Starting phenix.real_space_refine on Fri Mar 22 04:47:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uft_26480/03_2024/7uft_26480.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uft_26480/03_2024/7uft_26480.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uft_26480/03_2024/7uft_26480.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uft_26480/03_2024/7uft_26480.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uft_26480/03_2024/7uft_26480.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uft_26480/03_2024/7uft_26480.pdb" } resolution = 2.9 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= 0.003 sd= 1.032 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 Zn 4 6.06 5 S 176 5.16 5 C 20384 2.51 5 N 5592 2.21 5 O 6168 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 205": "OD1" <-> "OD2" Residue "A ASP 218": "OD1" <-> "OD2" Residue "A ASP 251": "OD1" <-> "OD2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A PHE 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 616": "OD1" <-> "OD2" Residue "A ASP 691": "OD1" <-> "OD2" Residue "A ASP 721": "OD1" <-> "OD2" Residue "A ASP 768": "OD1" <-> "OD2" Residue "A ASP 785": "OD1" <-> "OD2" Residue "A ASP 873": "OD1" <-> "OD2" Residue "A ASP 949": "OD1" <-> "OD2" Residue "A GLU 995": "OE1" <-> "OE2" Residue "A GLU 1015": "OE1" <-> "OE2" Residue "B PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 205": "OD1" <-> "OD2" Residue "B ASP 218": "OD1" <-> "OD2" Residue "B ASP 251": "OD1" <-> "OD2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 554": "OE1" <-> "OE2" Residue "B PHE 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 616": "OD1" <-> "OD2" Residue "B ASP 691": "OD1" <-> "OD2" Residue "B ASP 721": "OD1" <-> "OD2" Residue "B ASP 768": "OD1" <-> "OD2" Residue "B ASP 785": "OD1" <-> "OD2" Residue "B ASP 873": "OD1" <-> "OD2" Residue "B ASP 949": "OD1" <-> "OD2" Residue "B GLU 995": "OE1" <-> "OE2" Residue "B GLU 1015": "OE1" <-> "OE2" Residue "C PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 205": "OD1" <-> "OD2" Residue "C ASP 218": "OD1" <-> "OD2" Residue "C ASP 251": "OD1" <-> "OD2" Residue "C PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 554": "OE1" <-> "OE2" Residue "C PHE 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 616": "OD1" <-> "OD2" Residue "C ASP 691": "OD1" <-> "OD2" Residue "C ASP 721": "OD1" <-> "OD2" Residue "C ASP 768": "OD1" <-> "OD2" Residue "C ASP 785": "OD1" <-> "OD2" Residue "C ASP 873": "OD1" <-> "OD2" Residue "C ASP 949": "OD1" <-> "OD2" Residue "C GLU 995": "OE1" <-> "OE2" Residue "C GLU 1015": "OE1" <-> "OE2" Residue "D PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 205": "OD1" <-> "OD2" Residue "D ASP 218": "OD1" <-> "OD2" Residue "D ASP 251": "OD1" <-> "OD2" Residue "D PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 554": "OE1" <-> "OE2" Residue "D PHE 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 616": "OD1" <-> "OD2" Residue "D ASP 691": "OD1" <-> "OD2" Residue "D ASP 721": "OD1" <-> "OD2" Residue "D ASP 768": "OD1" <-> "OD2" Residue "D ASP 785": "OD1" <-> "OD2" Residue "D ASP 873": "OD1" <-> "OD2" Residue "D ASP 949": "OD1" <-> "OD2" Residue "D GLU 995": "OE1" <-> "OE2" Residue "D GLU 1015": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 32324 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8080 Classifications: {'peptide': 1032} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 56, 'TRANS': 975} Chain: "B" Number of atoms: 8080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8080 Classifications: {'peptide': 1032} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 56, 'TRANS': 975} Chain: "C" Number of atoms: 8080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8080 Classifications: {'peptide': 1032} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 56, 'TRANS': 975} Chain: "D" Number of atoms: 8080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8080 Classifications: {'peptide': 1032} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 56, 'TRANS': 975} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 16.59, per 1000 atoms: 0.51 Number of scatterers: 32324 At special positions: 0 Unit cell: (97.15, 144.05, 169.51, 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) Zn 4 29.99 S 176 16.00 O 6168 8.00 N 5592 7.00 C 20384 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: 11.57 Conformation dependent library (CDL) restraints added in 6.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 272 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 594 " pdb=" ZN B1101 " pdb="ZN ZN B1101 " - pdb=" NE2 HIS B 272 " pdb="ZN ZN B1101 " - pdb=" NE2 HIS B 594 " pdb=" ZN C1101 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 272 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 594 " pdb=" ZN D1101 " pdb="ZN ZN D1101 " - pdb=" NE2 HIS D 272 " pdb="ZN ZN D1101 " - pdb=" NE2 HIS D 594 " 8240 Ramachandran restraints generated. 4120 Oldfield, 0 Emsley, 4120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7640 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 48 sheets defined 29.1% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.60 Creating SS restraints... Processing helix chain 'A' and resid 3 through 20 removed outlier: 3.552A pdb=" N ASP A 10 " --> pdb=" O ASN A 6 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG A 11 " --> pdb=" O ARG A 7 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL A 20 " --> pdb=" O MET A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 23 No H-bonds generated for 'chain 'A' and resid 21 through 23' Processing helix chain 'A' and resid 44 through 54 removed outlier: 3.574A pdb=" N THR A 50 " --> pdb=" O ALA A 46 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG A 51 " --> pdb=" O ALA A 47 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N SER A 54 " --> pdb=" O THR A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 211 removed outlier: 3.563A pdb=" N SER A 210 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU A 211 " --> pdb=" O VAL A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 233 removed outlier: 4.203A pdb=" N TRP A 222 " --> pdb=" O ASP A 218 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA A 227 " --> pdb=" O LYS A 223 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN A 229 " --> pdb=" O ALA A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 250 removed outlier: 4.078A pdb=" N LEU A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA A 249 " --> pdb=" O LEU A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 297 removed outlier: 3.839A pdb=" N THR A 284 " --> pdb=" O PRO A 280 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLU A 285 " --> pdb=" O VAL A 281 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ARG A 286 " --> pdb=" O ARG A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 322 removed outlier: 3.561A pdb=" N PHE A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 336 removed outlier: 3.672A pdb=" N GLU A 327 " --> pdb=" O PRO A 323 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG A 328 " --> pdb=" O ASP A 324 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL A 329 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU A 335 " --> pdb=" O ALA A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 372 Processing helix chain 'A' and resid 391 through 399 Processing helix chain 'A' and resid 407 through 412 removed outlier: 3.980A pdb=" N ASN A 412 " --> pdb=" O LEU A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 458 Processing helix chain 'A' and resid 481 through 487 removed outlier: 3.676A pdb=" N THR A 485 " --> pdb=" O ILE A 481 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET A 486 " --> pdb=" O ARG A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 521 Processing helix chain 'A' and resid 536 through 541 removed outlier: 3.593A pdb=" N THR A 539 " --> pdb=" O HIS A 536 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 540 " --> pdb=" O ARG A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 571 removed outlier: 3.536A pdb=" N LYS A 547 " --> pdb=" O GLN A 543 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG A 558 " --> pdb=" O GLU A 554 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N THR A 559 " --> pdb=" O SER A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 591 removed outlier: 3.504A pdb=" N SER A 591 " --> pdb=" O THR A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 635 