Starting phenix.real_space_refine on Sat Apr 13 21:50:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekk_28205/04_2024/8ekk_28205.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekk_28205/04_2024/8ekk_28205.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekk_28205/04_2024/8ekk_28205.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekk_28205/04_2024/8ekk_28205.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekk_28205/04_2024/8ekk_28205.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekk_28205/04_2024/8ekk_28205.pdb" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.016 sd= 0.951 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: 5 Type Number sf(0) Gaussians Ca 14 9.91 5 S 70 5.16 5 C 18655 2.51 5 N 4788 2.21 5 O 6097 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 453": "OD1" <-> "OD2" Residue "A ASP 471": "OD1" <-> "OD2" Residue "A TYR 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 787": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 453": "OD1" <-> "OD2" Residue "B ASP 471": "OD1" <-> "OD2" Residue "B ASP 561": "OD1" <-> "OD2" Residue "B TYR 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 815": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 624": "OD1" <-> "OD2" Residue "C ASP 867": "OD1" <-> "OD2" Residue "D ASP 239": "OD1" <-> "OD2" Residue "D GLU 251": "OE1" <-> "OE2" Residue "D ASP 471": "OD1" <-> "OD2" Residue "D ASP 624": "OD1" <-> "OD2" Residue "D GLU 710": "OE1" <-> "OE2" Residue "D PHE 815": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 453": "OD1" <-> "OD2" Residue "E ASP 465": "OD1" <-> "OD2" Residue "E GLU 522": "OE1" <-> "OE2" Residue "E TYR 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 709": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 453": "OD1" <-> "OD2" Residue "F GLU 524": "OE1" <-> "OE2" Residue "F TYR 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 453": "OD1" <-> "OD2" Residue "G GLU 522": "OE1" <-> "OE2" Residue "G ASP 568": "OD1" <-> "OD2" Residue "G ASP 572": "OD1" <-> "OD2" Residue "G ASP 582": "OD1" <-> "OD2" Residue "G TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 815": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 29624 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 4230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4230 Classifications: {'peptide': 533} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 510} Chain breaks: 6 Chain: "B" Number of atoms: 4230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4230 Classifications: {'peptide': 533} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 510} Chain breaks: 6 Chain: "C" Number of atoms: 4230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4230 Classifications: {'peptide': 533} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 510} Chain breaks: 6 Chain: "D" Number of atoms: 4230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4230 Classifications: {'peptide': 533} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 510} Chain breaks: 6 Chain: "E" Number of atoms: 4230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4230 Classifications: {'peptide': 533} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 510} Chain breaks: 6 Chain: "F" Number of atoms: 4230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4230 Classifications: {'peptide': 533} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 510} Chain breaks: 6 Chain: "G" Number of atoms: 4230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4230 Classifications: {'peptide': 533} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 510} Chain breaks: 6 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 15.60, per 1000 atoms: 0.53 Number of scatterers: 29624 At special positions: 0 Unit cell: (154.686, 156.464, 135.128, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 14 19.99 S 70 16.00 O 6097 8.00 N 4788 7.00 C 18655 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.59 Conformation dependent library (CDL) restraints added in 5.1 seconds 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7014 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 78 sheets defined 20.3% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.44 Creating SS restraints... Processing helix chain 'A' and resid 227 through 234 Processing helix chain 'A' and resid 246 through 253 removed outlier: 3.648A pdb=" N ALA A 250 " --> pdb=" O ASP A 247 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU A 251 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 279 Processing helix chain 'A' and resid 287 through 291 removed outlier: 3.611A pdb=" N ASP A 291 " --> pdb=" O GLU A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.923A pdb=" N ILE A 429 " --> pdb=" O GLU A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 471 Processing helix chain 'A' and resid 503 through 513 removed outlier: 4.590A pdb=" N SER A 508 " --> pdb=" O SER A 504 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLN A 509 " --> pdb=" O ASP A 505 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE A 513 " --> pdb=" O GLN A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 555 Processing helix chain 'A' and resid 581 through 593 removed outlier: 3.882A pdb=" N LYS A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 603 Processing helix chain 'A' and resid 757 through 765 removed outlier: 3.731A pdb=" N HIS A 765 " --> pdb=" O ILE A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 801 Processing helix chain 'A' and resid 829 through 831 No H-bonds generated for 'chain 'A' and resid 829 through 831' Processing helix chain 'A' and resid 841 through 845 Processing helix chain 'B' and resid 227 through 234 Processing helix chain 'B' and resid 246 through 253 removed outlier: 3.696A pdb=" N ALA B 250 " --> pdb=" O ASP B 247 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU B 251 " --> pdb=" O SER B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 279 Processing helix chain 'B' and resid 286 through 291 removed outlier: 3.654A pdb=" N ASP B 291 " --> pdb=" O GLU B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 471 Processing helix chain 'B' and resid 503 through 513 removed outlier: 4.616A pdb=" N SER B 508 " --> pdb=" O SER B 504 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N GLN B 509 " --> pdb=" O ASP B 505 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE B 513 " --> pdb=" O GLN B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 556 Processing helix chain 'B' and resid 581 through 595 removed outlier: 3.991A pdb=" N LYS B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N THR B 594 " --> pdb=" O ASP B 590 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU B 595 " --> pdb=" O SER B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 603 Processing helix chain 'B' and resid 757 through 765 removed outlier: 4.008A pdb=" N HIS B 765 " --> pdb=" O ILE B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 794 through 801 Processing helix chain 'B' and resid 829 through 831 No H-bonds generated for 'chain 'B' and resid 829 through 831' Processing helix chain 'B' and resid 843 through 845 No H-bonds generated for 'chain 'B' and resid 843 through 845' Processing helix chain 'C' and resid 227 through 234 Processing helix chain 'C' and resid 246 through 253 removed outlier: 3.577A pdb=" N ALA C 250 " --> pdb=" O ASP C 247 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU C 251 " --> pdb=" O SER C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 279 Processing helix chain 'C' and resid 286 through 291 removed outlier: 3.749A pdb=" N ASP C 291 " --> pdb=" O GLU C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 429 removed outlier: 3.921A pdb=" N ILE C 429 " --> pdb=" O GLU C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 471 Processing helix chain 'C' and resid 503 through 513 removed outlier: 4.619A pdb=" N SER C 508 " --> pdb=" O SER C 504 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N GLN C 509 " --> pdb=" O ASP C 505 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE C 513 " --> pdb=" O GLN C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 556 Processing helix chain 'C' and resid 581 through 595 removed outlier: 3.873A pdb=" N LYS C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N THR C 594 " --> pdb=" O ASP C 590 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU C 595 " --> pdb=" O SER C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 603 Processing helix chain 'C' and resid 757 through 765 removed outlier: 3.837A pdb=" N HIS C 765 " --> pdb=" O ILE C 761 " (cutoff:3.500A) Processing helix chain 'C' and resid 794 through 801 removed outlier: 3.600A pdb=" N ILE C 801 " --> pdb=" O ALA C 797 " (cutoff:3.500A) Processing helix chain 'C' and resid 829 through 831 No H-bonds generated for 'chain 'C' and resid 829 through 831' Processing helix chain 'C' and resid 841 through 845 Processing helix chain 'D' and resid 227 through 234 Processing helix chain 'D' and resid 246 through 253 removed outlier: 3.775A pdb=" N GLU D 251 " --> pdb=" O SER D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 279 Processing helix chain 'D' and resid 286 through 291 removed outlier: 3.736A pdb=" N ASP D 291 " --> pdb=" O GLU D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 429 removed outlier: 4.045A pdb=" N ILE D 429 " --> pdb=" O GLU D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 471 Processing helix chain 'D' and resid 503 through 513 removed outlier: 4.573A pdb=" N SER D 508 " --> pdb=" O SER D 504 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLN D 509 " --> pdb=" O ASP D 505 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE D 513 " --> pdb=" O GLN D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 555 Processing helix chain 'D' and resid 581 through 595 removed outlier: 3.823A pdb=" N LYS D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N THR D 594 " --> pdb=" O ASP D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 603 Processing helix chain 'D' and resid 757 through 765 removed outlier: 3.967A pdb=" N HIS D 765 " --> pdb=" O ILE D 761 " (cutoff:3.500A) Processing helix chain 'D' and resid 794 through 801 Processing helix chain 'D' and resid 829 through 831 No H-bonds generated for 'chain 'D' and resid 829 through 831' Processing helix chain 'D' and resid 841 through 845 Processing helix chain 'E' and resid 227 through 234 Processing helix chain 'E' and resid 246 through 253 removed outlier: 4.368A pdb=" N GLU E 251 " --> pdb=" O SER E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 279 Processing helix chain 'E' and resid 286 through 291 removed outlier: 3.595A pdb=" N ASP E 291 " --> pdb=" O GLU E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 429 removed outlier: 3.955A pdb=" N ILE E 429 " --> pdb=" O GLU E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 463 through 471 Processing helix chain 'E' and resid 503 through 513 removed outlier: 4.627A pdb=" N SER E 508 " --> pdb=" O SER E 504 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N GLN E 509 " --> pdb=" O ASP E 505 