Starting phenix.real_space_refine (version: dev) on Fri May 13 08:13:58 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vq8_21319/05_2022/6vq8_21319_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vq8_21319/05_2022/6vq8_21319.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vq8_21319/05_2022/6vq8_21319.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vq8_21319/05_2022/6vq8_21319.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vq8_21319/05_2022/6vq8_21319_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vq8_21319/05_2022/6vq8_21319_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.006 sd= 0.070 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 77": "OD1" <-> "OD2" Residue "o TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 60714 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 4651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4651 Classifications: {'peptide': 600} Link IDs: {'PTRANS': 29, 'TRANS': 569, 'PCIS': 1} Chain: "B" Number of atoms: 4651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4651 Classifications: {'peptide': 600} Link IDs: {'PTRANS': 29, 'TRANS': 569, 'PCIS': 1} Chain: "C" Number of atoms: 4651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4651 Classifications: {'peptide': 600} Link IDs: {'PTRANS': 29, 'TRANS': 569, 'PCIS': 1} Chain: "D" Number of atoms: 3595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3595 Classifications: {'peptide': 459} Link IDs: {'PTRANS': 26, 'TRANS': 431, 'PCIS': 1} Chain breaks: 1 Chain: "E" Number of atoms: 3595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3595 Classifications: {'peptide': 459} Link IDs: {'PTRANS': 26, 'TRANS': 431, 'PCIS': 1} Chain breaks: 1 Chain: "F" Number of atoms: 3595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3595 Classifications: {'peptide': 459} Link IDs: {'PTRANS': 26, 'TRANS': 431, 'PCIS': 1} Chain breaks: 1 Chain: "G" Number of atoms: 1790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 1790 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 325} Link IDs: {'PTRANS': 8, 'TRANS': 350, 'PCIS': 1} Chain breaks: 1 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1192 Unresolved non-hydrogen angles: 1522 Unresolved non-hydrogen dihedrals: 998 Unresolved non-hydrogen chiralities: 105 Planarities with less than four sites: {'GLN:plan1': 16, 'ARG:plan': 14, 'TYR:plan': 15, 'ASN:plan1': 22, 'TRP:plan': 6, 'HIS:plan': 6, 'PHE:plan': 14, 'GLU:plan': 25, 'ASP:plan': 24} Unresolved non-hydrogen planarities: 645 Chain: "H" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1726 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 3, 'TRANS': 210} Chain: "I" Number of atoms: 1607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1607 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 5, 'TRANS': 219} Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 268 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 13, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 132 Chain: "J" Number of atoms: 1602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1602 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 5, 'TRANS': 218} Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 268 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 13, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 132 Chain: "K" Number of atoms: 1607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1607 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 5, 'TRANS': 219} Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 268 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 13, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 132 Chain: "L" Number of atoms: 866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 866 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 105} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 714 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 2, 'TRANS': 111} Unresolved non-hydrogen bonds: 214 Unresolved non-hydrogen angles: 258 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 13, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 147 Chain: "N" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 714 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 2, 'TRANS': 111} Unresolved non-hydrogen bonds: 214 Unresolved non-hydrogen angles: 258 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 13, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 147 Chain: "O" Number of atoms: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 709 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 2, 'TRANS': 110} Unresolved non-hydrogen bonds: 213 Unresolved non-hydrogen angles: 257 Unresolved non-hydrogen dihedrals: 174 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 13, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 147 Chain: "Q" Number of atoms: 1878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1878 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 222} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 1824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1824 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 9, 'TRANS': 214} Chain: "S" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1722 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 8, 'TRANS': 203} Chain: "a" Number of atoms: 3703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 749, 3703 Classifications: {'peptide': 749} Incomplete info: {'truncation_to_alanine': 668} Link IDs: {'PTRANS': 31, 'TRANS': 717} Chain breaks: 2 Unresolved chain link angles: 31 Unresolved non-hydrogen bonds: 2555 Unresolved non-hydrogen angles: 3282 Unresolved non-hydrogen dihedrals: 2176 Unresolved non-hydrogen chiralities: 228 Planarities with less than four sites: {'GLN:plan1': 26, 'HIS:plan': 19, 'TYR:plan': 23, 'ASN:plan1': 41, 'TRP:plan': 12, 'ASP:plan': 22, 'PHE:plan': 63, 'GLU:plan': 47, 'ARG:plan': 39} Unresolved non-hydrogen planarities: 1418 Chain: "b" Number of atoms: 1503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1503 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 5, 'TRANS': 197} Chain: "c" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 337 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "d" Number of atoms: 2833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2833 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 13, 'TRANS': 336} Chain: "e" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 384 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 6, 'TRANS': 71} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 361 Unresolved non-hydrogen dihedrals: 242 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 5, 'HIS:plan': 1, 'PHE:plan': 7, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 137 Chain: "f" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 412 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 3, 'TRANS': 80} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 259 Unresolved non-hydrogen angles: 337 Unresolved non-hydrogen dihedrals: 219 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 7, 'GLU:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 141 Chain: "g" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "h" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "i" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "j" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "k" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "l" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "m" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "n" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "o" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "p" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 406 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 50} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 27.93, per 1000 atoms: 0.46 Number of scatterers: 60714 At special positions: 0 Unit cell: (173.84, 174.9, 272.42, 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) S 311 16.00 P 2 15.00 O 11426 8.00 N 10527 7.00 C 38448 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: 20.38 Conformation dependent library (CDL) restraints added in 7.5 seconds 16738 Ramachandran restraints generated. 