removed outlier: 3.587A pdb=" N HIS A 606 " --> pdb=" O ILE A 602 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASP A 622 " --> pdb=" O LYS A 618 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE A 623 " --> pdb=" O ALA A 619 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ARG A 625 " --> pdb=" O SER A 621 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA A 630 " --> pdb=" O ASP A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 739 removed outlier: 3.558A pdb=" N CYS A 738 " --> pdb=" O ASP A 734 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA A 739 " --> pdb=" O ALA A 735 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 734 through 739' Processing helix chain 'A' and resid 831 through 836 removed outlier: 3.963A pdb=" N PHE A 836 " --> pdb=" O GLU A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 924 Processing helix chain 'B' and resid 4 through 20 removed outlier: 3.551A pdb=" N ASP B 10 " --> pdb=" O ASN B 6 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG B 11 " --> pdb=" O ARG B 7 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL B 20 " --> pdb=" O MET B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 23 No H-bonds generated for 'chain 'B' and resid 21 through 23' Processing helix chain 'B' and resid 44 through 54 removed outlier: 3.574A pdb=" N THR B 50 " --> pdb=" O ALA B 46 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG B 51 " --> pdb=" O ALA B 47 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N SER B 54 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 211 removed outlier: 3.564A pdb=" N SER B 210 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU B 211 " --> pdb=" O VAL B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 233 removed outlier: 4.204A pdb=" N TRP B 222 " --> pdb=" O ASP B 218 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA B 227 " --> pdb=" O LYS B 223 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN B 229 " --> pdb=" O ALA B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 250 removed outlier: 4.078A pdb=" N LEU B 245 " --> pdb=" O ASN B 241 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA B 249 " --> pdb=" O LEU B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 297 removed outlier: 3.838A pdb=" N THR B 284 " --> pdb=" O PRO B 280 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLU B 285 " --> pdb=" O VAL B 281 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ARG B 286 " --> pdb=" O ARG B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 322 removed outlier: 3.560A pdb=" N PHE B 315 " --> pdb=" O ALA B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 336 removed outlier: 3.673A pdb=" N GLU B 327 " --> pdb=" O PRO B 323 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG B 328 " --> pdb=" O ASP B 324 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL B 329 " --> pdb=" O LEU B 325 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU B 335 " --> pdb=" O ALA B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 372 Processing helix chain 'B' and resid 391 through 399 Processing helix chain 'B' and resid 407 through 412 removed outlier: 3.980A pdb=" N ASN B 412 " --> pdb=" O LEU B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 458 Processing helix chain 'B' and resid 481 through 487 removed outlier: 3.677A pdb=" N THR B 485 " --> pdb=" O ILE B 481 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET B 486 " --> pdb=" O ARG B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 521 Processing helix chain 'B' and resid 536 through 541 removed outlier: 3.592A pdb=" N THR B 539 " --> pdb=" O HIS B 536 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU B 540 " --> pdb=" O ARG B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 571 removed outlier: 3.535A pdb=" N LYS B 547 " --> pdb=" O GLN B 543 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG B 558 " --> pdb=" O GLU B 554 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N THR B 559 " --> pdb=" O SER B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 591 removed outlier: 3.503A pdb=" N SER B 591 " --> pdb=" O THR B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 635 removed outlier: 3.588A pdb=" N HIS B 606 " --> pdb=" O ILE B 602 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP B 622 " --> pdb=" O LYS B 618 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE B 623 " --> pdb=" O ALA B 619 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N ARG B 625 " --> pdb=" O SER B 621 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA B 630 " --> pdb=" O ASP B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 739 removed outlier: 3.559A pdb=" N CYS B 738 " --> pdb=" O ASP B 734 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA B 739 " --> pdb=" O ALA B 735 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 734 through 739' Processing helix chain 'B' and resid 831 through 836 removed outlier: 3.964A pdb=" N PHE B 836 " --> pdb=" O GLU B 833 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 924 Processing helix chain 'C' and resid 4 through 20 removed outlier: 3.551A pdb=" N ASP C 10 " --> pdb=" O ASN C 6 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG C 11 " --> pdb=" O ARG C 7 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL C 20 " --> pdb=" O MET C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 23 No H-bonds generated for 'chain 'C' and resid 21 through 23' Processing helix chain 'C' and resid 44 through 54 removed outlier: 3.573A pdb=" N THR C 50 " --> pdb=" O ALA C 46 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG C 51 " --> pdb=" O ALA C 47 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N SER C 54 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 211 removed outlier: 3.564A pdb=" N SER C 210 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU C 211 " --> pdb=" O VAL C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 233 removed outlier: 4.204A pdb=" N TRP C 222 " --> pdb=" O ASP C 218 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA C 227 " --> pdb=" O LYS C 223 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN C 229 " --> pdb=" O ALA C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 250 removed outlier: 4.078A pdb=" N LEU C 245 " --> pdb=" O ASN C 241 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA C 249 " --> pdb=" O LEU C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 297 removed outlier: 3.839A pdb=" N THR C 284 " --> pdb=" O PRO C 280 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLU C 285 " --> pdb=" O VAL C 281 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ARG C 286 " --> pdb=" O ARG C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 322 removed outlier: 3.561A pdb=" N PHE C 315 " --> pdb=" O ALA C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 336 removed outlier: 3.672A pdb=" N GLU C 327 " --> pdb=" O PRO C 323 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG C 328 " --> pdb=" O ASP C 324 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU C 335 " --> pdb=" O ALA C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 372 Processing helix chain 'C' and resid 391 through 399 Processing helix chain 'C' and resid 407 through 412 removed outlier: 3.981A pdb=" N ASN C 412 " --> pdb=" O LEU C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 458 Processing helix chain 'C' and resid 481 through 487 removed outlier: 3.676A pdb=" N THR C 485 " --> pdb=" O ILE C 481 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET C 486 " --> pdb=" O ARG C 482 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 521 Processing helix chain 'C' and resid 536 through 541 removed outlier: 3.592A pdb=" N THR C 539 " --> pdb=" O HIS C 536 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU C 540 " --> pdb=" O ARG C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 571 removed outlier: 3.535A pdb=" N LYS C 547 " --> pdb=" O GLN C 543 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG C 558 " --> pdb=" O GLU C 554 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N THR C 559 " --> pdb=" O SER C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 591 removed outlier: 3.503A pdb=" N SER C 591 " --> pdb=" O THR C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 602 through 635 removed outlier: 3.587A pdb=" N HIS C 606 " --> pdb=" O ILE C 602 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASP C 622 " --> pdb=" O