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE E 513 " --> pdb=" O GLN E 509 " (cutoff:3.500A) Processing helix chain 'E' and resid 546 through 556 Processing helix chain 'E' and resid 581 through 595 removed outlier: 3.940A pdb=" N LYS E 593 " --> pdb=" O LYS E 589 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N THR E 594 " --> pdb=" O ASP E 590 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU E 595 " --> pdb=" O SER E 591 " (cutoff:3.500A) Processing helix chain 'E' and resid 599 through 603 Processing helix chain 'E' and resid 757 through 765 removed outlier: 3.982A pdb=" N HIS E 765 " --> pdb=" O ILE E 761 " (cutoff:3.500A) Processing helix chain 'E' and resid 794 through 801 Processing helix chain 'E' and resid 829 through 831 No H-bonds generated for 'chain 'E' and resid 829 through 831' Processing helix chain 'E' and resid 843 through 845 No H-bonds generated for 'chain 'E' and resid 843 through 845' Processing helix chain 'F' and resid 227 through 234 Processing helix chain 'F' and resid 246 through 253 removed outlier: 3.506A pdb=" N ALA F 250 " --> pdb=" O ASP F 247 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLU F 251 " --> pdb=" O SER F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 279 Processing helix chain 'F' and resid 286 through 291 removed outlier: 3.666A pdb=" N ASP F 291 " --> pdb=" O GLU F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 429 removed outlier: 3.882A pdb=" N ILE F 429 " --> pdb=" O GLU F 426 " (cutoff:3.500A) Processing helix chain 'F' and resid 463 through 471 Processing helix chain 'F' and resid 503 through 513 removed outlier: 4.566A pdb=" N SER F 508 " --> pdb=" O SER F 504 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLN F 509 " --> pdb=" O ASP F 505 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE F 513 " --> pdb=" O GLN F 509 " (cutoff:3.500A) Processing helix chain 'F' and resid 546 through 556 Processing helix chain 'F' and resid 581 through 595 removed outlier: 3.880A pdb=" N LYS F 593 " --> pdb=" O LYS F 589 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N THR F 594 " --> pdb=" O ASP F 590 " (cutoff:3.500A) Processing helix chain 'F' and resid 599 through 603 Processing helix chain 'F' and resid 757 through 765 removed outlier: 3.836A pdb=" N HIS F 765 " --> pdb=" O ILE F 761 " (cutoff:3.500A) Processing helix chain 'F' and resid 794 through 801 Processing helix chain 'F' and resid 829 through 831 No H-bonds generated for 'chain 'F' and resid 829 through 831' Processing helix chain 'F' and resid 841 through 845 Processing helix chain 'G' and resid 227 through 234 Processing helix chain 'G' and resid 246 through 251 removed outlier: 3.564A pdb=" N ALA G 250 " --> pdb=" O ASP G 247 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU G 251 " --> pdb=" O SER G 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 272 through 279 Processing helix chain 'G' and resid 286 through 291 removed outlier: 3.693A pdb=" N ASP G 291 " --> pdb=" O GLU G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 425 through 429 removed outlier: 3.931A pdb=" N ILE G 429 " --> pdb=" O GLU G 426 " (cutoff:3.500A) Processing helix chain 'G' and resid 463 through 471 Processing helix chain 'G' and resid 503 through 513 removed outlier: 4.751A pdb=" N SER G 508 " --> pdb=" O SER G 504 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N GLN G 509 " --> pdb=" O ASP G 505 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE G 513 " --> pdb=" O GLN G 509 " (cutoff:3.500A) Processing helix chain 'G' and resid 546 through 556 Processing helix chain 'G' and resid 581 through 595 removed outlier: 3.931A pdb=" N LYS G 593 " --> pdb=" O LYS G 589 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N THR G 594 " --> pdb=" O ASP G 590 " (cutoff:3.500A) Processing helix chain 'G' and resid 599 through 603 Processing helix chain 'G' and resid 757 through 765 removed outlier: 3.840A pdb=" N HIS G 765 " --> pdb=" O ILE G 761 " (cutoff:3.500A) Processing helix chain 'G' and resid 794 through 801 removed outlier: 3.511A pdb=" N ILE G 801 " --> pdb=" O ALA G 797 " (cutoff:3.500A) Processing helix chain 'G' and resid 829 through 831 No H-bonds generated for 'chain 'G' and resid 829 through 831' Processing helix chain 'G' and resid 843 through 845 No H-bonds generated for 'chain 'G' and resid 843 through 845' Processing sheet with id=AA1, first strand: chain 'A' and resid 235 through 238 Processing sheet with id=AA2, first strand: chain 'A' and resid 294 through 295 removed outlier: 4.824A pdb=" N ARG A 529 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 9.145A pdb=" N ILE A 611 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N SER A 516 " --> pdb=" O ILE A 611 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ILE A 613 " --> pdb=" O SER A 516 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE A 518 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 300 through 311 removed outlier: 5.643A pdb=" N VAL A 302 " --> pdb=" O TYR A 396 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N TYR A 396 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N MET A 304 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ARG A 394 " --> pdb=" O MET A 304 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS A 306 " --> pdb=" O ASN A 392 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 314 through 327 removed outlier: 3.529A pdb=" N SER A 316 " --> pdb=" O GLY A 378 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP A 369 " --> pdb=" O THR B 327 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER B 374 " --> pdb=" O GLY B 320 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N SER B 370 " --> pdb=" O SER B 324 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 313 through 323 current: chain 'D' and resid 313 through 327 removed outlier: 3.643A pdb=" N SER D 374 " --> pdb=" O GLY D 320 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N SER D 370 " --> pdb=" O SER D 324 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP D 369 " --> pdb=" O THR E 327 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG E 325 " --> pdb=" O ASN D 371 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER E 374 " --> pdb=" O GLY E 320 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER E 370 " --> pdb=" O SER E 324 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 313 through 323 current: chain 'G' and resid 313 through 323 Processing sheet with id=AA5, first strand: chain 'A' and resid 418 through 423 removed outlier: 6.813A pdb=" N LEU A 412 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N THR A 421 " --> pdb=" O THR A 410 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N THR A 410 " --> pdb=" O THR A 421 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N LYS A 423 " --> pdb=" O PRO A 408 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N LYS A 405 " --> pdb=" O ASN A 486 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ASN A 486 " --> pdb=" O LYS A 405 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLN A 482 " --> pdb=" O THR A 409 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ASN A 411 " --> pdb=" O THR A 480 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N THR A 480 " --> pdb=" O ASN A 411 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N VAL A 413 " --> pdb=" O LEU A 478 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N LEU A 478 " --> pdb=" O VAL A 413 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 489 through 490 Processing sheet with id=AA7, first strand: chain 'A' and resid 558 through 559 Processing sheet with id=AA8, first strand: chain 'A' and resid 618 through 620 Processing sheet with id=AA9, first strand: chain 'A' and resid 674 through 675 Processing sheet with id=AB1, first strand: chain 'A' and resid 768 through 771 removed outlier: 3.523A pdb=" N PHE A 769 " --> pdb=" O TYR A 787 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY A 785 " --> pdb=" O ASP A 771 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 820 through 821 removed outlier: 4.893A pdb=" N LYS A 803 " --> pdb=" O ILE A 863 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE A 863 " --> pdb=" O LYS A 803 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE A 860 " --> pdb=" O VAL A 872 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 826 through 827 Processing sheet with id=AB4, first strand: chain 'B' and resid 235 through 238 Processing sheet with id=AB5, first strand: chain 'B' and resid 300 through 311 removed outlier: 5.692A pdb=" N VAL B 302 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N TYR B 396 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N MET B 304 " --> pdb=" O ARG B 394 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ARG B 394 " --> pdb=" O MET B 304 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS B 306 " --> pdb=" O ASN B 392 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR B 439 " --> pdb=" O TYR B 395 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 418 through 423 removed outlier: 6.804A pdb=" N LEU B 412 " --> pdb=" O LEU B 419 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N THR B 421 " --> pdb=" O THR B 410 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR B 410 " --> pdb=" O THR B 421 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN B 482 " --> pdb=" O THR B 409 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ASN B 411 " --> pdb=" O THR B 480 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N THR B 480 " --> pdb=" O ASN B 411 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N VAL B 413 " --> pdb=" O LEU B 478 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N LEU B 478 " --> pdb=" O VAL B 413 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 489 through 490 Processing sheet with id=AB8, first strand: chain 'B' and resid 526 through 531 removed outlier: 9.077A pdb=" N ILE B 611 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N SER B 516 " --> pdb=" O ILE B 611 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ILE B 613 " --> pdb=" O SER B 516 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE B 518 " --> pdb=" O ILE B 613 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 558 through 559 Processing sheet with id=AC1, first strand: chain 'B' and resid 618 through 619 Processing sheet with id=AC2, first strand: chain 'B' and resid 674 through 675 removed outlier: 3.618A pdb=" N SER B 675 " --> pdb=" O THR B 705 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR B 705 " --> pdb=" O SER B 675 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 768 through 772 removed outlier: 6.316A pdb=" N PHE B 769 " --> pdb=" O MET B 786 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N MET B 786 " --> pdb=" O PHE B 769 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ASP B 771 " --> pdb=" O ASN B 784 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 820 through 821 removed outlier: 4.916A pdb=" N LYS B 803 " --> pdb=" O ILE B 863 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE B 863 " --> pdb=" O LYS B 803 