Starting phenix.real_space_refine on Thu Mar 5 17:15:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tcn_25814/03_2026/7tcn_25814_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tcn_25814/03_2026/7tcn_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_25814/03_2026/7tcn_25814.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tcn_25814/03_2026/7tcn_25814.map" model { file = "/net/cci-nas-00/data/ceres_data/7tcn_25814/03_2026/7tcn_25814_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tcn_25814/03_2026/7tcn_25814_neut.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 5.42, per 1000 atoms: 0.23 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: 1.72 Conformation dependent library (CDL) restraints added in 1.2 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: 1.11 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: 4.74 Time building geometry restraints manager: 2.25 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 604) selection = (chain 'E' and (resid 32 through 56 or resid 75 through 144 or resid 157 through \ 396 or resid 398 through 604)) selection = (chain 'I' and (resid 32 through 56 or resid 75 through 144 or resid 157 through \ 396 or resid 409 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: 2.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 23.030 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.620 ------------------------------------------------------------------------------- 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 : 3.96 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.007 0.001 ARG E 432 TYR 0.033 0.002 TYR H 91 PHE 0.018 0.002 PHE H 71 TRP 0.100 0.003 TRP F 610 HIS 0.006 0.002 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00480 (24228) covalent geometry : angle 0.84426 (32883) SS BOND : bond 0.00421 ( 39) SS BOND : angle 1.81059 ( 78) hydrogen bonds : bond 0.24250 ( 766) hydrogen bonds : angle 8.75122 ( 2151) link_ALPHA1-3 : bond 0.01068 ( 3) link_ALPHA1-3 : angle 3.02181 ( 9) link_BETA1-4 : bond 0.01626 ( 20) link_BETA1-4 : angle 4.87061 ( 60) link_NAG-ASN : bond 0.00810 ( 15) link_NAG-ASN : angle 5.16609 ( 45) *********************** 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 : 0.855 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: 0.1577 time to fit residues: 19.7054 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 : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.0010 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 7.9990 chunk 111 optimal weight: 8.9990 overall best weight: 3.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN B 607 ASN C 164 HIS C 171 GLN D 38 HIS D 137 ASN E 33 ASN F 577 GLN F 607 ASN H 38 HIS H 155 GLN I 33 ASN I 105 HIS K 102 HIS K 164 HIS K 171 GLN L 38 HIS L 137 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.036156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.029178 restraints weight = 288884.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.029935 restraints weight = 152567.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.030390 restraints weight = 100193.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.030671 restraints weight = 76995.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.030851 restraints weight = 65573.191| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1711 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= 0.191 Angle : 0.763 13.352 33075 Z= 0.374 Chirality : 0.051 0.747 3846 Planarity : 0.005 0.059 4124 Dihedral : 10.836 63.876 4211 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.58 % Favored : 94.38 % Rotamer: Outliers : 0.15 % Allowed : 2.71 % Favored : 97.