8369 Oldfield, 0 Emsley, 8369 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15618 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 291 helices and 40 sheets defined 59.1% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.33 Creating SS restraints... Processing helix chain 'A' and resid 106 through 113 Processing helix chain 'A' and resid 256 through 265 Processing helix chain 'A' and resid 281 through 293 Proline residue: A 292 - end of helix Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 321 through 340 removed outlier: 3.641A pdb=" N SER A 326 " --> pdb=" O ARG A 323 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY A 330 " --> pdb=" O ILE A 327 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE A 331 " --> pdb=" O TYR A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 364 Processing helix chain 'A' and resid 371 through 373 No H-bonds generated for 'chain 'A' and resid 371 through 373' Processing helix chain 'A' and resid 376 through 388 removed outlier: 4.358A pdb=" N GLY A 379 " --> pdb=" O ALA A 376 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA A 383 " --> pdb=" O ALA A 380 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A 384 " --> pdb=" O ARG A 381 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU A 387 " --> pdb=" O SER A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 415 No H-bonds generated for 'chain 'A' and resid 413 through 415' Processing helix chain 'A' and resid 420 through 426 Processing helix chain 'A' and resid 437 through 441 Processing helix chain 'A' and resid 458 through 468 removed outlier: 4.455A pdb=" N GLU A 463 " --> pdb=" O ARG A 459 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N TYR A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 496 removed outlier: 4.140A pdb=" N ILE A 492 " --> pdb=" O ASP A 488 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 518 Processing helix chain 'A' and resid 534 through 556 Processing helix chain 'A' and resid 567 through 573 Processing helix chain 'A' and resid 575 through 585 removed outlier: 4.968A pdb=" N LYS A 585 " --> pdb=" O LEU A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 615 Processing helix chain 'B' and resid 106 through 113 Processing helix chain 'B' and resid 232 through 235 No H-bonds generated for 'chain 'B' and resid 232 through 235' Processing helix chain 'B' and resid 256 through 266 Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 305 through 308 Processing helix chain 'B' and resid 320 through 340 removed outlier: 4.616A pdb=" N ILE B 327 " --> pdb=" O ARG B 323 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N TYR B 328 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N MET B 340 " --> pdb=" O TYR B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 364 Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 378 through 386 Processing helix chain 'B' and resid 420 through 426 Processing helix chain 'B' and resid 437 through 441 Processing helix chain 'B' and resid 458 through 468 removed outlier: 4.282A pdb=" N GLU B 463 " --> pdb=" O ARG B 459 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N TYR B 464 " --> pdb=" O ALA B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 496 removed outlier: 3.867A pdb=" N LEU B 495 " --> pdb=" O GLU B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 518 Processing helix chain 'B' and resid 534 through 557 Processing helix chain 'B' and resid 567 through 573 Processing helix chain 'B' and resid 575 through 586 removed outlier: 5.130A pdb=" N LYS B 585 " --> pdb=" O LEU B 581 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N PHE B 586 " --> pdb=" O SER B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 615 Processing helix chain 'C' and resid 106 through 112 removed outlier: 3.652A pdb=" N SER C 111 " --> pdb=" O SER C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 254 No H-bonds generated for 'chain 'C' and resid 252 through 254' Processing helix chain 'C' and resid 257 through 266 Processing helix chain 'C' and resid 281 through 293 Proline residue: C 292 - end of helix Processing helix chain 'C' and resid 305 through 307 No H-bonds generated for 'chain 'C' and resid 305 through 307' Processing helix chain 'C' and resid 320 through 340 removed outlier: 4.594A pdb=" N ILE C 327 " --> pdb=" O ARG C 323 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N TYR C 328 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N MET C 340 " --> pdb=" O TYR C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 364 Processing helix chain 'C' and resid 371 through 373 No H-bonds generated for 'chain 'C' and resid 371 through 373' Processing helix chain 'C' and resid 378 through 388 removed outlier: 3.725A pdb=" N ARG C 388 " --> pdb=" O SER C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 415 No H-bonds generated for 'chain 'C' and resid 413 through 415' Processing helix