LYS C 618 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE C 623 " --> pdb=" O ALA C 619 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ARG C 625 " --> pdb=" O SER C 621 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA C 630 " --> pdb=" O ASP C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 739 removed outlier: 3.558A pdb=" N CYS C 738 " --> pdb=" O ASP C 734 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA C 739 " --> pdb=" O ALA C 735 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 734 through 739' Processing helix chain 'C' and resid 831 through 836 removed outlier: 3.964A pdb=" N PHE C 836 " --> pdb=" O GLU C 833 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 924 Processing helix chain 'D' and resid 4 through 20 removed outlier: 3.552A pdb=" N ASP D 10 " --> pdb=" O ASN D 6 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG D 11 " --> pdb=" O ARG D 7 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL D 20 " --> pdb=" O MET D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 23 No H-bonds generated for 'chain 'D' and resid 21 through 23' Processing helix chain 'D' and resid 44 through 54 removed outlier: 3.573A pdb=" N THR D 50 " --> pdb=" O ALA D 46 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG D 51 " --> pdb=" O ALA D 47 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER D 54 " --> pdb=" O THR D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 211 removed outlier: 3.565A pdb=" N SER D 210 " --> pdb=" O VAL D 206 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU D 211 " --> pdb=" O VAL D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 233 removed outlier: 4.204A pdb=" N TRP D 222 " --> pdb=" O ASP D 218 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA D 227 " --> pdb=" O LYS D 223 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN D 229 " --> pdb=" O ALA D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 250 removed outlier: 4.077A pdb=" N LEU D 245 " --> pdb=" O ASN D 241 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS D 248 " --> pdb=" O ALA D 244 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA D 249 " --> pdb=" O LEU D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 297 removed outlier: 3.839A pdb=" N THR D 284 " --> pdb=" O PRO D 280 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLU D 285 " --> pdb=" O VAL D 281 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ARG D 286 " --> pdb=" O ARG D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 322 removed outlier: 3.560A pdb=" N PHE D 315 " --> pdb=" O ALA D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 336 removed outlier: 3.672A pdb=" N GLU D 327 " --> pdb=" O PRO D 323 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG D 328 " --> pdb=" O ASP D 324 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL D 329 " --> pdb=" O LEU D 325 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU D 335 " --> pdb=" O ALA D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 372 Processing helix chain 'D' and resid 391 through 399 Processing helix chain 'D' and resid 407 through 412 removed outlier: 3.980A pdb=" N ASN D 412 " --> pdb=" O LEU D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 458 Processing helix chain 'D' and resid 481 through 487 removed outlier: 3.676A pdb=" N THR D 485 " --> pdb=" O ILE D 481 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET D 486 " --> pdb=" O ARG D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 521 Processing helix chain 'D' and resid 536 through 541 removed outlier: 3.592A pdb=" N THR D 539 " --> pdb=" O HIS D 536 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU D 540 " --> pdb=" O ARG D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 571 removed outlier: 3.535A pdb=" N LYS D 547 " --> pdb=" O GLN D 543 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG D 558 " --> pdb=" O GLU D 554 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N THR D 559 " --> pdb=" O SER D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 591 removed outlier: 3.504A pdb=" N SER D 591 " --> pdb=" O THR D 587 " (cutoff:3.500A) Processing helix chain 'D' and resid 602 through 635 removed outlier: 3.589A pdb=" N HIS D 606 " --> pdb=" O ILE D 602 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP D 622 " --> pdb=" O LYS D 618 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE D 623 " --> pdb=" O ALA D 619 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ARG D 625 " --> pdb=" O SER D 621 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA D 630 " --> pdb=" O ASP D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 734 through 739 removed outlier: 3.559A pdb=" N CYS D 738 " --> pdb=" O ASP D 734 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA D 739 " --> pdb=" O ALA D 735 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 734 through 739' Processing helix chain 'D' and resid 831 through 836 removed outlier: 3.963A pdb=" N PHE D 836 " --> pdb=" O GLU D 833 " (cutoff:3.500A) Processing helix chain 'D' and resid 912 through 924 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 30 removed outlier: 6.963A pdb=" N ILE A 190 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA A 92 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LEU A 95 " --> pdb=" O PRO A 133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 38 removed outlier: 3.656A pdb=" N GLY A 81 " --> pdb=" O PHE A 151 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N PHE A 151 " --> pdb=" O GLY A 81 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ALA A 112 " --> pdb=" O ALA A 124 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N ALA A 124 " --> pdb=" O ALA A 112 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ALA A 114 " --> pdb=" O ILE A 122 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 467 through 471 removed outlier: 6.341A pdb=" N THR A 264 " --> pdb=" O GLY A 467 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N LEU A 469 " --> pdb=" O THR A 264 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N THR A 266 " --> pdb=" O LEU A 469 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N PHE A 471 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N MET A 268 " --> pdb=" O PHE A 471 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 307 through 309 removed outlier: 6.453A pdb=" N TYR A 307 " --> pdb=" O ILE A 339 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 379 through 381 removed outlier: 6.682A pdb=" N ILE A 380 " --> pdb=" O LEU A 405 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 644 through 646 removed outlier: 3.662A pdb=" N ALA A 658 " --> pdb=" O ARG A 645 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 668 through 669 removed outlier: 3.763A pdb=" N SER A 696 " --> pdb=" O HIS A 687 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG A 704 " --> pdb=" O ASP A 699 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 740 through 741 removed outlier: 3.632A pdb=" N THR A 740 " --> pdb=" O ILE A 718 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LYS A 797 " --> pdb=" O ALA A 886 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ALA A 886 " --> pdb=" O LYS A 797 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU A 799 " --> pdb=" O LEU A 884 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N GLY A 862 " --> pdb=" O SER A 883 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 746 through 752 removed outlier: 3.749A pdb=" N HIS A 746 " --> pdb=" O LYS A 763 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL A 761 " --> pdb=" O VAL A 748 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ILE A 750 " --> pdb=" O VAL A 759 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL A 759 " --> pdb=" O ILE A 750 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP A 769 " --> pdb=" O TYR A 766 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N PHE A 843 " --> pdb=" O GLU A 815 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU A 815 " --> pdb=" O PHE A 843 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N HIS A 847 " --> pdb=" O ARG A 811 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ARG A 811 " --> pdb=" O HIS A 847 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 937 through 943 removed outlier: 3.615A pdb=" N MET A 976 " --> pdb=" O GLU A 940 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LYS A 974 " --> pdb=" O ILE A 942 