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.16), residues: 2901 helix: 1.82 (0.29), residues: 349 sheet: -0.82 (0.16), residues: 941 loop : -1.19 (0.15), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 169 TYR 0.022 0.002 TYR E 191 PHE 0.018 0.002 PHE H 71 TRP 0.029 0.002 TRP F 610 HIS 0.005 0.001 HIS I 417 Details of bonding type rmsd covalent geometry : bond 0.00415 (24228) covalent geometry : angle 0.72782 (32883) SS BOND : bond 0.00407 ( 39) SS BOND : angle 1.23046 ( 78) hydrogen bonds : bond 0.04288 ( 766) hydrogen bonds : angle 6.22628 ( 2151) link_ALPHA1-3 : bond 0.00275 ( 3) link_ALPHA1-3 : angle 2.83883 ( 9) link_BETA1-4 : bond 0.01075 ( 20) link_BETA1-4 : angle 3.65810 ( 60) link_NAG-ASN : bond 0.00939 ( 15) link_NAG-ASN : angle 4.36514 ( 45) *********************** 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 62 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.7804 (mpp) cc_final: 0.7365 (mpp) REVERT: B 626 MET cc_start: 0.5819 (tmm) cc_final: 0.5220 (tmm) REVERT: C 89 MET cc_start: 0.8226 (ttp) cc_final: 0.7907 (ttm) REVERT: E 100 MET cc_start: 0.8907 (ptt) cc_final: 0.8468 (pmm) REVERT: F 530 MET cc_start: 0.6993 (mpp) cc_final: 0.6635 (mpp) outliers start: 4 outliers final: 0 residues processed: 62 average time/residue: 0.1493 time to fit residues: 16.2261 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 : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 83 optimal weight: 8.9990 chunk 130 optimal weight: 0.6980 chunk 292 optimal weight: 5.9990 chunk 290 optimal weight: 7.9990 chunk 119 optimal weight: 9.9990 chunk 49 optimal weight: 20.0000 chunk 102 optimal weight: 20.0000 chunk 187 optimal weight: 20.0000 chunk 241 optimal weight: 10.0000 chunk 266 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 38 HIS D 147 GLN E 33 ASN H 38 HIS J 625 ASN K 6 GLN L 38 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.034133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.027138 restraints weight = 292476.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.027842 restraints weight = 153893.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.028290 restraints weight = 102684.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.028564 restraints weight = 79460.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.028708 restraints weight = 67873.821| |-----------------------------------------------------------------------------| r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 24305 Z= 0.198 Angle : 0.699 13.678 33075 Z= 0.348 Chirality : 0.047 0.528 3846 Planarity : 0.005 0.050 4124 Dihedral : 8.861 56.501 4211 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.89 % Favored : 94.07 % Rotamer: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.16), residues: 2901 helix: 1.50 (0.29), residues: 373 sheet: -0.74 (0.16), residues: 918 loop : -1.21 (0.15), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 94 TYR 0.020 0.002 TYR E 191 PHE 0.024 0.002 PHE L 71 TRP 0.018 0.002 TRP H 96 HIS 0.005 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00440 (24228) covalent geometry : angle 0.67081 (32883) SS BOND : bond 0.00408 ( 39) SS BOND : angle 1.01671 ( 78) hydrogen bonds : bond 0.05095 ( 766) hydrogen bonds : angle 5.81006 ( 2151) link_ALPHA1-3 : bond 0.00896 ( 3) link_ALPHA1-3 : angle 1.26357 ( 9) link_BETA1-4 : bond 0.00892 ( 20) link_BETA1-4 : angle 3.04868 ( 60) link_NAG-ASN : bond 0.00474 ( 15) link_NAG-ASN : angle 3.92335 ( 45) *********************** 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 55 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 89 MET cc_start: 0.8529 (ttp) cc_final: 0.8183 (ttm) REVERT: E 100 MET cc_start: 0.8967 (ptt) cc_final: 0.8597 (pmm) REVERT: F 530 MET cc_start: 0.7152 (mpp) cc_final: 0.6626 (mpp) REVERT: I 396 MET cc_start: 0.8588 (ptt) cc_final: 0.8290 (mtt) REVERT: J 530 MET cc_start: 0.6651 (mmp) cc_final: 0.6412 (mmp) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1471 time to fit residues: 14.0110 Evaluate side-chains 49 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 129 optimal weight: 4.9990 chunk 193 optimal weight: 40.0000 chunk 210 optimal weight: 3.9990 chunk 273 optimal weight: 6.9990 chunk 241 optimal weight: 20.0000 chunk 132 optimal weight: 8.9990 chunk 225 optimal weight: 4.9990 chunk 182 optimal weight: 10.0000 chunk 73 optimal weight: 20.0000 chunk 168 optimal weight: 0.1980 chunk 140 optimal weight: 20.0000 overall best weight: 4.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS A 374 HIS D 210 ASN L 210 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.033744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.026758 restraints weight = 294673.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.027478 restraints weight = 155491.