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ILE B 860 " --> pdb=" O VAL B 872 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 826 through 827 Processing sheet with id=AC6, first strand: chain 'C' and resid 235 through 238 Processing sheet with id=AC7, first strand: chain 'C' and resid 294 through 295 removed outlier: 4.782A pdb=" N ARG C 529 " --> pdb=" O ALA C 295 " (cutoff:3.500A) removed outlier: 9.113A pdb=" N ILE C 611 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N SER C 516 " --> pdb=" O ILE C 611 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N ILE C 613 " --> pdb=" O SER C 516 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ILE C 518 " --> pdb=" O ILE C 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 300 through 302 Processing sheet with id=AC9, first strand: chain 'C' and resid 306 through 311 removed outlier: 3.832A pdb=" N LYS C 306 " --> pdb=" O ASN C 392 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA C 391 " --> pdb=" O LEU C 449 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 418 through 423 removed outlier: 6.777A pdb=" N LEU C 412 " --> pdb=" O LEU C 419 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N THR C 421 " --> pdb=" O THR C 410 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N THR C 410 " --> pdb=" O THR C 421 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N LYS C 423 " --> pdb=" O PRO C 408 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N LYS C 405 " --> pdb=" O ASN C 486 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ASN C 486 " --> pdb=" O LYS C 405 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN C 482 " --> pdb=" O THR C 409 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ASN C 411 " --> pdb=" O THR C 480 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N THR C 480 " --> pdb=" O ASN C 411 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL C 413 " --> pdb=" O LEU C 478 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N LEU C 478 " --> pdb=" O VAL C 413 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 489 through 490 Processing sheet with id=AD3, first strand: chain 'C' and resid 558 through 559 Processing sheet with id=AD4, first strand: chain 'C' and resid 618 through 620 removed outlier: 3.613A pdb=" N TYR C 618 " --> pdb=" O ILE C 738 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 674 through 675 removed outlier: 3.558A pdb=" N THR C 705 " --> pdb=" O SER C 675 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 768 through 771 removed outlier: 3.557A pdb=" N PHE C 769 " --> pdb=" O TYR C 787 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 820 through 821 removed outlier: 4.888A pdb=" N LYS C 803 " --> pdb=" O ILE C 863 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE C 863 " --> pdb=" O LYS C 803 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE C 860 " --> pdb=" O VAL C 872 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 826 through 827 Processing sheet with id=AD9, first strand: chain 'D' and resid 235 through 237 Processing sheet with id=AE1, first strand: chain 'D' and resid 294 through 295 removed outlier: 4.843A pdb=" N ARG D 529 " --> pdb=" O ALA D 295 " (cutoff:3.500A) removed outlier: 9.143A pdb=" N ILE D 611 " --> pdb=" O SER D 514 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N SER D 516 " --> pdb=" O ILE D 611 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N ILE D 613 " --> pdb=" O SER D 516 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE D 518 " --> pdb=" O ILE D 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 300 through 311 removed outlier: 5.618A pdb=" N VAL D 302 " --> pdb=" O TYR D 396 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N TYR D 396 " --> pdb=" O VAL D 302 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N MET D 304 " --> pdb=" O ARG D 394 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ARG D 394 " --> pdb=" O MET D 304 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS D 306 " --> pdb=" O ASN D 392 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 418 through 423 removed outlier: 6.795A pdb=" N LEU D 412 " --> pdb=" O LEU D 419 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N THR D 421 " --> pdb=" O THR D 410 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N THR D 410 " --> pdb=" O THR D 421 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N LYS D 423 " --> pdb=" O PRO D 408 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N VAL D 406 " --> pdb=" O SER D 484 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N SER D 484 " --> pdb=" O VAL D 406 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N GLN D 482 " --> pdb=" O PRO D 408 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N THR D 410 " --> pdb=" O THR D 480 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR D 480 " --> pdb=" O THR D 410 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N LEU D 412 " --> pdb=" O LEU D 478 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N LEU D 478 " --> pdb=" O LEU D 412 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 489 through 490 Processing sheet with id=AE5, first strand: chain 'D' and resid 558 through 559 Processing sheet with id=AE6, first strand: chain 'D' and resid 618 through 619 Processing sheet with id=AE7, first strand: chain 'D' and resid 768 through 772 removed outlier: 6.231A pdb=" N PHE D 769 " --> pdb=" O MET D 786 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N MET D 786 " --> pdb=" O PHE D 769 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ASP D 771 " --> pdb=" O ASN D 784 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 820 through 821 removed outlier: 4.867A pdb=" N LYS D 803 " --> pdb=" O ILE D 863 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE D 863 " --> pdb=" O LYS D 803 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ILE D 860 " --> pdb=" O VAL D 872 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 826 through 827 Processing sheet with id=AF1, first strand: chain 'E' and resid 235 through 238 Processing sheet with id=AF2, first strand: chain 'E' and resid 300 through 311 removed outlier: 5.599A pdb=" N VAL E 302 " --> pdb=" O TYR E 396 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N TYR E 396 " --> pdb=" O VAL E 302 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N MET E 304 " --> pdb=" O ARG E 394 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ARG E 394 " --> pdb=" O MET E 304 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS E 306 " --> pdb=" O ASN E 392 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 403 through 413 removed outlier: 4.825A pdb=" N LYS E 423 " --> pdb=" O PRO E 408 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N THR E 410 " --> pdb=" O THR E 421 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N THR E 421 " --> pdb=" O THR E 410 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU E 412 " --> pdb=" O LEU E 419 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 489 through 490 Processing sheet with id=AF5, first strand: chain 'E' and resid 526 through 531 removed outlier: 9.110A pdb=" N ILE E 611 " --> pdb=" O SER E 514 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N SER E 516 " --> pdb=" O ILE E 611 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N ILE E 613 " --> pdb=" O SER E 516 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE E 518 " --> pdb=" O ILE E 613 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 558 through 559 Processing sheet with id=AF7, first strand: chain 'E' and resid 618 through 620 removed outlier: 3.559A pdb=" N TYR E 618 " --> pdb=" O ILE E 738 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 674 through 675 Processing sheet with id=AF9, first strand: chain 'E' and resid 768 through 772 removed outlier: 6.226A pdb=" N PHE E 769 " --> pdb=" O MET E 786 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N MET E 786 " --> pdb=" O PHE E 769 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ASP E 771 " --> pdb=" O ASN E 784 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 820 through 821 removed outlier: 4.891A pdb=" N LYS E 803 " --> pdb=" O ILE E 863 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE E 863 " --> pdb=" O LYS E 803 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE E 860 " --> pdb=" O VAL E 872 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 826 through 827 Processing sheet with id=AG3, first strand: chain 'F' and resid 235 through 238 Processing sheet with id=AG4, first strand: chain 'F' and resid 294 through 295 removed outlier: 4.812A pdb=" N ARG F 529 " --> pdb=" O ALA F 295 " (cutoff:3.500A) removed outlier: 9.136A pdb=" N ILE F 611 " --> pdb=" O SER F 514 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N SER F 516 " --> pdb=" O ILE F 611 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N ILE F 613 " --> pdb=" O SER F 516 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ILE F 518 " --> pdb=" O ILE F 613 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 300 through 302 removed outlier: 3.503A pdb=" N TYR F 439 " --> pdb=" O TYR F 395 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 306 through 311 removed outlier: 3.720A pdb=" N LYS F 306 " --> pdb=" O ASN F 392 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA F 391 " --> pdb=" O LEU F 449 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 418 through 423 removed outlier: 6.764A pdb=" N LEU F 412 " --> pdb=" O LEU F 419 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N THR F 421 " --> pdb=" O THR F 410 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N THR F 410 " --> pdb=" O THR F 421 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N LYS F 423 " --> pdb=" O PRO F 408 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N VAL F 406 " --> pdb=" O SER F 484 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N SER F 484 " --> pdb=" O VAL F 406 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLN F 482 " --> pdb=" O PRO F 408 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N THR F 410 " --> pdb=" O THR F 480 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N THR F 480 " --> pdb=" O THR F 410 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N LEU F 412 " --> pdb=" O LEU F 478 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N LEU F 478 " --> pdb=" O LEU F 412 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'F' and resid 489 through 490 Processing sheet with id=AG9, first strand: chain 'F' and resid 558 through 559 Processing sheet with id=AH1, first strand: chain 'F' and resid 618 through 620 removed outlier: 3.563A pdb=" N TYR F 618 " --> pdb=" O ILE F 738 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'F' and resid 674 through 675 removed outlier: 3.505A pdb=" N THR F 705 " --> pdb=" O SER F 675 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'F' and resid 768 through 771 removed outlier: 3.539A pdb=" N PHE F 769 " --> pdb=" O TYR F 787 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'F' and resid 815 through 821 removed outlier: 6.076A pdb=" N VAL F 806 " --> pdb=" O ILE F 818 