chain 'C' and resid 420 through 426 Processing helix chain 'C' and resid 438 through 441 No H-bonds generated for 'chain 'C' and resid 438 through 441' Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 472 through 496 removed outlier: 4.598A pdb=" N GLU C 491 " --> pdb=" O GLU C 487 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ILE C 492 " --> pdb=" O ASP C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 518 Processing helix chain 'C' and resid 534 through 558 removed outlier: 3.810A pdb=" N THR C 558 " --> pdb=" O ALA C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 573 Processing helix chain 'C' and resid 575 through 586 removed outlier: 4.851A pdb=" N LYS C 585 " --> pdb=" O LEU C 581 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N PHE C 586 " --> pdb=" O SER C 582 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 615 removed outlier: 3.971A pdb=" N LEU C 615 " --> pdb=" O ALA C 611 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 127 No H-bonds generated for 'chain 'D' and resid 125 through 127' Processing helix chain 'D' and resid 175 through 178 No H-bonds generated for 'chain 'D' and resid 175 through 178' Processing helix chain 'D' and resid 199 through 209 removed outlier: 3.601A pdb=" N ARG D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 250 Processing helix chain 'D' and resid 254 through 256 No H-bonds generated for 'chain 'D' and resid 254 through 256' Processing helix chain 'D' and resid 270 through 272 No H-bonds generated for 'chain 'D' and resid 270 through 272' Processing helix chain 'D' and resid 274 through 287 Processing helix chain 'D' and resid 300 through 313 Processing helix chain 'D' and resid 327 through 335 Processing helix chain 'D' and resid 357 through 359 No H-bonds generated for 'chain 'D' and resid 357 through 359' Processing helix chain 'D' and resid 364 through 372 Processing helix chain 'D' and resid 381 through 386 removed outlier: 4.049A pdb=" N ARG D 386 " --> pdb=" O GLN D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 405 No H-bonds generated for 'chain 'D' and resid 402 through 405' Processing helix chain 'D' and resid 415 through 439 removed outlier: 4.343A pdb=" N VAL D 438 " --> pdb=" O ALA D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 443 No H-bonds generated for 'chain 'D' and resid 441 through 443' Processing helix chain 'D' and resid 446 through 461 removed outlier: 4.348A pdb=" N TYR D 451 " --> pdb=" O ASP D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 486 removed outlier: 4.005A pdb=" N ILE D 486 " --> pdb=" O GLN D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 491 No H-bonds generated for 'chain 'D' and resid 489 through 491' Processing helix chain 'D' and resid 497 through 503 removed outlier: 5.012A pdb=" N GLU D 502 " --> pdb=" O SER D 498 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 127 No H-bonds generated for 'chain 'E' and resid 125 through 127' Processing helix chain 'E' and resid 175 through 178 No H-bonds generated for 'chain 'E' and resid 175 through 178' Processing helix chain 'E' and resid 199 through 209 Processing helix chain 'E' and resid 238 through 250 Processing helix chain 'E' and resid 254 through 256 No H-bonds generated for 'chain 'E' and resid 254 through 256' Processing helix chain 'E' and resid 270 through 287 removed outlier: 3.580A pdb=" N THR E 274 " --> pdb=" O ARG E 271 " (cutoff:3.500A) Proline residue: E 275 - end of helix removed outlier: 3.591A pdb=" N ALA E 278 " --> pdb=" O PRO E 275 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU E 279 " --> pdb=" O ARG E 276 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR E 280 " --> pdb=" O LEU E 277 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA E 286 " --> pdb=" O GLU E 283 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR E 287 " --> pdb=" O PHE E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 313 Processing helix chain 'E' and resid 320 through 322 No H-bonds generated for 'chain 'E' and resid 320 through 322' Processing helix chain 'E' and resid 327 through 335 removed outlier: 3.852A pdb=" N ILE E 334 " --> pdb=" O ASP E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 359 No H-bonds generated for 'chain 'E' and resid 357 through 359' Processing helix chain 'E' and resid 364 through 372 Processing helix chain 'E' and resid 382 through 385 No