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.027927 restraints weight = 103025.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.028208 restraints weight = 79396.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.028346 restraints weight = 67588.280| |-----------------------------------------------------------------------------| r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 24305 Z= 0.176 Angle : 0.665 12.536 33075 Z= 0.331 Chirality : 0.047 0.493 3846 Planarity : 0.004 0.047 4124 Dihedral : 8.243 56.379 4211 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.58 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.16), residues: 2901 helix: 1.62 (0.28), residues: 390 sheet: -0.70 (0.16), residues: 927 loop : -1.28 (0.16), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG D 108 TYR 0.018 0.002 TYR H 91 PHE 0.019 0.002 PHE L 71 TRP 0.031 0.002 TRP B 631 HIS 0.004 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00394 (24228) covalent geometry : angle 0.63597 (32883) SS BOND : bond 0.00372 ( 39) SS BOND : angle 1.17139 ( 78) hydrogen bonds : bond 0.03921 ( 766) hydrogen bonds : angle 5.56393 ( 2151) link_ALPHA1-3 : bond 0.00390 ( 3) link_ALPHA1-3 : angle 2.71534 ( 9) link_BETA1-4 : bond 0.00850 ( 20) link_BETA1-4 : angle 2.85977 ( 60) link_NAG-ASN : bond 0.00471 ( 15) link_NAG-ASN : angle 3.83830 ( 45) *********************** 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 55 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7975 (ppp) cc_final: 0.7665 (ppp) REVERT: B 530 MET cc_start: 0.7334 (mmm) cc_final: 0.6694 (mmp) REVERT: B 626 MET cc_start: 0.6262 (tmm) cc_final: 0.5713 (tmm) REVERT: C 89 MET cc_start: 0.8459 (ttp) cc_final: 0.8132 (ttm) REVERT: E 100 MET cc_start: 0.8951 (ptt) cc_final: 0.8649 (pmm) REVERT: F 530 MET cc_start: 0.7219 (mpp) cc_final: 0.6680 (mpp) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1398 time to fit residues: 13.6326 Evaluate side-chains 49 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 137 optimal weight: 1.9990 chunk 184 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 282 optimal weight: 9.9990 chunk 165 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 162 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 244 optimal weight: 0.7980 chunk 1 optimal weight: 10.0000 chunk 179 optimal weight: 4.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN A 374 HIS A 461 ASN I 321AGLN I 334 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.033091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.026117 restraints weight = 294542.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.026813 restraints weight = 155031.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.027256 restraints weight = 102937.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.027531 restraints weight = 79491.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.027676 restraints weight = 67770.953| |-----------------------------------------------------------------------------| r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 24305 Z= 0.166 Angle : 0.640 12.562 33075 Z= 0.319 Chirality : 0.045 0.464 3846 Planarity : 0.004 0.041 4124 Dihedral : 7.852 56.400 4211 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.15), residues: 2901 helix: 1.67 (0.28), residues: 391 sheet: -0.68 (0.17), residues: 855 loop : -1.34 (0.15), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 501 TYR 0.017 0.001 TYR L 91 PHE 0.019 0.002 PHE L 71 TRP 0.022 0.002 TRP E 427 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00367 (24228) covalent geometry : angle 0.61418 (32883) SS BOND : bond 0.00362 ( 39) SS BOND : angle 1.11282 ( 78) hydrogen bonds : bond 0.03929 ( 766) hydrogen bonds : angle 5.40389 ( 2151) link_ALPHA1-3 : bond 0.00570 ( 3) link_ALPHA1-3 : angle 2.13614 ( 9) link_BETA1-4 : bond 0.00903 ( 20) link_BETA1-4 : angle 2.58629 ( 60) link_NAG-ASN : bond 0.00337 ( 15) link_NAG-ASN : angle 3.71651 ( 45) *********************** 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 51 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8130 (ppp) cc_final: 0.7725 (ppp) REVERT: B 530 MET cc_start: 0.7537 (mmm) cc_final: 0.7234 (mmp) REVERT: C 89 MET cc_start: 