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N THR F 820 " --> pdb=" O TYR F 804 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N TYR F 804 " --> pdb=" O THR F 820 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N LYS F 803 " --> pdb=" O ILE F 863 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE F 863 " --> pdb=" O LYS F 803 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE F 860 " --> pdb=" O VAL F 872 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'F' and resid 826 through 827 Processing sheet with id=AH6, first strand: chain 'G' and resid 235 through 238 Processing sheet with id=AH7, first strand: chain 'G' and resid 294 through 295 removed outlier: 4.811A pdb=" N ARG G 529 " --> pdb=" O ALA G 295 " (cutoff:3.500A) removed outlier: 9.072A pdb=" N ILE G 611 " --> pdb=" O SER G 514 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N SER G 516 " --> pdb=" O ILE G 611 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N ILE G 613 " --> pdb=" O SER G 516 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE G 518 " --> pdb=" O ILE G 613 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'G' and resid 300 through 311 removed outlier: 5.636A pdb=" N VAL G 302 " --> pdb=" O TYR G 396 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N TYR G 396 " --> pdb=" O VAL G 302 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N MET G 304 " --> pdb=" O ARG G 394 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ARG G 394 " --> pdb=" O MET G 304 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS G 306 " --> pdb=" O ASN G 392 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'G' and resid 418 through 423 removed outlier: 6.811A pdb=" N LEU G 412 " --> pdb=" O LEU G 419 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N THR G 421 " --> pdb=" O THR G 410 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N THR G 410 " --> pdb=" O THR G 421 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N LYS G 423 " --> pdb=" O PRO G 408 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL G 406 " --> pdb=" O SER G 484 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N SER G 484 " --> pdb=" O VAL G 406 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N GLN G 482 " --> pdb=" O PRO G 408 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N THR G 410 " --> pdb=" O THR G 480 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N THR G 480 " --> pdb=" O THR G 410 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N LEU G 412 " --> pdb=" O LEU G 478 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N LEU G 478 " --> pdb=" O LEU G 412 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'G' and resid 489 through 490 Processing sheet with id=AI2, first strand: chain 'G' and resid 558 through 559 Processing sheet with id=AI3, first strand: chain 'G' and resid 618 through 619 removed outlier: 3.604A pdb=" N TYR G 618 " --> pdb=" O ILE G 738 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'G' and resid 768 through 772 removed outlier: 6.349A pdb=" N PHE G 769 " --> pdb=" O MET G 786 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N MET G 786 " --> pdb=" O PHE G 769 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ASP G 771 " --> pdb=" O ASN G 784 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'G' and resid 820 through 821 removed outlier: 4.876A pdb=" N LYS G 803 " --> pdb=" O ILE G 863 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE G 863 " --> pdb=" O LYS G 803 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE G 860 " --> pdb=" O VAL G 872 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'G' and resid 826 through 827 819 hydrogen bonds defined for protein. 2028 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: 10.95 Time building geometry restraints manager: 11.53 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: 9600 1.34 - 1.45: 4248 1.45 - 1.57: 16160 1.57 - 1.69: 1 1.69 - 1.81: 133 Bond restraints: 30142 Sorted by residual: bond pdb=" CB GLU E 522 " pdb=" CG GLU E 522 " ideal model delta sigma weight residual 1.520 1.575 -0.055 3.00e-02 1.11e+03 3.30e+00 bond pdb=" CB GLU G 522 " pdb=" CG GLU G 522 " ideal model delta sigma weight residual 1.520 1.565 -0.045 3.00e-02 1.11e+03 2.29e+00 bond pdb=" C TYR D 297 " pdb=" O TYR D 297 " ideal model delta sigma weight residual 1.249 1.237 0.012 8.50e-03 1.38e+04 1.87e+00 bond pdb=" CB ASP C 561 " pdb=" CG ASP C 561 " ideal model delta sigma weight residual 1.516 1.550 -0.034 2.50e-02 1.60e+03 1.80e+00 bond pdb=" CA GLU E 522 " pdb=" CB GLU E 522 " ideal model delta sigma weight residual 1.533 1.550 -0.017 1.37e-02 5.33e+03 1.53e+00 ... (remaining 30137 not shown) Histogram of bond angle deviations from ideal: 100.10 - 106.87: 700 106.87 - 113.65: 16357 113.65 - 120.43: 11140 120.43 - 127.20: 12431 127.20 - 133.98: 175 Bond angle restraints: 40803 Sorted by residual: angle pdb=" CA GLU E 522 " pdb=" CB GLU E 522 " pdb=" CG GLU E 522 " ideal model delta sigma weight residual 114.10 124.72 -10.62 2.00e+00 2.50e-01 2.82e+01 angle pdb=" CB GLU E 522 " pdb=" CG GLU E 522 " pdb=" CD GLU E 522 " ideal model delta sigma weight residual 112.60 119.72 -7.12 1.70e+00 3.46e-01 1.75e+01 angle pdb=" CB GLU G 522 " pdb=" CG GLU G 522 " pdb=" CD GLU G 522 " ideal model delta sigma weight residual 112.60 119.11 -6.51 1.70e+00 3.46e-01 1.47e+01 angle pdb=" CA GLU G 522 " pdb=" CB GLU G 522 " pdb=" CG GLU G 522 " ideal model delta sigma weight residual 114.10 120.92 -6.82 2.00e+00 2.50e-01 1.16e+01 angle pdb=" C MET D 762 " pdb=" N ASP D 763 " pdb=" CA ASP D 763 " ideal model delta sigma weight residual 122.06 116.26 5.80 1.86e+00 2.89e-01 9.74e+00 ... (remaining 40798 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 15485 17.43 - 34.86: 2099 34.86 - 52.29: 532 52.29 - 69.71: 106 69.71 - 87.14: 55 Dihedral angle restraints: 18277 sinusoidal: 7322 harmonic: 10955 Sorted by residual: dihedral pdb=" CA ASN C 223 " pdb=" C ASN C 223 " pdb=" N ASP C 224 " pdb=" CA ASP C 224 " ideal model delta harmonic sigma weight residual 180.00 161.01 18.99 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA ASN E 223 " pdb=" C ASN E 223 " pdb=" N ASP E 224 " pdb=" CA ASP E 224 " ideal model delta harmonic sigma weight residual 180.00 161.20 18.80 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA PHE A 566 " pdb=" C PHE A 566 " pdb=" N ASN A 567 " pdb=" CA ASN A 567 " ideal model delta harmonic sigma weight residual 180.00 161.36 18.64 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 18274 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 3687 0.052 - 0.103: 656 0.103 - 0.155: 193 0.155 - 0.207: 5 0.207 - 0.258: 2 Chirality restraints: 4543 Sorted by residual: chirality pdb=" CB THR G 521 " pdb=" CA THR G 521 " pdb=" OG1 THR G 521 " pdb=" CG2 THR G 521 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CB THR D 521 " pdb=" CA THR D 521 " pdb=" OG1 THR D 521 " pdb=" CG2 THR D 521 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA ASN D 523 " pdb=" N ASN D 523 " pdb=" C ASN D 523 " pdb=" CB ASN D 523 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.21e-01 ... (remaining 4540 not shown) Planarity restraints: 5285 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU E 522 " -0.021 2.00e-02 2.50e+03 4.23e-02 1.79e+01 pdb=" CD GLU E 522 " 0.073 2.00e-02 2.50e+03 pdb=" OE1 GLU E 522 " -0.026 2.00e-02 2.50e+03 pdb=" OE2 GLU E 522 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU G 522 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.84e+00 pdb=" CD GLU G 522 " 0.045 2.00e-02 2.50e+03 pdb=" OE1 GLU G 522 " -0.017 2.00e-02 2.50e+03 pdb=" OE2 GLU G 522 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU G 522 " 0.012 2.00e-02 2.50e+03 2.51e-02 6.30e+00 pdb=" C GLU G 522 " -0.043 2.00e-02 2.50e+03 pdb=" O GLU G 522 " 0.017 2.00e-02 2.50e+03 pdb=" N ASN G 523 " 0.014 2.00e-02 2.50e+03 ... (remaining 5282 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 2063 2.73 - 3.27: 27355 3.27 - 3.82: 45305 3.82 - 4.36: 55945 4.36 - 4.90: 101081 Nonbonded interactions: 231749 Sorted by model distance: nonbonded pdb=" OG SER C 672 " pdb=" OG SER C 708 " model vdw 2.191 2.440 nonbonded pdb=" OD1 ASP G 222 " pdb="CA CA G 902 " model vdw 2.233 2.510 nonbonded pdb=" OD1 ASP F 581 " pdb=" OG1 THR F 584 " model vdw 2.245 2.440 nonbonded pdb=" OD1 ASP C 581 " pdb=" OG1 THR C 584 " model vdw 2.247 2.440 nonbonded pdb=" OG SER E 672 " pdb=" OG SER E 708 " model vdw 2.249 2.440 ... (remaining 231744 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.170 Check model and map are aligned: 0.480 Set scattering table: 0.260 Process input model: 74.780 Find NCS groups from input model: 2.070 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 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 : 0.002 0.055 30142 Z= 0.157 Angle : 0.480 10.623 40803 Z= 0.258 Chirality : 0.043 0.258 4543 Planarity : 0.003 0.042 5285 Dihedral : 17.363 87.144 11263 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.15 % Allowed : 27.27 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.14), residues: 3633 helix: -0.07 (0.22), residues: 539 sheet: -0.90 (0.17), residues: 973 loop : -0.78 (0.13), residues: 2121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 375 HIS 0.002 0.001 HIS F 314 PHE 0.013 0.001 PHE C 707 TYR 0.010 0.001 TYR D 439 ARG 0.006 0.000 ARG B 458 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 3304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 237 time to evaluate : 3.392 Fit side-chains revert: symmetry clash REVERT: G 709 TYR cc_start: 0.8364 (m-80) cc_final: 0.8156 (m-80) outliers start: 5 outliers final: 1 residues processed: 240 average time/residue: 0.4025 time to fit residues: 158.1070 Evaluate side-chains 219 residues out of total 3304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 218 time to evaluate : 3.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 870 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 313 optimal weight: 0.8980 chunk 281 optimal weight: 1.9990 chunk 156 optimal weight: 6.9990 chunk 96 optimal weight: 0.9980 chunk 189 optimal weight: 6.9990 chunk 150 optimal weight: 10.0000 chunk 290 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 176 optimal weight: 5.9990 chunk 216 optimal weight: 0.4980 chunk 336 optimal weight: 5.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN A 834 GLN B 368 GLN ** B 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 GLN C 834 GLN E 368 GLN E 773 ASN E 784 ASN F 368 GLN F 501 ASN F 834 GLN G 834 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.0610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 30142 Z= 0.154 Angle : 0.457 8.986 40803 Z= 0.246 Chirality : 0.043 0.179 4543 Planarity : 0.003 0.035 5285 Dihedral : 4.059 33.441 4041 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.21 % Allowed : 26.39 % Favored : 71.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.14), residues: 3633 helix: 0.26 (0.22), residues: 546 sheet: -0.80 (0.16), residues: 1015 loop : -0.58 (0.14), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 375 HIS 0.002 0.000 HIS F 314 PHE 0.009 0.001 PHE D 707 TYR 0.013 0.001 TYR G 669 ARG 0.004 0.000 ARG C 458 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 3304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 238 time to evaluate : 3.