H-bonds generated for 'chain 'E' and resid 382 through 385' Processing helix chain 'E' and resid 400 through 403 removed outlier: 4.189A pdb=" N LYS E 403 " --> pdb=" O ARG E 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 400 through 403' Processing helix chain 'E' and resid 415 through 439 removed outlier: 4.031A pdb=" N VAL E 438 " --> pdb=" O ALA E 434 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 443 No H-bonds generated for 'chain 'E' and resid 441 through 443' Processing helix chain 'E' and resid 446 through 461 Processing helix chain 'E' and resid 473 through 486 removed outlier: 3.830A pdb=" N ILE E 486 " --> pdb=" O GLN E 482 " (cutoff:3.500A) Processing helix chain 'E' and resid 489 through 491 No H-bonds generated for 'chain 'E' and resid 489 through 491' Processing helix chain 'E' and resid 497 through 503 Processing helix chain 'F' and resid 160 through 162 No H-bonds generated for 'chain 'F' and resid 160 through 162' Processing helix chain 'F' and resid 175 through 177 No H-bonds generated for 'chain 'F' and resid 175 through 177' Processing helix chain 'F' and resid 199 through 209 Processing helix chain 'F' and resid 238 through 250 Processing helix chain 'F' and resid 253 through 256 Processing helix chain 'F' and resid 268 through 288 removed outlier: 3.580A pdb=" N ILE F 272 " --> pdb=" O THR F 268 " (cutoff:3.500A) Proline residue: F 275 - end of helix Processing helix chain 'F' and resid 300 through 313 Processing helix chain 'F' and resid 320 through 322 No H-bonds generated for 'chain 'F' and resid 320 through 322' Processing helix chain 'F' and resid 327 through 335 Processing helix chain 'F' and resid 357 through 359 No H-bonds generated for 'chain 'F' and resid 357 through 359' Processing helix chain 'F' and resid 364 through 372 removed outlier: 3.845A pdb=" N ILE F 372 " --> pdb=" O LEU F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 385 No H-bonds generated for 'chain 'F' and resid 382 through 385' Processing helix chain 'F' and resid 402 through 405 No H-bonds generated for 'chain 'F' and resid 402 through 405' Processing helix chain 'F' and resid 415 through 439 removed outlier: 3.691A pdb=" N VAL F 438 " --> pdb=" O ALA F 434 " (cutoff:3.500A) Processing helix chain 'F' and resid 446 through 461 Processing helix chain 'F' and resid 473 through 486 removed outlier: 4.109A pdb=" N ILE F 486 " --> pdb=" O GLN F 482 " (cutoff:3.500A) Processing helix chain 'F' and resid 489 through 491 No H-bonds generated for 'chain 'F' and resid 489 through 491' Processing helix chain 'F' and resid 497 through 503 Processing helix chain 'G' and resid 14 through 21 Processing helix chain 'G' and resid 28 through 31 Processing helix chain 'G' and resid 48 through 79 Processing helix chain 'G' and resid 98 through 103 Processing helix chain 'G' and resid 118 through 156 Processing helix chain 'G' and resid 166 through 168 No H-bonds generated for 'chain 'G' and resid 166 through 168' Processing helix chain 'G' and resid 172 through 174 No H-bonds generated for 'chain 'G' and resid 172 through 174' Processing helix chain 'G' and resid 191 through 203 removed outlier: 5.311A pdb=" N ASN G 195 " --> pdb=" O LEU G 192 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N TYR G 201 " --> pdb=" O ILE G 198 " (cutoff:3.500A) Processing helix chain 'G' and resid 231 through 243 removed outlier: 4.064A pdb=" N ASP G 235 " --> pdb=" O LYS G 232 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE G 237 " --> pdb=" O VAL G 234 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG G 238 " --> pdb=" O ASP G 235 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 310 Proline residue: G 278 - end of helix Processing helix chain 'G' and resid 328 through 340 Processing helix chain 'H' and resid 13 through 76 Processing helix chain 'H' and resid 79 through 85 Processing helix chain 'H' and resid 128 through 174 Processing helix chain 'H' and resid 176 through 215 Processing helix chain 'I' and resid 5 through 106 Processing helix chain 'I' and resid 109 through 127 removed outlier: 4.629A pdb=" N VAL I 114 " --> pdb=" O THR I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 138 through 158 Proline residue: I 142 - end of helix removed outlier: 3.833A pdb=" N LYS I 145 " --> pdb=" O PRO I 142 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS I 150 " --> pdb=" O ALA I 