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 946 through 948 Processing sheet with id=AB3, first strand: chain 'A' and resid 946 through 948 Processing sheet with id=AB4, first strand: chain 'B' and resid 25 through 30 removed outlier: 6.963A pdb=" N ILE B 190 " --> pdb=" O LEU B 28 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA B 92 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LEU B 95 " --> pdb=" O PRO B 133 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 32 through 38 removed outlier: 3.656A pdb=" N GLY B 81 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N PHE B 151 " --> pdb=" O GLY B 81 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ALA B 112 " --> pdb=" O ALA B 124 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N ALA B 124 " --> pdb=" O ALA B 112 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ALA B 114 " --> pdb=" O ILE B 122 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 467 through 471 removed outlier: 6.341A pdb=" N THR B 264 " --> pdb=" O GLY B 467 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N LEU B 469 " --> pdb=" O THR B 264 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N THR B 266 " --> pdb=" O LEU B 469 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N PHE B 471 " --> pdb=" O THR B 266 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N MET B 268 " --> pdb=" O PHE B 471 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 307 through 309 removed outlier: 6.452A pdb=" N TYR B 307 " --> pdb=" O ILE B 339 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 379 through 381 removed outlier: 6.681A pdb=" N ILE B 380 " --> pdb=" O LEU B 405 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 644 through 646 removed outlier: 3.661A pdb=" N ALA B 658 " --> pdb=" O ARG B 645 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 668 through 669 removed outlier: 3.762A pdb=" N SER B 696 " --> pdb=" O HIS B 687 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG B 704 " --> pdb=" O ASP B 699 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 740 through 741 removed outlier: 3.631A pdb=" N THR B 740 " --> pdb=" O ILE B 718 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LYS B 797 " --> pdb=" O ALA B 886 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N ALA B 886 " --> pdb=" O LYS B 797 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU B 799 " --> pdb=" O LEU B 884 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N GLY B 862 " --> pdb=" O SER B 883 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 746 through 752 removed outlier: 3.749A pdb=" N HIS B 746 " --> pdb=" O LYS B 763 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL B 761 " --> pdb=" O VAL B 748 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ILE B 750 " --> pdb=" O VAL B 759 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL B 759 " --> pdb=" O ILE B 750 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP B 769 " --> pdb=" O TYR B 766 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N PHE B 843 " --> pdb=" O GLU B 815 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU B 815 " --> pdb=" O PHE B 843 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N HIS B 847 " --> pdb=" O ARG B 811 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ARG B 811 " --> pdb=" O HIS B 847 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 937 through 943 removed outlier: 3.615A pdb=" N MET B 976 " --> pdb=" O GLU B 940 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LYS B 974 " --> pdb=" O ILE B 942 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 946 through 948 Processing sheet with id=AC6, first strand: chain 'B' and resid 946 through 948 Processing sheet with id=AC7, first strand: chain 'C' and resid 25 through 30 removed outlier: 6.963A pdb=" N ILE C 190 " --> pdb=" O LEU C 28 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA C 92 " --> pdb=" O LEU C 193 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LEU C 95 " --> pdb=" O PRO C 133 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 32 through 38 removed outlier: 3.656A pdb=" N GLY C 81 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N PHE C 151 " --> pdb=" O GLY C 81 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ALA C 112 " --> pdb=" O ALA C 124 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N ALA C 124 " --> pdb=" O ALA C 112 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ALA C 114 " --> pdb=" O ILE C 122 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 467 through 471 removed outlier: 6.340A pdb=" N THR C 264 " --> pdb=" O GLY C 467 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N LEU C 469 " --> pdb=" O THR C 264 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N THR C 266 " --> pdb=" O LEU C 469 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N PHE C 471 " --> pdb=" O THR C 266 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N MET C 268 " --> pdb=" O PHE C 471 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 307 through 309 removed outlier: 6.452A pdb=" N TYR C 307 " --> pdb=" O ILE C 339 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 379 through 381 removed outlier: 6.681A pdb=" N ILE C 380 " --> pdb=" O LEU C 405 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 644 through 646 removed outlier: 3.661A pdb=" N ALA C 658 " --> pdb=" O ARG C 645 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 668 through 669 removed outlier: 3.762A pdb=" N SER C 696 " --> pdb=" O HIS C 687 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG C 704 " --> pdb=" O ASP C 699 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 740 through 741 removed outlier: 3.631A pdb=" N THR C 740 " --> pdb=" O ILE C 718 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N LYS C 797 " --> pdb=" O ALA C 886 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ALA C 886 " --> pdb=" O LYS C 797 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU C 799 " --> pdb=" O LEU C 884 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N GLY C 862 " --> pdb=" O SER C 883 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 746 through 752 removed outlier: 3.750A pdb=" N HIS C 746 " --> pdb=" O LYS C 763 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL C 761 " --> pdb=" O VAL C 748 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ILE C 750 " --> pdb=" O VAL C 759 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL C 759 " --> pdb=" O ILE C 750 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP C 769 " --> pdb=" O TYR C 766 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N PHE C 843 " --> pdb=" O GLU C 815 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLU C 815 " --> pdb=" O PHE C 843 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N HIS C 847 " --> pdb=" O ARG C 811 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ARG C 811 " --> pdb=" O HIS C 847 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 937 through 943 removed outlier: 3.616A pdb=" N MET C 976 " --> pdb=" O GLU C 940 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LYS C 974 " --> pdb=" O ILE C 942 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 946 through 948 Processing sheet with id=AD9, first strand: chain 'C' and resid 946 through 948 Processing sheet with id=AE1, first strand: chain 'D' and resid 25 through 30 removed outlier: 6.964A pdb=" N ILE D 190 " --> pdb=" O LEU D 28 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA D 92 " --> pdb=" O LEU D 193 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LEU D 95 " --> pdb=" O PRO D 133 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 32 through 38 removed outlier: 3.656A pdb=" N GLY D 81 " --> pdb=" O PHE D 151 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE D 151 " --> pdb=" O GLY D 81 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ALA D 112 " --> pdb=" O ALA D 124 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N ALA D 124 " --> pdb=" O ALA D 112 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ALA D 114 " --> pdb=" O ILE D 122 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 467 through 471 removed outlier: 6.341A pdb=" N THR D 264 " --> pdb=" O GLY D 467 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N LEU D 469 " --> pdb=" O THR D 264 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N THR D 266 " --> pdb=" O LEU D 469 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N PHE