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 319 GLN cc_start: 0.7712 (pt0) cc_final: 0.7382 (tt0) REVERT: C 825 MET cc_start: 0.8484 (mmt) cc_final: 0.8109 (mmt) REVERT: E 217 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7407 (tt0) outliers start: 73 outliers final: 39 residues processed: 301 average time/residue: 0.3868 time to fit residues: 192.6918 Evaluate side-chains 253 residues out of total 3304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 213 time to evaluate : 3.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 505 ASP Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 793 THR Chi-restraints excluded: chain B residue 822 ASP Chi-restraints excluded: chain B residue 874 SER Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain D residue 371 ASN Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 757 THR Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 822 ASP Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 414 LEU Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 757 THR Chi-restraints excluded: chain E residue 793 THR Chi-restraints excluded: chain E residue 802 GLN Chi-restraints excluded: chain E residue 822 ASP Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 582 ASP Chi-restraints excluded: chain F residue 625 TYR Chi-restraints excluded: chain G residue 263 GLU Chi-restraints excluded: chain G residue 272 THR Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 763 ASP Chi-restraints excluded: chain G residue 822 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 187 optimal weight: 5.9990 chunk 104 optimal weight: 9.9990 chunk 280 optimal weight: 7.9990 chunk 229 optimal weight: 7.9990 chunk 92 optimal weight: 20.0000 chunk 337 optimal weight: 6.9990 chunk 364 optimal weight: 9.9990 chunk 300 optimal weight: 9.9990 chunk 334 optimal weight: 6.9990 chunk 115 optimal weight: 2.9990 chunk 270 optimal weight: 3.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN ** B 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 583 ASN C 368 GLN D 368 GLN E 368 GLN E 784 ASN F 368 GLN F 501 ASN G 368 GLN G 784 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.0937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 30142 Z= 0.420 Angle : 0.590 10.126 40803 Z= 0.316 Chirality : 0.048 0.181 4543 Planarity : 0.004 0.041 5285 Dihedral : 4.717 23.404 4039 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 3.66 % Allowed : 26.57 % Favored : 69.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.14), residues: 3633 helix: -0.09 (0.22), residues: 553 sheet: -0.89 (0.16), residues: 994 loop : -0.85 (0.14), residues: 2086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 245 HIS 0.003 0.001 HIS F 314 PHE 0.021 0.002 PHE B 707 TYR 0.016 0.002 TYR D 839 ARG 0.003 0.000 ARG B 458 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 3304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 211 time to evaluate : 3.455 Fit side-chains revert: symmetry clash REVERT: A 414 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8406 (tp) REVERT: A 822 ASP cc_start: 0.7181 (OUTLIER) cc_final: 0.6898 (m-30) REVERT: C 668 ARG cc_start: 0.8170 (ptm-80) cc_final: 0.7892 (ptm-80) REVERT: C 740 GLU cc_start: 0.7657 (pt0) cc_final: 0.7423 (pt0) REVERT: D 239 ASP cc_start: 0.7828 (t0) cc_final: 0.7594 (t0) REVERT: D 414 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8263 (tp) REVERT: E 217 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7504 (tt0) REVERT: G 228 ASP cc_start: 0.6521 (p0) cc_final: 0.6285 (p0) outliers start: 121 outliers final: 95 residues processed: 321 average time/residue: 0.3806 time to fit residues: 203.8085 Evaluate side-chains 294 residues out of total 3304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 195 time to evaluate : 3.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 325 ARG Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 793 THR Chi-restraints excluded: chain A residue 822 ASP Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 452 MET Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 793 THR Chi-restraints excluded: chain B residue 822 ASP Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 874 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 793 THR Chi-restraints excluded: chain C residue 874 SER Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 371 ASN Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain D residue 757 THR Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 822 ASP Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 377 THR Chi-restraints excluded: chain E residue 381 ILE Chi-restraints excluded: chain E residue 414 LEU Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 542 THR Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 757 THR Chi-restraints excluded: chain E residue 793 THR Chi-restraints excluded: chain E residue 822 ASP Chi-restraints excluded: chain E residue 870 LEU Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 407 THR Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain F residue 452 MET Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 530 VAL Chi-restraints excluded: chain F residue 542 THR Chi-restraints excluded: chain F residue 582 ASP Chi-restraints excluded: chain F residue 625 TYR Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 791 THR Chi-restraints excluded: chain F residue 793 THR Chi-restraints excluded: chain F residue 822 ASP Chi-restraints excluded: chain F residue 870 LEU Chi-restraints excluded: chain G residue 272 THR Chi-restraints excluded: chain G residue 308 ILE Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 381 ILE Chi-restraints excluded: chain G residue 407 THR Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 421 THR Chi-restraints excluded: chain G residue 480 THR Chi-restraints excluded: chain G residue 569 ILE Chi-restraints excluded: chain G residue 582 ASP Chi-restraints excluded: chain G residue 763 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 333 optimal weight: 1.9990 chunk 253 optimal weight: 20.0000 chunk 175 optimal weight: 0.0570 chunk 37 optimal weight: 0.0370 chunk 161 optimal weight: 3.9990 chunk 226 optimal weight: 3.9990 chunk 338 optimal weight: 3.9990 chunk 358 optimal weight: 1.9990 chunk 176 optimal weight: 5.9990 chunk 321 optimal weight: 7.9990 chunk 96 optimal weight: 0.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 GLN ** B 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 GLN D 368 GLN E 368 GLN E 773 ASN E 784 ASN F 368 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.0861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 30142 Z= 0.131 Angle : 0.445 9.823 40803 Z= 0.237 Chirality : 0.043 0.186 4543 Planarity : 0.003 0.036 5285 Dihedral : 4.067 19.284 4039 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.81 % Allowed : 27.36 % Favored : 69.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.14), residues: 3633 helix: 0.29 (0.22), residues: 553 sheet: -0.57 (0.16), residues: 1057 loop : -0.71 (0.14), residues: 2023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 375 HIS 0.001 0.000 HIS G 314 PHE 0.009 0.001 PHE A 487 TYR 0.009 0.001 TYR G 669 ARG 0.003 0.000 ARG C 458 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 3304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 230 time to evaluate : 3.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 371 ASN cc_start: 0.7633 (p0) cc_final: 0.7380 (p0) REVERT: C 319 GLN cc_start: 0.7728 (pt0) cc_final: 0.7421 (tt0) REVERT: C 371 ASN cc_start: 0.8037 (p0) cc_final: 0.7185 (p0) REVERT: C 668 ARG cc_start: 0.8220 (ptm-80) cc_final: 0.7893 (ptm-80) REVERT: D 239 ASP cc_start: 0.7803 (t0) cc_final: 0.7562 (t0) REVERT: D 561 ASP cc_start: 0.7207 (t0) cc_final: 0.7004 (t0) REVERT: E 217 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7573 (tt0) REVERT: E 707 PHE cc_start: 0.5641 (OUTLIER) cc_final: 0.4817 (p90) outliers start: 93 outliers final: 61 residues processed: 311 average time/residue: 0.3969 time to fit residues: 202.4269 Evaluate side-chains 275 residues out of total 3304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 212 time to evaluate : 3.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 833 ASN Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 822 ASP Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 456 SER Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 757 THR Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 822 ASP Chi-restraints excluded: chain D residue 874 SER Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 310 SER Chi-restraints excluded: chain E residue 377 THR Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 707 PHE Chi-restraints excluded: chain E residue 757 THR Chi-restraints excluded: chain E residue 802 GLN Chi-restraints excluded: chain E residue 870 LEU Chi-restraints excluded: chain F residue 263 GLU Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 452 MET Chi-restraints excluded: chain F residue 489 THR Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 822 ASP Chi-restraints excluded: chain G residue 263 GLU Chi-restraints excluded: chain G residue 307 LEU Chi-restraints excluded: chain G residue 308 ILE Chi-restraints excluded: chain G residue 377 THR Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 480 THR Chi-restraints excluded: chain G residue 505 ASP Chi-restraints excluded: chain G residue 569 ILE Chi-restraints excluded: chain G residue 757 THR Chi-restraints excluded: chain G residue 763 ASP Chi-restraints excluded: chain G residue 822 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 298 optimal weight: 9.9990 chunk 203 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 267 optimal weight: 0.7980 chunk 147 optimal weight: 20.0000 chunk 306 optimal weight: 0.9990 chunk 247 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 183 optimal weight: 0.7980 chunk 321 optimal weight: 10.0000 chunk 90 optimal weight: 9.9990 overall best weight: 4.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 GLN ** B 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 GLN D 368 GLN E 368 GLN E 501 ASN F 368 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 30142 Z= 0.349 Angle : 0.545 9.823 40803 Z= 0.291 Chirality : 0.046 0.193 4543 Planarity : 0.004 0.042 5285 Dihedral : 4.543 22.515 4039 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 4.12 % Allowed : 26.85 % Favored : 69.