REVERT: F 530 MET cc_start: 0.7691 (mpp) cc_final: 0.6971 (mpp) REVERT: I 104 MET cc_start: 0.9467 (tpp) cc_final: 0.9138 (tpt) REVERT: I 145 MET cc_start: 0.6480 (mtp) cc_final: 0.6198 (mtp) REVERT: J 626 MET cc_start: 0.7579 (tmm) cc_final: 0.7307 (tmm) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.3455 time to fit residues: 30.5422 Evaluate side-chains 50 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 2.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 275 optimal weight: 10.0000 chunk 229 optimal weight: 20.0000 chunk 135 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 25 optimal weight: 10.0000 chunk 147 optimal weight: 8.9990 chunk 232 optimal weight: 0.0010 chunk 271 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 200 optimal weight: 20.0000 chunk 234 optimal weight: 9.9990 overall best weight: 3.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 ASN E 374 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.031967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.025210 restraints weight = 297925.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.025875 restraints weight = 157398.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.026294 restraints weight = 104743.863| |-----------------------------------------------------------------------------| r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.5456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24305 Z= 0.156 Angle : 0.633 12.664 33075 Z= 0.315 Chirality : 0.045 0.448 3846 Planarity : 0.004 0.054 4124 Dihedral : 7.501 57.866 4211 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % 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: -1.27 (0.15), residues: 2901 helix: 1.64 (0.29), residues: 399 sheet: -0.62 (0.17), residues: 843 loop : -1.65 (0.14), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP L 96 HIS 0.004 0.001 HIS E 374 PHE 0.018 0.002 PHE L 71 TYR 0.015 0.001 TYR E 191 ARG 0.003 0.000 ARG A 467 Details of bonding type rmsd link_NAG-ASN : bond 0.00409 ( 15) link_NAG-ASN : angle 3.99733 ( 45) link_BETA1-4 : bond 0.00808 ( 20) link_BETA1-4 : angle 2.43502 ( 60) link_ALPHA1-3 : bond 0.00643 ( 3) link_ALPHA1-3 : angle 2.02984 ( 9) hydrogen bonds : bond 0.03817 ( 766) hydrogen bonds : angle 5.38965 ( 2151) SS BOND : bond 0.00333 ( 39) SS BOND : angle 0.90702 ( 78) covalent geometry : bond 0.00348 (24228) covalent geometry : angle 0.60645 (32883) *********************** 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 51 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 2.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8451 (ppp) cc_final: 0.8170 (ppp) REVERT: A 396 MET cc_start: 0.8263 (pmm) cc_final: 0.7729 (pmm) REVERT: B 530 MET cc_start: 0.7957 (mmm) cc_final: 0.7555 (mmp) REVERT: E 100 MET cc_start: 0.9051 (ptt) cc_final: 0.8672 (pmm) REVERT: E 396 MET cc_start: 0.8795 (pmm) cc_final: 0.7753 (mtt) REVERT: F 530 MET cc_start: 0.7583 (mpp) cc_final: 0.6883 (mpp) REVERT: I 145 MET cc_start: 0.6763 (mtp) cc_final: 0.6482 (mtp) REVERT: J 626 MET cc_start: 0.7708 (tmm) cc_final: 0.7405 (tmm) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.3436 time to fit residues: 31.4862 Evaluate side-chains 51 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 2.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 16 optimal weight: 10.0000 chunk 251 optimal weight: 8.9990 chunk 273 optimal weight: 8.9990 chunk 102 optimal weight: 8.9990 chunk 163 optimal weight: 4.9990 chunk 19 optimal weight: 8.9990 chunk 120 optimal weight: 0.6980 chunk 279 optimal weight: 8.9990 chunk 281 optimal weight: 6.9990 chunk 147 optimal weight: 10.0000 chunk 247 optimal weight: 0.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** 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 = 0.3390 r_free = 0.3390 target = 0.038550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.026618 restraints weight = 251570.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.027696 restraints weight = 153779.