0.8578 (ttp) cc_final: 0.8027 (ttp) REVERT: E 100 MET cc_start: 0.8952 (ptt) cc_final: 0.8583 (pmm) REVERT: F 530 MET cc_start: 0.7263 (mpp) cc_final: 0.6698 (mpp) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1446 time to fit residues: 13.1115 Evaluate side-chains 49 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 208 optimal weight: 10.0000 chunk 8 optimal weight: 20.0000 chunk 190 optimal weight: 20.0000 chunk 68 optimal weight: 9.9990 chunk 177 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 109 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 118 optimal weight: 7.9990 chunk 65 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN A 321AGLN A 334 ASN A 428 GLN E 321AGLN E 334 ASN G 164 HIS H 210 ASN I 280 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.032131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.025160 restraints weight = 301135.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.025825 restraints weight = 158884.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.026260 restraints weight = 106170.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.026518 restraints weight = 81955.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.026689 restraints weight = 70051.768| |-----------------------------------------------------------------------------| r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.4746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 24305 Z= 0.243 Angle : 0.724 12.544 33075 Z= 0.358 Chirality : 0.047 0.501 3846 Planarity : 0.005 0.056 4124 Dihedral : 8.061 57.357 4211 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.00 % Favored : 92.97 % Rotamer: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.15), residues: 2901 helix: 1.70 (0.29), residues: 394 sheet: -0.78 (0.17), residues: 854 loop : -1.59 (0.15), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 501 TYR 0.019 0.002 TYR G 100E PHE 0.021 0.002 PHE L 71 TRP 0.018 0.002 TRP B 610 HIS 0.005 0.001 HIS I 374 Details of bonding type rmsd covalent geometry : bond 0.00546 (24228) covalent geometry : angle 0.69743 (32883) SS BOND : bond 0.00509 ( 39) SS BOND : angle 0.98552 ( 78) hydrogen bonds : bond 0.04326 ( 766) hydrogen bonds : angle 5.59144 ( 2151) link_ALPHA1-3 : bond 0.00564 ( 3) link_ALPHA1-3 : angle 2.47613 ( 9) link_BETA1-4 : bond 0.00817 ( 20) link_BETA1-4 : angle 2.74892 ( 60) link_NAG-ASN : bond 0.00624 ( 15) link_NAG-ASN : angle 4.12523 ( 45) *********************** 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 50 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8296 (ppp) cc_final: 0.7899 (ppp) REVERT: B 530 MET cc_start: 0.7702 (mmm) cc_final: 0.7297 (mmp) REVERT: C 89 MET cc_start: 0.8600 (ttp) cc_final: 0.7971 (ttp) REVERT: E 396 MET cc_start: 0.8847 (pmm) cc_final: 0.7702 (mtt) REVERT: F 530 MET cc_start: 0.7573 (mpp) cc_final: 0.7116 (mpp) REVERT: I 104 MET cc_start: 0.9566 (ttm) cc_final: 0.9364 (ttp) REVERT: I 145 MET cc_start: 0.6686 (mtp) cc_final: 0.6431 (mtp) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1443 time to fit residues: 12.5710 Evaluate side-chains 49 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 99 optimal weight: 7.9990 chunk 86 optimal weight: 6.9990 chunk 205 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 chunk 225 optimal weight: 10.0000 chunk 151 optimal weight: 6.9990 chunk 186 optimal weight: 10.0000 chunk 31 optimal weight: 0.0470 chunk 269 optimal weight: 6.9990 chunk 267 optimal weight: 5.9990 chunk 82 optimal weight: 20.0000 overall best weight: 5.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN I 374 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.038730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.026824 restraints weight = 249918.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.027918 restraints weight = 164759.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.028183 restraints weight = 101237.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.028275 restraints weight = 101423.