147 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE I 152 " --> pdb=" O GLN I 149 " (cutoff:3.500A) Proline residue: I 153 - end of helix removed outlier: 3.692A pdb=" N LYS I 156 " --> pdb=" O PRO I 153 " (cutoff:3.500A) Processing helix chain 'I' and resid 196 through 216 removed outlier: 3.949A pdb=" N GLN I 206 " --> pdb=" O LEU I 202 " (cutoff:3.500A) Proline residue: I 209 - end of helix Processing helix chain 'J' and resid 5 through 106 removed outlier: 3.574A pdb=" N LYS J 52 " --> pdb=" O THR J 48 " (cutoff:3.500A) Processing helix chain 'J' and resid 110 through 127 Processing helix chain 'J' and resid 138 through 159 Proline residue: J 142 - end of helix removed outlier: 3.750A pdb=" N LYS J 145 " --> pdb=" O PRO J 142 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ILE J 152 " --> pdb=" O GLN J 149 " (cutoff:3.500A) Proline residue: J 153 - end of helix removed outlier: 3.722A pdb=" N LYS J 156 " --> pdb=" O PRO J 153 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE J 157 " --> pdb=" O MET J 154 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR J 159 " --> pdb=" O LYS J 156 " (cutoff:3.500A) Processing helix chain 'J' and resid 196 through 204 Processing helix chain 'J' and resid 208 through 216 removed outlier: 3.613A pdb=" N GLY J 213 " --> pdb=" O PRO J 209 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 106 Processing helix chain 'K' and resid 110 through 127 Processing helix chain 'K' and resid 138 through 159 Proline residue: K 142 - end of helix removed outlier: 3.713A pdb=" N LYS K 145 " --> pdb=" O PRO K 142 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS K 150 " --> pdb=" O ALA K 147 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ILE K 152 " --> pdb=" O GLN K 149 " (cutoff:3.500A) Proline residue: K 153 - end of helix removed outlier: 3.695A pdb=" N LYS K 156 " --> pdb=" O PRO K 153 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR K 159 " --> pdb=" O LYS K 156 " (cutoff:3.500A) Processing helix chain 'K' and resid 196 through 206 Processing helix chain 'K' and resid 208 through 216 removed outlier: 3.507A pdb=" N GLY K 213 " --> pdb=" O PRO K 209 " (cutoff:3.500A) Processing helix chain 'L' and resid 14 through 22 Processing helix chain 'L' and resid 45 through 56 Processing helix chain 'L' and resid 68 through 73 Processing helix chain 'L' and resid 75 through 80 Processing helix chain 'L' and resid 104 through 108 Processing helix chain 'M' and resid 4 through 90 removed outlier: 4.043A pdb=" N SER M 70 " --> pdb=" O GLN M 66 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ALA M 71 " --> pdb=" O GLY M 67 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU M 72 " --> pdb=" O ASN M 68 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ARG M 90 " --> pdb=" O SER M 86 " (cutoff:3.500A) Processing helix chain 'M' and resid 92 through 104 Processing helix chain 'N' and resid 4 through 103 removed outlier: 3.793A pdb=" N GLN N 66 " --> pdb=" O ALA N 62 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU N 74 " --> pdb=" O SER N 70 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN N 91 " --> pdb=" O SER N 87 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N GLU N 93 " --> pdb=" O GLN N 89 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N ARG N 94 " --> pdb=" O ARG N 90 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 90 removed outlier: 3.845A pdb=" N GLN O 66 " --> pdb=" O ALA O 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 92 through 104 Processing helix chain 'Q' and resid 15 through 36 Processing helix chain 'Q' and resid 43 through 48 Processing helix chain 'Q' and resid 50 through 55 removed outlier: 5.008A pdb=" N TRP Q 55 " --> pdb=" O ASP Q 51 " (cutoff:3.500A) Processing helix chain 'Q' and resid 62 through 70 Processing helix chain 'Q' and resid 78 through 98 removed outlier: 3.907A pdb=" N LEU Q 88 " --> pdb=" O ARG Q 84 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU Q 91 " --> pdb=" O ILE Q 87 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE Q 98 " --> pdb=" O LEU Q 94 " (cutoff:3.500A) Processing helix chain 'Q' and resid 105 through 116 Processing helix chain 'Q' and resid 125 through 141 removed outlier: 3.524A pdb=" N LEU Q 140 " --> pdb=" O LEU Q 136 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS Q 141 " --> pdb=" O THR Q 137 " (cutoff:3.500A) Processing