D 471 " --> pdb=" O THR D 266 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N MET D 268 " --> pdb=" O PHE D 471 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 307 through 309 removed outlier: 6.452A pdb=" N TYR D 307 " --> pdb=" O ILE D 339 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'D' and resid 379 through 381 removed outlier: 6.681A pdb=" N ILE D 380 " --> pdb=" O LEU D 405 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 644 through 646 removed outlier: 3.661A pdb=" N ALA D 658 " --> pdb=" O ARG D 645 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 668 through 669 removed outlier: 3.763A pdb=" N SER D 696 " --> pdb=" O HIS D 687 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG D 704 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 740 through 741 removed outlier: 3.631A pdb=" N THR D 740 " --> pdb=" O ILE D 718 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LYS D 797 " --> pdb=" O ALA D 886 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ALA D 886 " --> pdb=" O LYS D 797 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU D 799 " --> pdb=" O LEU D 884 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N GLY D 862 " --> pdb=" O SER D 883 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 746 through 752 removed outlier: 3.749A pdb=" N HIS D 746 " --> pdb=" O LYS D 763 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL D 761 " --> pdb=" O VAL D 748 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ILE D 750 " --> pdb=" O VAL D 759 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL D 759 " --> pdb=" O ILE D 750 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP D 769 " --> pdb=" O TYR D 766 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N PHE D 843 " --> pdb=" O GLU D 815 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU D 815 " --> pdb=" O PHE D 843 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N HIS D 847 " --> pdb=" O ARG D 811 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ARG D 811 " --> pdb=" O HIS D 847 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 937 through 943 removed outlier: 3.615A pdb=" N MET D 976 " --> pdb=" O GLU D 940 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LYS D 974 " --> pdb=" O ILE D 942 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 946 through 948 Processing sheet with id=AF3, first strand: chain 'D' and resid 946 through 948 1265 hydrogen bonds defined for protein. 3555 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: 15.09 Time building geometry restraints manager: 12.64 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: 10872 1.34 - 1.46: 7494 1.46 - 1.58: 14446 1.58 - 1.70: 0 1.70 - 1.82: 308 Bond restraints: 33120 Sorted by residual: bond pdb=" C SER D 621 " pdb=" N ASP D 622 " ideal model delta sigma weight residual 1.332 1.303 0.030 1.40e-02 5.10e+03 4.52e+00 bond pdb=" C SER A 621 " pdb=" N ASP A 622 " ideal model delta sigma weight residual 1.332 1.303 0.030 1.40e-02 5.10e+03 4.48e+00 bond pdb=" C SER C 621 " pdb=" N ASP C 622 " ideal model delta sigma weight residual 1.332 1.303 0.030 1.40e-02 5.10e+03 4.48e+00 bond pdb=" C SER B 621 " pdb=" N ASP B 622 " ideal model delta sigma weight residual 1.332 1.303 0.029 1.40e-02 5.10e+03 4.44e+00 bond pdb=" C ASP A 216 " pdb=" N ALA A 217 " ideal model delta sigma weight residual 1.332 1.307 0.026 1.40e-02 5.10e+03 3.42e+00 ... (remaining 33115 not shown) Histogram of bond angle deviations from ideal: 98.91 - 105.94: 882 105.94 - 112.96: 17753 112.96 - 119.98: 11303 119.98 - 127.01: 14518 127.01 - 134.03: 564 Bond angle restraints: 45020 Sorted by residual: angle pdb=" N ILE A 24 " pdb=" CA ILE A 24 " pdb=" C ILE A 24 " ideal model delta sigma weight residual 111.62 108.33 3.29 7.90e-01 1.60e+00 1.73e+01 angle pdb=" N ILE B 24 " pdb=" CA ILE B 24 " pdb=" C ILE B 24 " ideal model delta sigma weight residual 111.62 108.35 3.27 7.90e-01 1.60e+00 1.71e+01 angle pdb=" N ILE C 24 " pdb=" CA ILE C 24 " pdb=" C ILE C 24 " ideal model delta sigma weight residual 111.62 108.37 3.25 7.90e-01 1.60e+00 1.69e+01 angle pdb=" N ILE D 24 " pdb=" CA ILE D 24 " pdb=" C ILE D 24 " ideal model delta sigma weight residual 111.62 108.37 3.25 7.90e-01 1.60e+00 1.69e+01 angle pdb=" N ASP C 475 " pdb=" CA ASP C 475 " pdb=" CB ASP C 475 " ideal model delta sigma weight residual 114.17 109.77 4.40 1.14e+00 7.69e-01 1.49e+01 ... (remaining 45015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 17703 17.69 - 35.38: 1701 35.38 - 53.07: 276 53.07 - 70.75: 56 70.75 - 88.44: 20 Dihedral angle restraints: 19756 sinusoidal: 7872 harmonic: 11884 Sorted by residual: dihedral pdb=" CA SER C 186 " pdb=" C SER C 186 " pdb=" N SER C 187 " pdb=" CA SER C 187 " ideal model delta harmonic sigma weight residual 180.00 151.07 28.93 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA SER A 186 " pdb=" C SER A 186 " pdb=" N SER A 187 " pdb=" CA SER A 187 " ideal model delta harmonic sigma weight residual 180.00 151.07 28.93 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA SER D 186 " pdb=" C SER D 186 " pdb=" N SER D 187 " pdb=" CA SER D 187 " ideal model delta harmonic sigma weight residual 180.00 151.13 28.87 0 5.00e+00 4.00e-02 3.33e+01 ... (remaining 19753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2444 0.031 - 0.062: 1493 0.062 - 0.093: 544 0.093 - 0.124: 297 0.124 - 0.155: 78 Chirality restraints: 4856 Sorted by residual: chirality pdb=" CA ILE A 750 " pdb=" N ILE A 750 " pdb=" C ILE A 750 " pdb=" CB ILE A 750 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.98e-01 chirality pdb=" CA ILE B 190 " pdb=" N ILE B 190 " pdb=" C ILE B 190 " pdb=" CB ILE B 190 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.83e-01 chirality pdb=" CA ASP A 465 " pdb=" N ASP A 465 " pdb=" C ASP A 465 " pdb=" CB ASP A 465 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.76e-01 ... (remaining 4853 not shown) Planarity restraints: 5900 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 198 " 0.023 2.00e-02 2.50e+03 2.14e-02 7.98e+00 pdb=" CG PHE A 198 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE A 198 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 198 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 198 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 198 " 0.013 2.00e-02 2.50e+03 pdb=" CZ PHE A 198 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 198 " -0.022 2.00e-02 2.50e+03 2.12e-02 7.84e+00 pdb=" CG PHE C 198 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE C 198 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE C 198 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE C 198 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 198 " -0.013 2.00e-02 2.50e+03 pdb=" CZ PHE C 198 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 198 " 0.023 2.00e-02 2.50e+03 2.11e-02 7.80e+00 pdb=" CG PHE B 198 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE B 198 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE B 198 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE B 198 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 198 " 0.013 2.00e-02 2.50e+03 pdb=" CZ PHE B 198 " -0.000 2.00e-02 2.50e+03 ... (remaining 5897 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 192 2.51 - 3.11: 23752 3.11 - 3.70: 46810 3.70 - 4.30: 70104 4.30 - 4.90: 121105 Nonbonded interactions: 261963 Sorted by model distance: nonbonded pdb=" OD1 ASP C 274 " pdb="ZN ZN C1101 " model vdw 1.910 2.230 nonbonded pdb=" OD1 ASP D 274 " pdb="ZN ZN D1101 " model vdw 1.911 2.230 nonbonded pdb=" OD1 ASP B 274 " pdb="ZN ZN B1101 " model vdw 1.911 2.230 nonbonded pdb=" OD2 ASP C 384 " pdb="ZN ZN C1101 " model vdw 1.911 2.230 nonbonded pdb=" OD2 ASP A 384 " pdb="ZN ZN A1101 " model vdw 1.911 2.230 ... (remaining 261958 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' } 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: 14.040 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: 42.530 Check model and map are aligned: 0.480 Set scattering table: 0.300 Process input model: 90.050 Find NCS groups from input model: 1.970 Set up NCS constraints: 0.210 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:12.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 162.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 33120 Z= 0.460 Angle : 0.744 7.438 45020 Z= 0.442 Chirality : 0.049 0.155 4856 Planarity : 0.005 0.055 5900 Dihedral : 13.891 88.443 12116 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 0.94 % Allowed : 5.81 % Favored : 93.