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.028296 restraints weight = 89092.661| |-----------------------------------------------------------------------------| r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.5077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 24305 Z= 0.203 Angle : 0.664 12.591 33075 Z= 0.332 Chirality : 0.046 0.463 3846 Planarity : 0.004 0.052 4124 Dihedral : 7.900 59.376 4211 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.15), residues: 2901 helix: 1.68 (0.28), residues: 396 sheet: -0.78 (0.17), residues: 854 loop : -1.63 (0.15), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L 108 TYR 0.017 0.002 TYR H 91 PHE 0.020 0.002 PHE L 71 TRP 0.031 0.002 TRP H 96 HIS 0.005 0.001 HIS C 100D Details of bonding type rmsd covalent geometry : bond 0.00453 (24228) covalent geometry : angle 0.63916 (32883) SS BOND : bond 0.00389 ( 39) SS BOND : angle 0.92522 ( 78) hydrogen bonds : bond 0.04073 ( 766) hydrogen bonds : angle 5.49183 ( 2151) link_ALPHA1-3 : bond 0.00634 ( 3) link_ALPHA1-3 : angle 2.29707 ( 9) link_BETA1-4 : bond 0.00806 ( 20) link_BETA1-4 : angle 2.50432 ( 60) link_NAG-ASN : bond 0.00416 ( 15) link_NAG-ASN : angle 3.84498 ( 45) *********************** 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 51 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.7641 (mpp) cc_final: 0.7416 (mpp) REVERT: A 95 MET cc_start: 0.7980 (ppp) cc_final: 0.7562 (ppp) REVERT: A 396 MET cc_start: 0.7752 (ppp) cc_final: 0.7517 (mtt) REVERT: B 530 MET cc_start: 0.7639 (mmm) cc_final: 0.7255 (mmp) REVERT: C 89 MET cc_start: 0.8490 (ttp) cc_final: 0.7905 (ttp) REVERT: E 396 MET cc_start: 0.8997 (pmm) cc_final: 0.7708 (mtt) REVERT: F 530 MET cc_start: 0.7371 (mpp) cc_final: 0.6800 (mpp) REVERT: I 145 MET cc_start: 0.6578 (mtp) cc_final: 0.6319 (mtp) REVERT: J 626 MET cc_start: 0.7921 (tmm) cc_final: 0.7686 (tmm) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1422 time to fit residues: 12.6951 Evaluate side-chains 49 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 165 optimal weight: 2.9990 chunk 209 optimal weight: 6.9990 chunk 81 optimal weight: 0.5980 chunk 244 optimal weight: 9.9990 chunk 150 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 213 optimal weight: 20.0000 chunk 69 optimal weight: 10.0000 chunk 268 optimal weight: 10.0000 chunk 9 optimal weight: 20.0000 overall best weight: 4.5188 ------------------------------------------------------------------------------- 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 = 0.3392 r_free = 0.3392 target = 0.038614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.026720 restraints weight = 249883.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.027826 restraints weight = 166198.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.028169 restraints weight = 100901.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.028260 restraints weight = 99612.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.028278 restraints weight = 86646.252| |-----------------------------------------------------------------------------| r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.5346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 24305 Z= 0.179 Angle : 0.648 12.417 33075 Z= 0.322 Chirality : 0.045 0.468 3846 Planarity : 0.004 0.055 4124 Dihedral : 7.589 57.918 4211 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.15), residues: 2901 helix: 1.68 (0.28), residues: 396 sheet: -0.69 (0.17), residues: 855 loop : -1.67 (0.15), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 501 TYR 0.014 0.002 TYR E 191 PHE 0.019 0.002 PHE L 71 TRP 0.035 0.002 TRP D 96 HIS 0.005 0.001 HIS I 374 Details of bonding type rmsd covalent geometry : bond 0.00399 (24228) covalent geometry : angle 0.62336 (32883) SS BOND : bond 0.00358 ( 39) SS BOND : angle 0.83961 ( 78) hydrogen bonds : bond 0.03858 ( 766) hydrogen bonds : angle 5.38420 ( 2151) link_ALPHA1-3 : bond 0.00586 ( 3) link_ALPHA1-3 : angle 2.17558 ( 9) link_BETA1-4 : bond 0.00801 ( 20) link_BETA1-4 : angle 2.44772 ( 60) link_NAG-ASN : bond 0.00407 ( 15) link_NAG-ASN : angle 3.80353 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8053 (ppp) cc_final: 0.7678 (ppp) REVERT: B 530 MET cc_start: 0.7638 (mmm) cc_final: 0.7165 (mmp) REVERT: C 89 MET cc_start: 0.8476 (ttp) cc_final: 0.7866 (ttp) REVERT: E 100 MET cc_start: 0.9105 (ptt) cc_final: 0.8608 (pmm) REVERT: E 396 MET cc_start: 