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.14), residues: 3633 helix: 0.11 (0.22), residues: 553 sheet: -0.63 (0.16), residues: 1043 loop : -0.83 (0.14), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 245 HIS 0.003 0.001 HIS F 314 PHE 0.018 0.002 PHE B 707 TYR 0.014 0.001 TYR D 839 ARG 0.002 0.000 ARG B 458 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 206 time to evaluate : 3.560 Fit side-chains revert: symmetry clash REVERT: A 822 ASP cc_start: 0.7172 (OUTLIER) cc_final: 0.6849 (m-30) REVERT: B 371 ASN cc_start: 0.7667 (p0) cc_final: 0.7404 (p0) REVERT: D 239 ASP cc_start: 0.8002 (t0) cc_final: 0.7781 (t0) REVERT: D 414 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8284 (tp) REVERT: D 561 ASP cc_start: 0.7353 (t0) cc_final: 0.7145 (t0) REVERT: E 217 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7527 (tt0) REVERT: E 414 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8321 (tp) REVERT: E 707 PHE cc_start: 0.5893 (OUTLIER) cc_final: 0.5156 (p90) outliers start: 136 outliers final: 109 residues processed: 332 average time/residue: 0.3864 time to fit residues: 213.9705 Evaluate side-chains 310 residues out of total 3304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 196 time to evaluate : 3.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 325 ARG Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 822 ASP Chi-restraints excluded: chain A residue 833 ASN Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 793 THR Chi-restraints excluded: chain B residue 822 ASP Chi-restraints excluded: chain B residue 833 ASN Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 874 SER Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 793 THR Chi-restraints excluded: chain C residue 822 ASP Chi-restraints excluded: chain C residue 870 LEU Chi-restraints excluded: chain C residue 874 SER Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 456 SER Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain D residue 757 THR Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 822 ASP Chi-restraints excluded: chain D residue 844 SER Chi-restraints excluded: chain D residue 874 SER Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 377 THR Chi-restraints excluded: chain E residue 381 ILE Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 414 LEU Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 578 LEU Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 707 PHE Chi-restraints excluded: chain E residue 757 THR Chi-restraints excluded: chain E residue 793 THR Chi-restraints excluded: chain E residue 802 GLN Chi-restraints excluded: chain E residue 822 ASP Chi-restraints excluded: chain E residue 870 LEU Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 452 MET Chi-restraints excluded: chain F residue 479 GLU Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 489 THR Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 530 VAL Chi-restraints excluded: chain F residue 582 ASP Chi-restraints excluded: chain F residue 625 TYR Chi-restraints excluded: chain F residue 705 THR Chi-restraints excluded: chain F residue 793 THR Chi-restraints excluded: chain F residue 822 ASP Chi-restraints excluded: chain F residue 844 SER Chi-restraints excluded: chain F residue 874 SER Chi-restraints excluded: chain G residue 272 THR Chi-restraints excluded: chain G residue 307 LEU Chi-restraints excluded: chain G residue 308 ILE Chi-restraints excluded: chain G residue 377 THR Chi-restraints excluded: chain G residue 407 THR Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 480 THR Chi-restraints excluded: chain G residue 505 ASP Chi-restraints excluded: chain G residue 542 THR Chi-restraints excluded: chain G residue 569 ILE Chi-restraints excluded: chain G residue 582 ASP Chi-restraints excluded: chain G residue 757 THR Chi-restraints excluded: chain G residue 763 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 120 optimal weight: 2.9990 chunk 322 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 210 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 358 optimal weight: 20.0000 chunk 297 optimal weight: 5.9990 chunk 166 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 118 optimal weight: 7.9990 chunk 188 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 GLN ** B 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 GLN D 368 GLN E 368 GLN E 784 ASN F 368 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 30142 Z= 0.236 Angle : 0.495 9.813 40803 Z= 0.264 Chirality : 0.044 0.203 4543 Planarity : 0.004 0.038 5285 Dihedral : 4.397 21.960 4039 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 4.24 % Allowed : 26.79 % Favored : 68.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.14), residues: 3633 helix: 0.18 (0.22), residues: 553 sheet: -0.68 (0.16), residues: 1057 loop : -0.77 (0.14), residues: 2023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 245 HIS 0.003 0.001 HIS F 314 PHE 0.013 0.001 PHE B 707 TYR 0.012 0.001 TYR B 261 ARG 0.003 0.000 ARG C 668 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 3304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 211 time to evaluate : 3.363 Fit side-chains REVERT: A 373 GLU cc_start: 0.7811 (pt0) cc_final: 0.7412 (pt0) REVERT: A 414 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8281 (tp) REVERT: A 625 TYR cc_start: 0.7888 (OUTLIER) cc_final: 0.5835 (m-80) REVERT: A 822 ASP cc_start: 0.7223 (OUTLIER) cc_final: 0.6916 (m-30) REVERT: B 371 ASN cc_start: 0.7604 (p0) cc_final: 0.7339 (p0) REVERT: B 561 ASP cc_start: 0.7431 (t0) cc_final: 0.7229 (t0) REVERT: C 371 ASN cc_start: 0.7964 (p0) cc_final: 0.7260 (p0) REVERT: C 668 ARG cc_start: 0.8210 (ptm-80) cc_final: 0.7986 (ptm-80) REVERT: D 239 ASP cc_start: 0.7973 (t0) cc_final: 0.7748 (t0) REVERT: E 217 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7512 (tt0) REVERT: E 414 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8276 (tp) REVERT: E 707 PHE cc_start: 0.5776 (OUTLIER) cc_final: 0.4952 (p90) REVERT: F 505 ASP cc_start: 0.8794 (OUTLIER) cc_final: 0.8527 (m-30) REVERT: F 707 PHE cc_start: 0.6235 (OUTLIER) cc_final: 0.4152 (p90) REVERT: G 802 GLN cc_start: 0.7229 (OUTLIER) cc_final: 0.6819 (mt0) outliers start: 140 outliers final: 121 residues processed: 338 average time/residue: 0.3811 time to fit residues: 214.4542 Evaluate side-chains 335 residues out of total 3304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 205 time to evaluate : 3.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 325 ARG Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 625 TYR Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 793 THR Chi-restraints excluded: chain A residue 802 GLN Chi-restraints excluded: chain A residue 822 ASP Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 793 THR Chi-restraints excluded: chain B residue 822 ASP Chi-restraints excluded: chain B residue 833 ASN Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 874 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 793 THR Chi-restraints excluded: chain C residue 822 ASP Chi-restraints excluded: chain C residue 870 LEU Chi-restraints excluded: chain C residue 874 SER Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 371 ASN Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 456 SER Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 582 ASP Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain D residue 757 THR Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 822 ASP Chi-restraints excluded: chain D residue 874 SER Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 310 SER Chi-restraints excluded: chain E residue 377 THR Chi-restraints excluded: chain E residue 381 ILE Chi-restraints excluded: chain E residue 407 THR Chi-restraints excluded: chain E residue 414 LEU Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 578 LEU Chi-restraints excluded: chain E residue 582 ASP Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 707 PHE Chi-restraints excluded: chain E residue 757 THR Chi-restraints excluded: chain E residue 793 THR Chi-restraints excluded: chain E residue 802 GLN Chi-restraints excluded: chain E residue 822 ASP Chi-restraints excluded: chain E residue 870 LEU Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 407 THR Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 452 MET Chi-restraints excluded: chain F residue 479 GLU Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 489 THR Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 505 ASP Chi-restraints excluded: chain F residue 530 VAL Chi-restraints excluded: chain F residue 542 THR Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 582 ASP Chi-restraints excluded: chain F residue 707 PHE Chi-restraints excluded: chain F residue 791 THR Chi-restraints excluded: chain F residue 793 THR Chi-restraints excluded: chain F residue 822 ASP Chi-restraints excluded: chain F residue 844 SER Chi-restraints excluded: chain F residue 874 SER Chi-restraints excluded: chain G residue 263 GLU Chi-restraints excluded: chain G residue 272 THR Chi-restraints excluded: chain G residue 307 LEU Chi-restraints excluded: chain G residue 308 ILE Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 377 THR Chi-restraints excluded: chain G residue 381 ILE Chi-restraints excluded: chain G residue 407 THR Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 480 THR Chi-restraints excluded: chain G residue 505 ASP Chi-restraints excluded: chain G residue 542 THR Chi-restraints excluded: chain G residue 569 ILE Chi-restraints excluded: chain G residue 582 ASP Chi-restraints excluded: chain G residue 757 THR Chi-restraints excluded: chain G residue 763 ASP Chi-restraints excluded: chain G residue 802 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 346 optimal weight: 5.9990 chunk 40 optimal weight: 30.0000 chunk 204 optimal weight: 2.9990 chunk 262 optimal weight: 10.0000 chunk 203 optimal weight: 10.0000 chunk 302 optimal weight: 9.9990 chunk 200 optimal weight: 4.9990 chunk 357 optimal weight: 20.0000 chunk 223 optimal weight: 30.0000 chunk 218 optimal weight: 2.9990 chunk 165 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 GLN ** B 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 GLN D 368 GLN E 368 GLN F 368 GLN F 742 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 30142 Z= 0.348 Angle : 0.548 10.030 40803 Z= 0.292 Chirality : 0.046 0.204 4543 Planarity : 0.004 0.043 5285 Dihedral : 4.641 27.944 4039 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 5.12 % Allowed : 25.94 % Favored : 68.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.14), residues: 3633 helix: 0.04 (0.22), residues: 553 sheet: -0.67 (0.16), residues: 1036 loop : -0.90 (0.14), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 245 HIS 0.004 0.001 HIS F 314 PHE 0.017 0.002 PHE B 707 TYR 0.013 0.001 TYR B 261 ARG 0.003 0.000 ARG C 668 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 196 time to evaluate : 3.441 Fit side-chains REVERT: A 414 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8327 (tp) REVERT: A 625 TYR cc_start: 0.8012 (OUTLIER) cc_final: 0.5900 (m-80) REVERT: A 822 ASP cc_start: 0.7203 (OUTLIER) cc_final: 0.6861 (m-30) REVERT: A 825 MET cc_start: 0.8347 (tpp) cc_final: 0.7944 (mmt) REVERT: B 371 ASN cc_start: 0.7593 (p0) cc_final: 0.7309 (p0) REVERT: B 561 ASP cc_start: 0.7415 (t0) cc_final: 0.7192 (t0) REVERT: C 371 ASN cc_start: 0.8001 (p0) cc_final: 0.7287 (p0) REVERT: D 239 ASP cc_start: 0.7999 (t0) cc_final: 0.7742 (t70) REVERT: D 414 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8290 (tp) REVERT: D 458 ARG cc_start: 0.9157 (OUTLIER) cc_final: 0.8207 (ttt-90) REVERT: E 217 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7546 (tt0) REVERT: E 414 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8327 (tp) REVERT: E 480 THR cc_start: 0.8830 (OUTLIER) cc_final: 0.8587 (t) REVERT: E 707 PHE cc_start: 0.5876 (OUTLIER) cc_final: 0.4887 (p90) REVERT: G 668 ARG cc_start: 0.8312 (ptm-80) cc_final: 0.7950 (ptm-80) REVERT: G 802 GLN cc_start: 0.7251 (OUTLIER) cc_final: 0.6805 (mt0) outliers start: 169 outliers final: 139 residues processed: 352 average time/residue: 0.3791 time to fit residues: 221.5147 Evaluate side-chains 341 residues out of total 3304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 192 time to evaluate : 3.