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.81 (0.11), residues: 4120 helix: -1.99 (0.13), residues: 1088 sheet: -1.95 (0.15), residues: 1000 loop : -3.17 (0.10), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 904 HIS 0.007 0.001 HIS B 899 PHE 0.048 0.003 PHE A 198 TYR 0.020 0.002 TYR D 388 ARG 0.005 0.000 ARG C 367 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8240 Ramachandran restraints generated. 4120 Oldfield, 0 Emsley, 4120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8240 Ramachandran restraints generated. 4120 Oldfield, 0 Emsley, 4120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 608 time to evaluate : 3.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 GLU cc_start: 0.8423 (mp0) cc_final: 0.8167 (mp0) REVERT: A 252 LYS cc_start: 0.8799 (mttt) cc_final: 0.8497 (mmmt) REVERT: A 1002 ASP cc_start: 0.8240 (p0) cc_final: 0.7891 (p0) REVERT: B 212 GLU cc_start: 0.8405 (mp0) cc_final: 0.8152 (mp0) REVERT: B 252 LYS cc_start: 0.8817 (mttt) cc_final: 0.8517 (mmmt) REVERT: B 1002 ASP cc_start: 0.8255 (p0) cc_final: 0.7899 (p0) REVERT: C 212 GLU cc_start: 0.8424 (mp0) cc_final: 0.8168 (mp0) REVERT: C 252 LYS cc_start: 0.8791 (mttt) cc_final: 0.8488 (mmmt) REVERT: C 1002 ASP cc_start: 0.8239 (p0) cc_final: 0.7886 (p0) REVERT: D 212 GLU cc_start: 0.8409 (mp0) cc_final: 0.8145 (mp0) REVERT: D 252 LYS cc_start: 0.8819 (mttt) cc_final: 0.8523 (mmmt) REVERT: D 1002 ASP cc_start: 0.8254 (p0) cc_final: 0.7900 (p0) outliers start: 32 outliers final: 8 residues processed: 628 average time/residue: 1.5094 time to fit residues: 1113.1404 Evaluate side-chains 401 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 393 time to evaluate : 3.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 734 ASP Chi-restraints excluded: chain B residue 652 VAL Chi-restraints excluded: chain B residue 734 ASP Chi-restraints excluded: chain C residue 652 VAL Chi-restraints excluded: chain C residue 734 ASP Chi-restraints excluded: chain D residue 652 VAL Chi-restraints excluded: chain D residue 734 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 347 optimal weight: 7.9990 chunk 312 optimal weight: 1.9990 chunk 173 optimal weight: 8.9990 chunk 106 optimal weight: 8.9990 chunk 210 optimal weight: 9.9990 chunk 166 optimal weight: 9.9990 chunk 322 optimal weight: 6.9990 chunk 124 optimal weight: 0.9980 chunk 196 optimal weight: 3.9990 chunk 240 optimal weight: 0.9980 chunk 374 optimal weight: 5.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 543 GLN A 544 GLN A 857 ASN A 900 HIS A 929 ASN ** B 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 GLN B 544 GLN B 857 ASN B 900 HIS B 929 ASN ** C 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 543 GLN C 544 GLN C 857 ASN C 900 HIS C 929 ASN ** D 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 GLN D 544 GLN D 857 ASN D 900 HIS D 929 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 33120 Z= 0.328 Angle : 0.641 7.254 45020 Z= 0.339 Chirality : 0.048 0.160 4856 Planarity : 0.005 0.048 5900 Dihedral : 5.286 29.629 4512 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 3.67 % Allowed : 13.56 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.12), residues: 4120 helix: -0.19 (0.15), residues: 1112 sheet: -1.40 (0.15), residues: 1032 loop : -2.72 (0.12), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 904 HIS 0.005 0.001 HIS C 899 PHE 0.028 0.002 PHE A 198 TYR 0.016 0.001 TYR C 388 ARG 0.008 0.000 ARG D 487 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8240 Ramachandran restraints generated. 4120 Oldfield, 0 Emsley, 4120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8240 Ramachandran restraints generated. 4120 Oldfield, 0 Emsley, 4120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 434 time to evaluate : 3.488 Fit side-chains REVERT: A 178 LYS cc_start: 0.8159 (mmpt) cc_final: 0.7411 (mtpp) REVERT: A 252 LYS cc_start: 0.8869 (mttt) cc_final: 0.8591 (mmmt) REVERT: A 554 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7037 (tt0) REVERT: A 570 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7670 (tp30) REVERT: A 1002 ASP cc_start: 0.8341 (p0) cc_final: 0.8057 (p0) REVERT: B 178 LYS cc_start: 0.8181 (mmpt) cc_final: 0.7419 (mtpp) REVERT: B 252 LYS cc_start: 0.8875 (mttt) cc_final: 0.8595 (mmmt) REVERT: B 354 CYS cc_start: 0.7350 (OUTLIER) cc_final: 0.7141 (p) REVERT: B 554 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7038 (tt0) REVERT: B 1002 ASP cc_start: 0.8338 (p0) cc_final: 0.8060 (p0) REVERT: C 178 LYS cc_start: 0.8189 (mmpt) cc_final: 0.7415 (mtpp) REVERT: C 252 LYS cc_start: 0.8873 (mttt) cc_final: 0.8589 (mmmt) REVERT: C 554 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7040 (tt0) REVERT: C 570 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7666 (tp30) REVERT: C 691 ASP cc_start: 0.7799 (m-30) cc_final: 0.7595 (p0) REVERT: C 1002 ASP cc_start: 0.8337 (p0) cc_final: 0.8054 (p0) REVERT: D 178 LYS cc_start: 0.8129 (mmpt) cc_final: 0.7403 (mtpp) REVERT: D 252 LYS cc_start: 0.8873 (mttt) cc_final: 0.8600 (mmmt) REVERT: D 554 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7031 (tt0) REVERT: D 770 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7879 (mt-10) REVERT: D 1002 ASP cc_start: 0.8346 (p0) cc_final: 0.8068 (p0) outliers start: 125 outliers final: 38 residues processed: 514 average time/residue: 1.3966 time to fit residues: 855.3480 Evaluate side-chains 423 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 377 time to evaluate : 3.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 734 ASP Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 838 SER Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 956 ASP Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 652 VAL Chi-restraints excluded: chain B residue 734 ASP Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 838 SER Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 956 ASP Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 570 GLU Chi-restraints excluded: chain C residue 652 VAL Chi-restraints excluded: chain C residue 734 ASP Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain C residue 838 SER Chi-restraints excluded: chain C residue 855 VAL Chi-restraints excluded: chain C residue 956 ASP Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 554 GLU Chi-restraints excluded: chain D residue 652 VAL Chi-restraints excluded: chain D residue 734 ASP Chi-restraints excluded: chain D residue 770 GLU Chi-restraints excluded: chain D residue 810 SER Chi-restraints excluded: chain D residue 838 SER Chi-restraints excluded: chain D residue 855 VAL Chi-restraints excluded: chain D residue 956 ASP Chi-restraints excluded: chain D residue 982 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 207 optimal weight: 0.9980 chunk 116 optimal weight: 6.9990 chunk 311 optimal weight: 6.9990 chunk 254 optimal weight: 5.9990 chunk 103 optimal weight: 0.0470 chunk 374 optimal weight: 7.9990 chunk 404 optimal weight: 8.9990 chunk 333 optimal weight: 3.9990 chunk 371 optimal weight: 0.9990 chunk 127 optimal weight: 0.7980 chunk 300 optimal weight: 0.9990 overall best weight: 0.7682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 857 ASN B 857 ASN C 857 ASN D 857 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 33120 Z= 0.153 Angle : 0.537 6.918 45020 Z= 0.281 Chirality : 0.044 0.147 4856 Planarity : 0.004 0.046 5900 Dihedral : 4.732 27.226 4512 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 3.23 % Allowed : 16.17 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.12), residues: 4120 helix: 0.43 (0.16), residues: 1136 sheet: -1.03 (0.15), residues: 1032 loop : -2.39 (0.12), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 904 HIS 0.004 0.001 HIS B 594 PHE 0.014 0.001 PHE D 843 TYR 0.016 0.001 TYR A 388 ARG 0.003 0.000 ARG A 894 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8240 Ramachandran restraints generated. 4120 Oldfield, 0 Emsley, 4120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8240 Ramachandran restraints generated. 