0.8963 (pmm) cc_final: 0.7747 (mtt) REVERT: F 530 MET cc_start: 0.7398 (mpp) cc_final: 0.6795 (mpp) REVERT: I 145 MET cc_start: 0.6554 (mtp) cc_final: 0.6273 (mtp) REVERT: I 426 MET cc_start: 0.8105 (tpt) cc_final: 0.7553 (tpp) REVERT: J 626 MET cc_start: 0.7970 (tmm) cc_final: 0.7706 (tmm) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1494 time to fit residues: 13.6350 Evaluate side-chains 49 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 131 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 72 optimal weight: 20.0000 chunk 18 optimal weight: 9.9990 chunk 276 optimal weight: 1.9990 chunk 118 optimal weight: 8.9990 chunk 126 optimal weight: 8.9990 chunk 123 optimal weight: 20.0000 chunk 179 optimal weight: 20.0000 chunk 36 optimal weight: 8.9990 chunk 224 optimal weight: 0.6980 overall best weight: 2.6584 ------------------------------------------------------------------------------- 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 = 0.3405 r_free = 0.3405 target = 0.038759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.027313 restraints weight = 251422.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.028124 restraints weight = 153887.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.028514 restraints weight = 100016.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.028566 restraints weight = 100276.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.028601 restraints weight = 86671.983| |-----------------------------------------------------------------------------| r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.5483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24305 Z= 0.121 Angle : 0.603 12.555 33075 Z= 0.300 Chirality : 0.045 0.436 3846 Planarity : 0.004 0.052 4124 Dihedral : 7.194 58.453 4211 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.16), residues: 2901 helix: 1.62 (0.28), residues: 408 sheet: -0.54 (0.18), residues: 833 loop : -1.53 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 467 TYR 0.016 0.001 TYR L 91 PHE 0.017 0.001 PHE L 71 TRP 0.025 0.001 TRP L 96 HIS 0.003 0.001 HIS E 249 Details of bonding type rmsd covalent geometry : bond 0.00265 (24228) covalent geometry : angle 0.57882 (32883) SS BOND : bond 0.00271 ( 39) SS BOND : angle 0.83046 ( 78) hydrogen bonds : bond 0.03504 ( 766) hydrogen bonds : angle 5.21815 ( 2151) link_ALPHA1-3 : bond 0.00656 ( 3) link_ALPHA1-3 : angle 1.83636 ( 9) link_BETA1-4 : bond 0.00842 ( 20) link_BETA1-4 : angle 2.35007 ( 60) link_NAG-ASN : bond 0.00370 ( 15) link_NAG-ASN : angle 3.63184 ( 45) *********************** 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 52 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7952 (ppp) cc_final: 0.7558 (ppp) REVERT: B 530 MET cc_start: 0.7680 (mmm) cc_final: 0.7188 (mmp) REVERT: C 89 MET cc_start: 0.8487 (ttp) cc_final: 0.7857 (ttp) REVERT: E 396 MET cc_start: 0.8970 (pmm) cc_final: 0.7778 (mtt) REVERT: F 530 MET cc_start: 0.7285 (mpp) cc_final: 0.6617 (mpp) REVERT: I 104 MET cc_start: 0.9217 (ttp) cc_final: 0.8965 (ppp) REVERT: I 145 MET cc_start: 0.6392 (mtp) cc_final: 0.6131 (mtp) REVERT: J 626 MET cc_start: 0.8004 (tmm) cc_final: 0.7778 (tmm) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1465 time to fit residues: 13.4215 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 : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 227 optimal weight: 6.9990 chunk 140 optimal weight: 0.0770 chunk 216 optimal weight: 9.9990 chunk 17 optimal weight: 20.0000 chunk 181 optimal weight: 9.9990 chunk 225 optimal weight: 9.9990 chunk 68 optimal weight: 5.9990 chunk 230 optimal weight: 2.9990 chunk 99 optimal weight: 8.9990 chunk 187 optimal weight: 20.0000 chunk 37 optimal weight: 10.0000 overall best weight: 5.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 171 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.038511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.026788 restraints weight = 249895.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.027638 restraints weight = 155942.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.027741 restraints weight = 101509.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.027871 restraints weight = 105635.