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 325 ARG Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 625 TYR Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 793 THR Chi-restraints excluded: chain A residue 802 GLN Chi-restraints excluded: chain A residue 822 ASP Chi-restraints excluded: chain A residue 833 ASN Chi-restraints excluded: chain A residue 844 SER Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 793 THR Chi-restraints excluded: chain B residue 822 ASP Chi-restraints excluded: chain B residue 833 ASN Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 844 SER Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 874 SER Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 793 THR Chi-restraints excluded: chain C residue 822 ASP Chi-restraints excluded: chain C residue 844 SER Chi-restraints excluded: chain C residue 870 LEU Chi-restraints excluded: chain C residue 874 SER Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 371 ASN Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 456 SER Chi-restraints excluded: chain D residue 458 ARG Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 582 ASP Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain D residue 757 THR Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 822 ASP Chi-restraints excluded: chain D residue 844 SER Chi-restraints excluded: chain D residue 874 SER Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 310 SER Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 377 THR Chi-restraints excluded: chain E residue 381 ILE Chi-restraints excluded: chain E residue 407 THR Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 414 LEU Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain E residue 480 THR Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 578 LEU Chi-restraints excluded: chain E residue 582 ASP Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 707 PHE Chi-restraints excluded: chain E residue 757 THR Chi-restraints excluded: chain E residue 793 THR Chi-restraints excluded: chain E residue 802 GLN Chi-restraints excluded: chain E residue 822 ASP Chi-restraints excluded: chain E residue 844 SER Chi-restraints excluded: chain E residue 870 LEU Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 407 THR Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 452 MET Chi-restraints excluded: chain F residue 479 GLU Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 489 THR Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 530 VAL Chi-restraints excluded: chain F residue 542 THR Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 582 ASP Chi-restraints excluded: chain F residue 625 TYR Chi-restraints excluded: chain F residue 791 THR Chi-restraints excluded: chain F residue 793 THR Chi-restraints excluded: chain F residue 822 ASP Chi-restraints excluded: chain F residue 844 SER Chi-restraints excluded: chain F residue 874 SER Chi-restraints excluded: chain G residue 272 THR Chi-restraints excluded: chain G residue 307 LEU Chi-restraints excluded: chain G residue 308 ILE Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 377 THR Chi-restraints excluded: chain G residue 381 ILE Chi-restraints excluded: chain G residue 407 THR Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 480 THR Chi-restraints excluded: chain G residue 505 ASP Chi-restraints excluded: chain G residue 542 THR Chi-restraints excluded: chain G residue 569 ILE Chi-restraints excluded: chain G residue 582 ASP Chi-restraints excluded: chain G residue 757 THR Chi-restraints excluded: chain G residue 763 ASP Chi-restraints excluded: chain G residue 802 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 221 optimal weight: 4.9990 chunk 142 optimal weight: 10.0000 chunk 213 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 227 optimal weight: 6.9990 chunk 243 optimal weight: 10.0000 chunk 176 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 281 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 GLN ** B 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 GLN D 368 GLN E 368 GLN E 432 ASN F 368 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 30142 Z= 0.263 Angle : 0.511 9.807 40803 Z= 0.273 Chirality : 0.045 0.215 4543 Planarity : 0.004 0.039 5285 Dihedral : 4.514 29.293 4039 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 5.08 % Allowed : 26.00 % Favored : 68.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.14), residues: 3633 helix: 0.13 (0.22), residues: 553 sheet: -0.71 (0.16), residues: 1050 loop : -0.83 (0.14), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 245 HIS 0.003 0.001 HIS F 314 PHE 0.014 0.001 PHE B 707 TYR 0.013 0.001 TYR B 261 ARG 0.005 0.000 ARG B 668 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 3304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 204 time to evaluate : 3.714 Fit side-chains REVERT: A 373 GLU cc_start: 0.7817 (pt0) cc_final: 0.7437 (pt0) REVERT: A 414 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8267 (tp) REVERT: A 625 TYR cc_start: 0.8072 (OUTLIER) cc_final: 0.6134 (m-80) REVERT: A 822 ASP cc_start: 0.7166 (OUTLIER) cc_final: 0.6856 (m-30) REVERT: B 371 ASN cc_start: 0.7549 (p0) cc_final: 0.7284 (p0) REVERT: B 561 ASP cc_start: 0.7474 (t0) cc_final: 0.7259 (t0) REVERT: C 371 ASN cc_start: 0.7992 (p0) cc_final: 0.7255 (p0) REVERT: D 239 ASP cc_start: 0.7970 (t0) cc_final: 0.7705 (t70) REVERT: D 414 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8222 (tp) REVERT: D 458 ARG cc_start: 0.9162 (OUTLIER) cc_final: 0.8140 (ttt-90) REVERT: E 217 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7553 (tt0) REVERT: E 414 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8267 (tp) REVERT: E 480 THR cc_start: 0.8823 (OUTLIER) cc_final: 0.8584 (t) REVERT: E 707 PHE cc_start: 0.5729 (OUTLIER) cc_final: 0.4642 (p90) REVERT: F 707 PHE cc_start: 0.6323 (OUTLIER) cc_final: 0.4291 (p90) REVERT: G 668 ARG cc_start: 0.8346 (ptm-80) cc_final: 0.7998 (ptm-80) outliers start: 168 outliers final: 147 residues processed: 359 average time/residue: 0.3803 time to fit residues: 227.8320 Evaluate side-chains 355 residues out of total 3304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 198 time to evaluate : 3.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 325 ARG Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 625 TYR Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 793 THR Chi-restraints excluded: chain A residue 802 GLN Chi-restraints excluded: chain A residue 822 ASP Chi-restraints excluded: chain A residue 833 ASN Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 793 THR Chi-restraints excluded: chain B residue 822 ASP Chi-restraints excluded: chain B residue 833 ASN Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 874 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 793 THR Chi-restraints excluded: chain C residue 822 ASP Chi-restraints excluded: chain C residue 844 SER Chi-restraints excluded: chain C residue 870 LEU Chi-restraints excluded: chain C residue 874 SER Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 371 ASN Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 456 SER Chi-restraints excluded: chain D residue 458 ARG Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 582 ASP Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain D residue 757 THR Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 822 ASP Chi-restraints excluded: chain D residue 844 SER Chi-restraints excluded: chain D residue 874 SER Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 310 SER Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 371 ASN Chi-restraints excluded: chain E residue 377 THR Chi-restraints excluded: chain E residue 381 ILE Chi-restraints excluded: chain E residue 407 THR Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 414 LEU Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain E residue 480 THR Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 542 THR Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 578 LEU Chi-restraints excluded: chain E residue 582 ASP Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 707 PHE Chi-restraints excluded: chain E residue 757 THR Chi-restraints excluded: chain E residue 793 THR Chi-restraints excluded: chain E residue 802 GLN Chi-restraints excluded: chain E residue 822 ASP Chi-restraints excluded: chain E residue 844 SER Chi-restraints excluded: chain E residue 870 LEU Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 407 THR Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 452 MET Chi-restraints excluded: chain F residue 479 GLU Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 489 THR Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 530 VAL Chi-restraints excluded: chain F residue 542 THR Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 582 ASP Chi-restraints excluded: chain F residue 625 TYR Chi-restraints excluded: chain F residue 707 PHE Chi-restraints excluded: chain F residue 791 THR Chi-restraints excluded: chain F residue 793 THR Chi-restraints excluded: chain F residue 822 ASP Chi-restraints excluded: chain F residue 844 SER Chi-restraints excluded: chain F residue 874 SER Chi-restraints excluded: chain G residue 248 SER Chi-restraints excluded: chain G residue 263 GLU Chi-restraints excluded: chain G residue 272 THR Chi-restraints excluded: chain G residue 307 LEU Chi-restraints excluded: chain G residue 308 ILE Chi-restraints excluded: chain G residue 310 SER Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 377 THR Chi-restraints excluded: chain G residue 381 ILE Chi-restraints excluded: chain G residue 407 THR Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 480 THR Chi-restraints excluded: chain G residue 505 ASP Chi-restraints excluded: chain G residue 542 THR Chi-restraints excluded: chain G residue 569 ILE Chi-restraints excluded: chain G residue 582 ASP Chi-restraints excluded: chain G residue 594 THR Chi-restraints excluded: chain G residue 757 THR Chi-restraints excluded: chain G residue 763 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 325 optimal weight: 0.0670 chunk 342 optimal weight: 10.0000 chunk 312 optimal weight: 7.9990 chunk 333 optimal weight: 1.9990 chunk 200 optimal weight: 9.9990 chunk 145 optimal weight: 20.0000 chunk 261 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 chunk 301 optimal weight: 6.9990 chunk 315 optimal weight: 4.9990 chunk 332 optimal weight: 1.9990 overall best weight: 1.7524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 GLN ** B 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 GLN D 368 GLN E 368 GLN E 432 ASN F 368 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30142 Z= 0.170 Angle : 0.472 9.445 40803 Z= 0.252 Chirality : 0.043 0.221 4543 Planarity : 0.003 0.039 5285 Dihedral : 4.223 27.986 4039 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 4.21 % Allowed : 26.82 % Favored : 68.