4120 Oldfield, 0 Emsley, 4120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 477 time to evaluate : 3.726 Fit side-chains REVERT: A 252 LYS cc_start: 0.8819 (mttt) cc_final: 0.8547 (mmmt) REVERT: A 570 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7791 (tp30) REVERT: A 691 ASP cc_start: 0.7775 (p0) cc_final: 0.7240 (p0) REVERT: A 770 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7797 (mp0) REVERT: A 802 ASP cc_start: 0.8394 (p0) cc_final: 0.7956 (p0) REVERT: A 899 HIS cc_start: 0.7691 (t70) cc_final: 0.7404 (t70) REVERT: B 252 LYS cc_start: 0.8820 (mttt) cc_final: 0.8549 (mmmt) REVERT: B 354 CYS cc_start: 0.6684 (OUTLIER) cc_final: 0.6469 (p) REVERT: B 554 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.6982 (tt0) REVERT: B 570 GLU cc_start: 0.7915 (mp0) cc_final: 0.7661 (tp30) REVERT: B 691 ASP cc_start: 0.7802 (p0) cc_final: 0.7286 (p0) REVERT: B 770 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7838 (mp0) REVERT: B 802 ASP cc_start: 0.8399 (p0) cc_final: 0.7997 (p0) REVERT: B 899 HIS cc_start: 0.7720 (t70) cc_final: 0.7463 (t70) REVERT: C 252 LYS cc_start: 0.8821 (mttt) cc_final: 0.8549 (mmmt) REVERT: C 570 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7787 (tp30) REVERT: C 770 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7834 (mp0) REVERT: C 802 ASP cc_start: 0.8395 (p0) cc_final: 0.7963 (p0) REVERT: C 899 HIS cc_start: 0.7688 (t70) cc_final: 0.7403 (t70) REVERT: C 972 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8496 (pttp) REVERT: D 252 LYS cc_start: 0.8813 (mttt) cc_final: 0.8548 (mmmt) REVERT: D 570 GLU cc_start: 0.7919 (mp0) cc_final: 0.7687 (tp30) REVERT: D 691 ASP cc_start: 0.7813 (p0) cc_final: 0.7291 (p0) REVERT: D 770 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7794 (mp0) REVERT: D 802 ASP cc_start: 0.8392 (p0) cc_final: 0.7991 (p0) REVERT: D 899 HIS cc_start: 0.7692 (t70) cc_final: 0.7449 (t70) outliers start: 110 outliers final: 52 residues processed: 545 average time/residue: 1.2773 time to fit residues: 839.9833 Evaluate side-chains 464 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 403 time to evaluate : 3.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 734 ASP Chi-restraints excluded: chain A residue 770 GLU Chi-restraints excluded: chain A residue 808 SER Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 838 SER Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 956 ASP Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 652 VAL Chi-restraints excluded: chain B residue 734 ASP Chi-restraints excluded: chain B residue 770 GLU Chi-restraints excluded: chain B residue 808 SER Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 838 SER Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 939 LEU Chi-restraints excluded: chain B residue 956 ASP Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 570 GLU Chi-restraints excluded: chain C residue 652 VAL Chi-restraints excluded: chain C residue 734 ASP Chi-restraints excluded: chain C residue 770 GLU Chi-restraints excluded: chain C residue 808 SER Chi-restraints excluded: chain C residue 821 ILE Chi-restraints excluded: chain C residue 838 SER Chi-restraints excluded: chain C residue 855 VAL Chi-restraints excluded: chain C residue 939 LEU Chi-restraints excluded: chain C residue 956 ASP Chi-restraints excluded: chain C residue 972 LYS Chi-restraints excluded: chain C residue 1019 LEU Chi-restraints excluded: chain D residue 98 ASN Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 293 SER Chi-restraints excluded: chain D residue 652 VAL Chi-restraints excluded: chain D residue 734 ASP Chi-restraints excluded: chain D residue 770 GLU Chi-restraints excluded: chain D residue 808 SER Chi-restraints excluded: chain D residue 821 ILE Chi-restraints excluded: chain D residue 838 SER Chi-restraints excluded: chain D residue 855 VAL Chi-restraints excluded: chain D residue 939 LEU Chi-restraints excluded: chain D residue 956 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 370 optimal weight: 0.9990 chunk 281 optimal weight: 3.9990 chunk 194 optimal weight: 8.9990 chunk 41 optimal weight: 9.9990 chunk 178 optimal weight: 0.0030 chunk 251 optimal weight: 5.9990 chunk 376 optimal weight: 9.9990 chunk 398 optimal weight: 7.9990 chunk 196 optimal weight: 0.0040 chunk 356 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 overall best weight: 2.0008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 HIS A 213 ASN ** A 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 ASN B 213 ASN ** B 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 457 ASN C 126 HIS C 213 ASN ** C 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 457 ASN D 126 HIS D 213 ASN ** D 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 457 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 33120 Z= 0.251 Angle : 0.582 8.076 45020 Z= 0.303 Chirality : 0.046 0.166 4856 Planarity : 0.004 0.047 5900 Dihedral : 4.802 27.616 4512 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 4.14 % Allowed : 16.67 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.13), residues: 4120 helix: 0.78 (0.16), residues: 1132 sheet: -0.87 (0.15), residues: 1044 loop : -2.23 (0.13), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 904 HIS 0.004 0.001 HIS B 899 PHE 0.018 0.002 PHE D 843 TYR 0.013 0.001 TYR B 388 ARG 0.003 0.000 ARG C 894 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8240 Ramachandran restraints generated. 4120 Oldfield, 0 Emsley, 4120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8240 Ramachandran restraints generated. 4120 Oldfield, 0 Emsley, 4120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 418 time to evaluate : 3.690 Fit side-chains REVERT: A 252 LYS cc_start: 0.8837 (mttt) cc_final: 0.8552 (mmmt) REVERT: A 691 ASP cc_start: 0.8088 (p0) cc_final: 0.7540 (p0) REVERT: A 770 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7757 (mp0) REVERT: B 178 LYS cc_start: 0.8006 (mmmt) cc_final: 0.7604 (mppt) REVERT: B 252 LYS cc_start: 0.8846 (mttt) cc_final: 0.8557 (mmmt) REVERT: B 354 CYS cc_start: 0.7191 (OUTLIER) cc_final: 0.6914 (p) REVERT: B 554 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7107 (tt0) REVERT: B 570 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7712 (tp30) REVERT: B 691 ASP cc_start: 0.8081 (p0) cc_final: 0.7558 (p0) REVERT: B 770 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7779 (mp0) REVERT: C 252 LYS cc_start: 0.8843 (mttt) cc_final: 0.8550 (mmmt) REVERT: C 691 ASP cc_start: 0.8018 (p0) cc_final: 0.7556 (p0) REVERT: C 770 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7785 (mp0) REVERT: C 972 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8583 (pttp) REVERT: D 178 LYS cc_start: 0.8001 (mmmt) cc_final: 0.7594 (mppt) REVERT: D 252 LYS cc_start: 0.8835 (mttt) cc_final: 0.8553 (mmmt) REVERT: D 570 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7714 (tp30) REVERT: D 691 ASP cc_start: 0.8091 (p0) cc_final: 0.7555 (p0) outliers start: 141 outliers final: 76 residues processed: 508 average time/residue: 1.2442 time to fit residues: 765.5411 Evaluate side-chains 463 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 379 time to evaluate : 3.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 734 ASP Chi-restraints excluded: chain A residue 770 GLU Chi-restraints excluded: chain A residue 808 SER Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 859 SER Chi-restraints excluded: chain A residue 903 ASP Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 956 ASP Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 166 PHE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain B residue 652 VAL Chi-restraints excluded: chain B residue 734 ASP Chi-restraints excluded: chain B residue 770 GLU Chi-restraints excluded: chain B residue 808 SER Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 859 SER Chi-restraints excluded: chain B residue 903 ASP Chi-restraints excluded: chain B residue 939 LEU Chi-restraints excluded: chain B residue 956 ASP Chi-restraints excluded: chain B residue 1019 LEU Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 166 PHE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain C residue 652 VAL Chi-restraints excluded: chain C residue 734 ASP Chi-restraints excluded: chain C residue 770 GLU Chi-restraints excluded: chain C residue 808 SER Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain C residue 821 ILE Chi-restraints excluded: chain C residue 855 VAL Chi-restraints excluded: chain C residue 859 SER Chi-restraints excluded: chain C residue 903 ASP Chi-restraints excluded: chain C residue 939 LEU Chi-restraints excluded: chain C residue 956 ASP Chi-restraints excluded: chain C residue 972 LYS Chi-restraints excluded: chain C residue 1019 LEU Chi-restraints excluded: chain D residue 98 ASN Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 166 PHE Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 293 SER Chi-restraints excluded: chain D residue 522 SER Chi-restraints excluded: chain D residue 570 GLU Chi-restraints excluded: chain D residue 652 VAL Chi-restraints excluded: chain D residue 734 ASP Chi-restraints excluded: chain D residue 808 SER Chi-restraints excluded: chain D residue 810 SER Chi-restraints excluded: chain D residue 821 ILE Chi-restraints excluded: chain D residue 855 VAL Chi-restraints excluded: chain D residue 859 SER Chi-restraints excluded: chain D residue 903 ASP Chi-restraints excluded: chain D residue 939 LEU Chi-restraints excluded: chain D residue 956 ASP Chi-restraints excluded: chain D residue 1019 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 331 optimal weight: 5.9990 chunk 226 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 296 optimal weight: 0.8980 chunk 164 optimal weight: 0.8980 chunk 339 optimal weight: 6.9990 chunk 275 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 203 optimal weight: 6.9990 chunk 357 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 ASN ** B 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 457 ASN ** C 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 457 ASN ** D 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 457 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 33120 Z= 0.398 Angle : 0.655 8.677 45020 Z= 0.342 Chirality : 0.049 0.178 4856 Planarity : 0.005 0.049 5900 Dihedral : 5.141 28.668 4512 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 4.31 % Allowed : 18.25 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.13), residues: 4120 helix: 0.78 (0.16), residues: 1124 sheet: -0.88 (0.15), residues: 1064 loop : -2.25 (0.13), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 729 HIS 0.007 0.001 HIS A 899 PHE 0.026 0.002 PHE A 843 TYR 0.014 0.002 TYR B 221 ARG 0.003 0.000 ARG D 615 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8240 Ramachandran restraints generated. 4120 Oldfield, 0 Emsley, 4120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8240 Ramachandran restraints generated. 4120 Oldfield, 0 Emsley, 4120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 378 time to evaluate : 3.698 Fit side-chains REVERT: A 178 LYS cc_start: 0.7993 (mmmt) cc_final: 0.7541 (mmmt) REVERT: A 216 ASP cc_start: 0.7891 (p0) cc_final: 0.7585 (p0) REVERT: A 691 ASP cc_start: 0.8119 (p0) cc_final: 0.7621 (p0) REVERT: A 1002 ASP cc_start: 0.8447 (p0) cc_final: 0.8189 (p0) REVERT: B 178 LYS cc_start: 0.8014 (mmmt) cc_final: 0.7548 (mmmt) REVERT: B 216 ASP cc_start: 0.7892 (p0) cc_final: 0.7587 (p0) REVERT: B 252 LYS cc_start: 0.8889 (mttt) cc_final: 0.8588 (mmmt) REVERT: B 354 CYS cc_start: 0.7568 (OUTLIER) cc_final: 0.7345 (p) REVERT: B 554 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7130 (tt0) REVERT: B 570 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7738 (tp30) REVERT: B 691 ASP cc_start: 0.8116 (p0) cc_final: 0.7645 (p0) REVERT: B 1002 ASP cc_start: 0.8443 (p0) cc_final: 0.8184 (p0) REVERT: C 178 LYS cc_start: 0.8006 (mmmt) cc_final: 0.7540 (mmmt) REVERT: C 691 ASP cc_start: 0.8055 (p0) cc_final: 0.7617 (p0) REVERT: C 1002 ASP cc_start: 0.8448 (p0) cc_final: 0.8190 (p0) REVERT: D 178 LYS cc_start: 0.8004 (mmmt) cc_final: 0.7549 (mmmt) REVERT: D 570 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7741 (tp30) REVERT: D 691 ASP cc_start: 0.8117 (p0) cc_final: 0.7641 (p0) REVERT: D 1002 ASP cc_start: 0.8448 (p0) cc_final: 0.8192 (p0) outliers start: 147 outliers final: 78 residues processed: 490 average time/residue: 1.2796 time to fit residues: 762.0036 Evaluate side-chains 437 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 355 time to evaluate : 3.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 734 ASP Chi-restraints excluded: chain A residue 808 SER Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 859 SER Chi-restraints excluded: chain A residue 903 ASP Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 956 ASP Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain B residue 652 VAL Chi-restraints excluded: chain B residue 734 ASP Chi-restraints excluded: chain B residue 808 SER Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 859 SER Chi-restraints excluded: chain B residue 903 ASP Chi-restraints excluded: chain B residue 939 LEU Chi-restraints excluded: chain B residue 956 ASP Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 1019 LEU Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 389 THR Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain C residue 595 ASP Chi-restraints excluded: chain C residue 652 VAL Chi-restraints excluded: chain C residue 734 ASP Chi-restraints excluded: chain C residue 774 THR Chi-restraints excluded: chain C residue 808 SER Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain C residue 855 VAL Chi-restraints excluded: chain C residue 859 SER Chi-restraints excluded: chain C residue 895 THR Chi-restraints excluded: chain C residue 903 ASP Chi-restraints excluded: chain C residue 939 LEU Chi-restraints excluded: chain C residue 956 ASP Chi-restraints excluded: chain C residue 1019 LEU Chi-restraints excluded: chain D residue 98 ASN Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 293 SER Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 522 SER Chi-restraints excluded: chain D residue 570 GLU Chi-restraints excluded: chain D residue 652 VAL Chi-restraints excluded: chain D residue 734 ASP Chi-restraints excluded: chain D residue 808 SER Chi-restraints excluded: chain D residue 810 SER Chi-restraints excluded: chain D residue 855 VAL Chi-restraints excluded: chain D residue 859 SER Chi-restraints excluded: chain D residue 903 ASP Chi-restraints excluded: chain D residue 939 LEU Chi-restraints excluded: chain D residue 956 ASP Chi-restraints excluded: chain D residue 982 THR Chi-restraints excluded: chain D residue 1019 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.0944 > 50: distance: 73 - 89: 25.676 distance: 77 - 100: 29.332 distance: 83 - 108: 9.822 distance: 86 - 89: 25.486 distance: 89 - 90: 22.692 distance: 90 - 91: 30.193 distance: 90 - 93: 5.623 distance: 91 - 92: 20.310 distance: 91 - 100: 26.410 distance: 92 - 122: 40.614 distance: 93 - 94: 30.292 distance: 94 - 95: 21.523 distance: 95 - 96: 17.829 distance: 96 - 97: 7.358 distance: 97 - 98: 12.597 distance: 97 - 99: 14.341 distance: 100 - 101: 4.859 distance: 101 - 102: 34.244 distance: 101 - 104: 32.703 distance: 102 - 103: 17.478 distance: 102 - 108: 19.940 distance: 104 - 105: 38.466 distance: 104 - 106: 48.060 distance: 105 - 107: 15.582 distance: 108 - 109: 12.789 distance: 109 - 110: 7.495 distance: 109 - 112: 17.105 distance: 110 - 111: 45.444 distance: 110 - 113: 20.254 distance: 113 - 114: 6.658 distance: 114 - 115: 12.251 distance: 114 - 117: 3.264 distance: 115 - 116: 15.661 distance: 115 - 122: 18.563 distance: 117 - 118: 14.084 distance: 118 - 119: 24.431 distance: 119 - 120: 17.043 distance: 119 - 121: 22.855 distance: 122 - 123: 16.462 distance: 123 - 124: 36.197 distance: 124 - 125: 12.556 distance: 124 - 126: 22.486 distance: 126 - 127: 14.423 distance: 127 - 128: 15.732 distance: 127 - 130: 17.132 distance: 128 - 129: 19.028 distance: 128 - 137: 12.273 distance: 130 - 131: 23.022 distance: 131 - 132: 22.784 distance: 132 - 133: 18.331 distance: 133 - 134: 9.993 distance: 134 - 135: 10.108 distance: 134 - 136: 11.007 distance: 137 - 138: 17.311 distance: 138 - 139: 18.904 distance: 138 - 141: 11.808 distance: 139 - 140: 57.179 distance: 139 - 148: 24.778 distance: 141 - 142: 27.344 distance: 142 - 143: 11.447 distance: 142 - 144: 14.891 distance: 143 - 145: 22.599 distance: 144 - 146: 27.191 distance: 145 - 147: 29.476 distance: 148 - 149: 20.443 distance: 149 - 150: 12.116 distance: 149 - 152: 26.892 distance: 150 - 151: 27.261 distance: 150 - 156: 16.503 distance: 152 - 153: 33.522 distance: 152 - 154: 57.016 distance: 153 - 155: 22.042 distance: 156 - 157: 10.007 distance: 156 - 162: 34.636 distance: 157 - 158: 34.950 distance: 157 - 160: 13.871 distance: 158 - 159: 9.468 distance: 158 - 163: 29.324 distance: 160 - 161: 32.793 distance: 161 - 162: 24.108 distance: 163 - 164: 21.183 distance: 164 - 165: 10.341 distance: 164 - 167: 20.495 distance: 165 - 166: 10.355 distance: 165 - 170: 7.843 distance: 167 - 168: 5.321 distance: 167 - 169: 20.903