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.027917 restraints weight = 93681.937| |-----------------------------------------------------------------------------| r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.5717 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= 0.194 Angle : 0.653 12.496 33075 Z= 0.324 Chirality : 0.045 0.441 3846 Planarity : 0.004 0.052 4124 Dihedral : 7.289 57.987 4211 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.16), residues: 2901 helix: 1.59 (0.28), residues: 415 sheet: -0.57 (0.17), residues: 847 loop : -1.69 (0.15), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 108 TYR 0.015 0.002 TYR G 50 PHE 0.019 0.002 PHE L 71 TRP 0.026 0.002 TRP L 96 HIS 0.004 0.001 HIS D 38 Details of bonding type rmsd covalent geometry : bond 0.00434 (24228) covalent geometry : angle 0.62983 (32883) SS BOND : bond 0.00372 ( 39) SS BOND : angle 0.80481 ( 78) hydrogen bonds : bond 0.03871 ( 766) hydrogen bonds : angle 5.33323 ( 2151) link_ALPHA1-3 : bond 0.00512 ( 3) link_ALPHA1-3 : angle 1.94273 ( 9) link_BETA1-4 : bond 0.00818 ( 20) link_BETA1-4 : angle 2.45294 ( 60) link_NAG-ASN : bond 0.00397 ( 15) link_NAG-ASN : angle 3.71856 ( 45) ********************** 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 50 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8031 (ppp) cc_final: 0.7640 (ppp) REVERT: B 530 MET cc_start: 0.7611 (mmm) cc_final: 0.7116 (mmp) REVERT: C 89 MET cc_start: 0.8523 (ttp) cc_final: 0.7892 (ttp) REVERT: E 396 MET cc_start: 0.8963 (pmm) cc_final: 0.7758 (mtt) REVERT: F 530 MET cc_start: 0.7400 (mpp) cc_final: 0.6762 (mpp) REVERT: I 145 MET cc_start: 0.6284 (mtp) cc_final: 0.6022 (mtp) REVERT: I 426 MET cc_start: 0.8285 (tpt) cc_final: 0.7711 (tpp) REVERT: I 473 MET cc_start: 0.8919 (mmm) cc_final: 0.8089 (mmm) REVERT: J 626 MET cc_start: 0.7982 (tmm) cc_final: 0.7719 (tmm) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1507 time to fit residues: 13.1868 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 : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 163 optimal weight: 2.9990 chunk 263 optimal weight: 7.9990 chunk 61 optimal weight: 0.3980 chunk 67 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 45 optimal weight: 9.9990 chunk 175 optimal weight: 7.9990 chunk 216 optimal weight: 20.0000 chunk 76 optimal weight: 1.9990 chunk 151 optimal weight: 10.0000 chunk 189 optimal weight: 30.0000 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 171 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.038649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.027179 restraints weight = 250740.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.028011 restraints weight = 151297.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.028324 restraints weight = 98075.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.028404 restraints weight = 101364.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.028439 restraints weight = 86469.643| |-----------------------------------------------------------------------------| r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.5787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24305 Z= 0.114 Angle : 0.600 12.363 33075 Z= 0.297 Chirality : 0.044 0.429 3846 Planarity : 0.004 0.051 4124 Dihedral : 7.032 58.498 4211 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.16), residues: 2901 helix: 1.66 (0.28), residues: 408 sheet: -0.46 (0.18), residues: 833 loop : -1.56 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 467 TYR 0.015 0.001 TYR J 638 PHE 0.016 0.001 PHE L 71 TRP 0.019 0.001 TRP L 96 HIS 0.003 0.001 HIS E 249 Details of bonding type rmsd covalent geometry : bond 0.00250 (24228) covalent geometry : angle 0.57351 (32883) SS BOND : bond 0.00254 ( 39) SS BOND : angle 0.79176 ( 78) hydrogen bonds : bond 0.03463 ( 766) hydrogen bonds : angle 5.16013 ( 2151) link_ALPHA1-3 : bond 0.00578 ( 3) link_ALPHA1-3 : angle 1.68297 ( 9) link_BETA1-4 : bond 0.00795 ( 20) link_BETA1-4 : angle 2.33807 ( 60) link_NAG-ASN : bond 0.00385 ( 15) link_NAG-ASN : angle 3.88044 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3310.76 seconds wall clock time: 58 minutes 32.09 seconds (3512.09 seconds total)