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.14), residues: 3633 helix: 0.29 (0.22), residues: 560 sheet: -0.61 (0.16), residues: 1057 loop : -0.75 (0.14), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 375 HIS 0.002 0.001 HIS F 314 PHE 0.009 0.001 PHE B 707 TYR 0.011 0.001 TYR B 261 ARG 0.006 0.000 ARG E 668 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 3304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 215 time to evaluate : 3.456 Fit side-chains REVERT: A 625 TYR cc_start: 0.8041 (OUTLIER) cc_final: 0.6065 (m-80) REVERT: A 822 ASP cc_start: 0.7141 (OUTLIER) cc_final: 0.6845 (m-30) REVERT: A 825 MET cc_start: 0.8229 (tpp) cc_final: 0.7930 (mmt) REVERT: B 371 ASN cc_start: 0.7496 (p0) cc_final: 0.7267 (p0) REVERT: B 561 ASP cc_start: 0.7372 (t0) cc_final: 0.7171 (t0) REVERT: C 319 GLN cc_start: 0.7798 (pt0) cc_final: 0.7437 (tt0) REVERT: C 371 ASN cc_start: 0.8008 (p0) cc_final: 0.7293 (p0) REVERT: D 239 ASP cc_start: 0.7960 (t0) cc_final: 0.7726 (t0) REVERT: D 414 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8200 (tp) REVERT: D 458 ARG cc_start: 0.9151 (OUTLIER) cc_final: 0.8130 (ttt-90) REVERT: E 217 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7540 (tt0) REVERT: E 414 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8196 (tp) REVERT: E 480 THR cc_start: 0.8813 (OUTLIER) cc_final: 0.8578 (t) REVERT: G 668 ARG cc_start: 0.8346 (ptm-80) cc_final: 0.8021 (ptm-80) outliers start: 139 outliers final: 120 residues processed: 339 average time/residue: 0.3927 time to fit residues: 221.4227 Evaluate side-chains 333 residues out of total 3304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 206 time to evaluate : 3.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 325 ARG Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 625 TYR Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 793 THR Chi-restraints excluded: chain A residue 802 GLN Chi-restraints excluded: chain A residue 822 ASP Chi-restraints excluded: chain A residue 833 ASN Chi-restraints excluded: chain A residue 844 SER Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 833 ASN Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 844 SER Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 874 SER Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 793 THR Chi-restraints excluded: chain C residue 822 ASP Chi-restraints excluded: chain C residue 844 SER Chi-restraints excluded: chain C residue 870 LEU Chi-restraints excluded: chain C residue 874 SER Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 456 SER Chi-restraints excluded: chain D residue 458 ARG Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 757 THR Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 822 ASP Chi-restraints excluded: chain D residue 874 SER Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 377 THR Chi-restraints excluded: chain E residue 381 ILE Chi-restraints excluded: chain E residue 414 LEU Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain E residue 480 THR Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 757 THR Chi-restraints excluded: chain E residue 793 THR Chi-restraints excluded: chain E residue 802 GLN Chi-restraints excluded: chain E residue 822 ASP Chi-restraints excluded: chain E residue 844 SER Chi-restraints excluded: chain E residue 870 LEU Chi-restraints excluded: chain F residue 263 GLU Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 407 THR Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 452 MET Chi-restraints excluded: chain F residue 479 GLU Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 489 THR Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 530 VAL Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 625 TYR Chi-restraints excluded: chain F residue 793 THR Chi-restraints excluded: chain F residue 822 ASP Chi-restraints excluded: chain F residue 844 SER Chi-restraints excluded: chain F residue 870 LEU Chi-restraints excluded: chain F residue 874 SER Chi-restraints excluded: chain G residue 263 GLU Chi-restraints excluded: chain G residue 272 THR Chi-restraints excluded: chain G residue 307 LEU Chi-restraints excluded: chain G residue 308 ILE Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 377 THR Chi-restraints excluded: chain G residue 381 ILE Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 480 THR Chi-restraints excluded: chain G residue 505 ASP Chi-restraints excluded: chain G residue 542 THR Chi-restraints excluded: chain G residue 569 ILE Chi-restraints excluded: chain G residue 582 ASP Chi-restraints excluded: chain G residue 757 THR Chi-restraints excluded: chain G residue 763 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 218 optimal weight: 1.9990 chunk 352 optimal weight: 9.9990 chunk 215 optimal weight: 0.0270 chunk 167 optimal weight: 9.9990 chunk 244 optimal weight: 0.7980 chunk 369 optimal weight: 5.9990 chunk 340 optimal weight: 0.9980 chunk 294 optimal weight: 0.0870 chunk 30 optimal weight: 10.0000 chunk 227 optimal weight: 0.9990 chunk 180 optimal weight: 6.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 GLN ** B 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 GLN D 368 GLN E 368 GLN F 368 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 30142 Z= 0.123 Angle : 0.446 9.004 40803 Z= 0.236 Chirality : 0.042 0.236 4543 Planarity : 0.003 0.039 5285 Dihedral : 3.804 27.919 4039 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.91 % Allowed : 28.15 % Favored : 68.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.14), residues: 3633 helix: 0.55 (0.22), residues: 560 sheet: -0.35 (0.16), residues: 1050 loop : -0.63 (0.14), residues: 2023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 375 HIS 0.002 0.000 HIS F 314 PHE 0.007 0.001 PHE D 487 TYR 0.008 0.001 TYR C 261 ARG 0.006 0.000 ARG E 668 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 242 time to evaluate : 3.628 Fit side-chains REVERT: A 625 TYR cc_start: 0.7908 (OUTLIER) cc_final: 0.5966 (m-80) REVERT: A 825 MET cc_start: 0.8078 (tpp) cc_final: 0.7797 (mmt) REVERT: B 371 ASN cc_start: 0.7431 (p0) cc_final: 0.7148 (p0) REVERT: B 762 MET cc_start: 0.7999 (mmm) cc_final: 0.7726 (mmt) REVERT: C 371 ASN cc_start: 0.8003 (p0) cc_final: 0.7306 (p0) REVERT: C 668 ARG cc_start: 0.8185 (ptm-80) cc_final: 0.7927 (ptm-80) REVERT: D 458 ARG cc_start: 0.9142 (OUTLIER) cc_final: 0.8771 (ttt90) REVERT: E 217 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7552 (tt0) REVERT: E 414 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8155 (tp) REVERT: E 480 THR cc_start: 0.8790 (OUTLIER) cc_final: 0.8555 (t) REVERT: F 371 ASN cc_start: 0.8449 (p0) cc_final: 0.7873 (p0) REVERT: G 228 ASP cc_start: 0.6591 (p0) cc_final: 0.6280 (p0) REVERT: G 668 ARG cc_start: 0.8314 (ptm-80) cc_final: 0.8007 (ptm-80) outliers start: 96 outliers final: 73 residues processed: 328 average time/residue: 0.4094 time to fit residues: 219.9950 Evaluate side-chains 301 residues out of total 3304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 223 time to evaluate : 3.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 625 TYR Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 793 THR Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 844 SER Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 874 SER Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 793 THR Chi-restraints excluded: chain C residue 822 ASP Chi-restraints excluded: chain C residue 874 SER Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 456 SER Chi-restraints excluded: chain D residue 458 ARG Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 757 THR Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 822 ASP Chi-restraints excluded: chain D residue 874 SER Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 377 THR Chi-restraints excluded: chain E residue 381 ILE Chi-restraints excluded: chain E residue 414 LEU Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain E residue 480 THR Chi-restraints excluded: chain E residue 498 THR Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 757 THR Chi-restraints excluded: chain E residue 822 ASP Chi-restraints excluded: chain E residue 844 SER Chi-restraints excluded: chain E residue 870 LEU Chi-restraints excluded: chain F residue 263 GLU Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 452 MET Chi-restraints excluded: chain F residue 479 GLU Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 489 THR Chi-restraints excluded: chain F residue 530 VAL Chi-restraints excluded: chain F residue 625 TYR Chi-restraints excluded: chain F residue 793 THR Chi-restraints excluded: chain F residue 874 SER Chi-restraints excluded: chain G residue 263 GLU Chi-restraints excluded: chain G residue 307 LEU Chi-restraints excluded: chain G residue 308 ILE Chi-restraints excluded: chain G residue 377 THR Chi-restraints excluded: chain G residue 381 ILE Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 480 THR Chi-restraints excluded: chain G residue 505 ASP Chi-restraints excluded: chain G residue 542 THR Chi-restraints excluded: chain G residue 569 ILE Chi-restraints excluded: chain G residue 757 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 233 optimal weight: 0.7980 chunk 313 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 chunk 271 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 294 optimal weight: 0.8980 chunk 123 optimal weight: 7.9990 chunk 302 optimal weight: 5.9990 chunk 37 optimal weight: 0.3980 chunk 54 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 GLN ** B 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 GLN D 368 GLN E 368 GLN F 368 GLN G 368 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.138305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.112076 restraints weight = 39478.520| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.51 r_work: 0.3364 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 30142 Z= 0.124 Angle : 0.452 8.361 40803 Z= 0.239 Chirality : 0.042 0.242 4543 Planarity : 0.003 0.040 5285 Dihedral : 3.669 27.865 4039 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.54 % Allowed : 28.72 % Favored : 68.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.14), residues: 3633 helix: 0.74 (0.22), residues: 560 sheet: -0.19 (0.16), residues: 1050 loop : -0.52 (0.14), residues: 2023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 375 HIS 0.002 0.000 HIS G 314 PHE 0.008 0.001 PHE A 711 TYR 0.008 0.001 TYR C 526 ARG 0.005 0.000 ARG E 668 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5528.74 seconds wall clock time: 103 minutes 15.10 seconds (6195.10 seconds total)