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.028175 restraints weight = 98146.761| |-----------------------------------------------------------------------------| r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.5659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 24305 Z= 0.181 Angle : 0.650 12.589 33075 Z= 0.322 Chirality : 0.045 0.441 3846 Planarity : 0.004 0.053 4124 Dihedral : 7.402 58.034 4211 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % 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: -1.32 (0.15), residues: 2901 helix: 1.38 (0.28), residues: 420 sheet: -0.60 (0.17), residues: 846 loop : -1.69 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP L 96 HIS 0.004 0.001 HIS H 38 PHE 0.018 0.002 PHE L 71 TYR 0.017 0.002 TYR J 638 ARG 0.003 0.000 ARG A 501 Details of bonding type rmsd link_NAG-ASN : bond 0.00391 ( 15) link_NAG-ASN : angle 3.97145 ( 45) link_BETA1-4 : bond 0.00814 ( 20) link_BETA1-4 : angle 2.45052 ( 60) link_ALPHA1-3 : bond 0.00526 ( 3) link_ALPHA1-3 : angle 1.97842 ( 9) hydrogen bonds : bond 0.03887 ( 766) hydrogen bonds : angle 5.40401 ( 2151) SS BOND : bond 0.00370 ( 39) SS BOND : angle 0.89469 ( 78) covalent geometry : bond 0.00405 (24228) covalent geometry : angle 0.62387 (32883) ********************** 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 to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 2.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8194 (ppp) cc_final: 0.7873 (ppp) REVERT: A 396 MET cc_start: 0.8351 (pmm) cc_final: 0.7730 (pmm) REVERT: E 396 MET cc_start: 0.8964 (pmm) cc_final: 0.7779 (mtt) REVERT: F 530 MET cc_start: 0.7469 (mpp) cc_final: 0.6780 (mpp) REVERT: I 145 MET cc_start: 0.6526 (mtp) cc_final: 0.6273 (mtp) REVERT: I 473 MET cc_start: 0.8856 (mmm) cc_final: 0.8154 (mmm) REVERT: J 626 MET cc_start: 0.7949 (tmm) cc_final: 0.7711 (tmm) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.3316 time to fit residues: 30.2257 Evaluate side-chains 50 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 3.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 38 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 197 optimal weight: 20.0000 chunk 104 optimal weight: 5.9990 chunk 255 optimal weight: 5.9990 chunk 279 optimal weight: 6.9990 chunk 149 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 144 optimal weight: 5.9990 chunk 79 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** 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 = 0.3390 r_free = 0.3390 target = 0.038483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.027390 restraints weight = 250270.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.027629 restraints weight = 159526.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.027646 restraints weight = 118952.383| |-----------------------------------------------------------------------------| r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.5794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 24305 Z= 0.166 Angle : 0.642 12.856 33075 Z= 0.317 Chirality : 0.045 0.424 3846 Planarity : 0.004 0.052 4124 Dihedral : 7.296 58.096 4211 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % 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: -1.27 (0.15), residues: 2901 helix: 1.48 (0.28), residues: 417 sheet: -0.55 (0.17), residues: 843 loop : -1.68 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 96 HIS 0.003 0.001 HIS D 198 PHE 0.018 0.002 PHE L 71 TYR 0.033 0.002 TYR K 91 ARG 0.003 0.000 ARG A 467 Details of bonding type rmsd link_NAG-ASN : bond 0.00363 ( 15) link_NAG-ASN : angle 3.88743 ( 45) link_BETA1-4 : bond 0.00838 ( 20) link_BETA1-4 : angle 2.43051 ( 60) link_ALPHA1-3 : bond 0.00540 ( 3) link_ALPHA1-3 : angle 1.87798 ( 9) hydrogen bonds : bond 0.03763 ( 766) hydrogen bonds : angle 5.34181 ( 2151) SS BOND : bond 0.00336 ( 39) SS BOND : angle 0.87464 ( 78) covalent geometry : bond 0.00371 (24228) covalent geometry : angle 0.61674 (32883) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6710.06 seconds wall clock time: 121 minutes 15.92 seconds (7275.92 seconds total)