helix chain 'Q' and resid 147 through 166 Processing helix chain 'Q' and resid 173 through 187 Processing helix chain 'Q' and resid 193 through 204 Processing helix chain 'Q' and resid 219 through 232 removed outlier: 3.561A pdb=" N MET Q 229 " --> pdb=" O LEU Q 225 " (cutoff:3.500A) Processing helix chain 'R' and resid 15 through 36 Processing helix chain 'R' and resid 43 through 55 removed outlier: 3.673A pdb=" N TYR R 49 " --> pdb=" O ILE R 45 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ASP R 51 " --> pdb=" O GLU R 47 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL R 52 " --> pdb=" O ASP R 48 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N TRP R 55 " --> pdb=" O ASP R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 70 Processing helix chain 'R' and resid 78 through 96 Processing helix chain 'R' and resid 105 through 117 Processing helix chain 'R' and resid 121 through 123 No H-bonds generated for 'chain 'R' and resid 121 through 123' Processing helix chain 'R' and resid 125 through 142 removed outlier: 3.949A pdb=" N ASN R 142 " --> pdb=" O ASP R 138 " (cutoff:3.500A) Processing helix chain 'R' and resid 147 through 166 Processing helix chain 'R' and resid 173 through 186 Processing helix chain 'R' and resid 193 through 206 Processing helix chain 'R' and resid 219 through 234 Processing helix chain 'S' and resid 15 through 36 removed outlier: 3.506A pdb=" N HIS S 19 " --> pdb=" O SER S 15 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 53 removed outlier: 3.679A pdb=" N TYR S 49 " --> pdb=" O ILE S 45 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N ASP S 51 " --> pdb=" O GLU S 47 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL S 52 " --> pdb=" O ASP S 48 " (cutoff:3.500A) Processing helix chain 'S' and resid 63 through 71 Processing helix chain 'S' and resid 78 through 98 removed outlier: 4.015A pdb=" N ILE S 98 " --> pdb=" O LEU S 94 " (cutoff:3.500A) Processing helix chain 'S' and resid 105 through 116 Processing helix chain 'S' and resid 121 through 123 No H-bonds generated for 'chain 'S' and resid 121 through 123' Processing helix chain 'S' and resid 125 through 142 removed outlier: 3.694A pdb=" N LEU S 140 " --> pdb=" O LEU S 136 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS S 141 " --> pdb=" O THR S 137 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ASN S 142 " --> pdb=" O ASP S 138 " (cutoff:3.500A) Processing helix chain 'S' and resid 147 through 166 removed outlier: 3.541A pdb=" N GLN S 165 " --> pdb=" O MET S 161 " (cutoff:3.500A) Processing helix chain 'S' and resid 173 through 186 Processing helix chain 'S' and resid 194 through 206 Processing helix chain 'a' and resid 19 through 32 Processing helix chain 'a' and resid 46 through 49 No H-bonds generated for 'chain 'a' and resid 46 through 49' Processing helix chain 'a' and resid 52 through 74 Processing helix chain 'a' and resid 85 through 87 No H-bonds generated for 'chain 'a' and resid 85 through 87' Processing helix chain 'a' and resid 92 through 131 Processing helix chain 'a' and resid 180 through 190 Processing helix chain 'a' and resid 227 through 239 Processing helix chain 'a' and resid 252 through 308 Processing helix chain 'a' and resid 327 through 343 Processing helix chain 'a' and resid 371 through 381 removed outlier: 3.987A pdb=" N TYR a 381 " --> pdb=" O ILE a 377 " (cutoff:3.500A) Processing helix chain 'a' and resid 392 through 406 removed outlier: 4.686A pdb=" N ILE a 397 " --> pdb=" O PRO a 393 " (cutoff:3.500A) Proline residue: a 400 - end of helix Processing helix chain 'a' and resid 410 through 425 Processing helix chain 'a' and resid 427 through 431 Processing helix chain 'a' and resid 438 through 445 Processing helix chain 'a' and resid 447 through 464 Processing helix chain 'a' and resid 482 through 487 removed outlier: 3.631A pdb=" N ILE a 487 " --> pdb=" O PRO a 483 " (cutoff:3.500A) Processing helix chain 'a' and resid 493 through 499 removed outlier: 3.753A pdb=" N SER a 498 " --> pdb=" O THR a 494 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N SER a 499 " --> pdb=" O LEU a 495 " (cutoff:3.500A) Processing helix chain 'a' and resid 521 through 525 Processing helix chain 'a' and resid 529 through 562 removed outlier: 4.577A pdb=" N ASN a 534 " --> pdb=" O LEU a 530 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER a 556 " --> pdb=" O GLY a 552 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU a 557 " --> pdb=" O VAL a 553 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE a 558 " --> pdb=" O SER a 554 " (cutoff:3.500A) Processing helix chain 'a' and resid 566 through 570 Processing helix chain 'a' and resid 573 through 597 removed outlier: 4.227A pdb=" N TYR a 586 " --> pdb=" O SER a 582 " (cutoff:3.500A) Processing helix chain 'a' and resid 600 through 602 No H-bonds generated for 'chain 'a' and resid 600 through 602' Processing helix chain 'a' and resid 609 through 618 Processing helix chain 'a' and resid 633 through 646 Processing helix chain 'a' and resid 648 through 666 removed outlier: 5.798A pdb=" N LYS a 655 " --> pdb=" O MET a 651 " (cutoff:3.500A) Proline residue: a 656 - end of helix Processing helix chain 'a' and resid 714 through 758 removed outlier: 3.572A pdb=" N ILE a 733 " --> pdb=" O CYS a 729 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU a 740 " --> pdb=" O THR a 736 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ARG a 741 " --> pdb=" O ALA a 737 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N LEU a 742 " --> pdb=" O SER a 738 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N TRP a 743 " --> pdb=" O TYR a 739 " (cutoff:3.500A) Processing helix chain 'a' and resid 762 through 764 No H-bonds generated for 'chain 'a' and resid 762 through 764' Processing helix chain 'a' and resid 769 through 790 Processing helix chain 'a' and resid 794 through 809 Processing helix chain 'a' and resid 812 through 814 No H-bonds generated for 'chain 'a' and resid 812 through 814' Processing helix chain 'b' and resid 3 through 28 Processing helix chain 'b' and resid 37 through 43 Processing helix chain 'b' and resid 46 through 81 removed outlier: 3.666A pdb=" N SER b 61 " --> pdb=" O ALA b 57 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER b 75 " --> pdb=" O ILE b 71 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL b 81 " --> pdb=" O ILE b 77 " (cutoff:3.500A) Processing helix chain 'b' and resid 84 through 114 removed outlier: 3.596A pdb=" N LYS b 87 " --> pdb=" O PRO b 84 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ASN b 90 " --> pdb=" O LYS b 87 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N LEU b 91 " --> pdb=" O THR b 88 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE b 96 " --> pdb=" O SER b 93 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE b 106 " --> pdb=" O TYR b 103 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE b 111 " --> pdb=" O ALA b 108 " (cutoff:3.500A) Processing helix chain 'b' and resid 128 through 166 Processing helix chain 'b' and resid 170 through 197 removed outlier: 3.740A pdb=" N PHE b 173 " --> pdb=" O PRO b 170 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N VAL b 174 " --> pdb=" O SER b 171 " (cutoff:3.500A) Processing helix chain 'c' and resid 417 through 441 Processing helix chain 'd' and resid 9 through 26 removed outlier: 6.519A pdb=" N TYR d 15 " --> pdb=" O VAL d 11 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N LEU d 16 " --> pdb=" O ASP d 12 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY d 26 " --> pdb=" O GLY d 22 " (cutoff:3.500A) Processing helix chain 'd' and resid 30 through 37 Processing helix chain 'd' and resid 42 through 51 removed outlier: 3.914A pdb=" N SER d 51 " --> pdb=" O LEU d 47 " (cutoff:3.500A) Processing helix chain 'd' and resid 67 through 87 Processing helix chain 'd' and resid 91 through 115 removed outlier: 4.898A pdb=" N PHE d 96 " --> pdb=" O PRO d 92 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE d 100 " --> pdb=" O PHE d 96 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TYR d 104 " --> pdb=" O ILE d 100 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP d 107 " --> pdb=" O SER d 103 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N THR d 114 " --> pdb=" O ILE d 110 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY d 115 " --> pdb=" O LEU d 111 " (cutoff:3.500A) Processing helix chain 'd' and resid 122 through 128 Proline residue: d 127 - end of helix Processing helix chain 'd' and resid 147 through 156 Processing helix chain 'd' and resid 159 through 166 removed outlier: 4.100A pdb=" N ALA d 162 " --> pdb=" O PRO d 159 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP d 166 " --> pdb=" O PHE d 163 " (cutoff:3.500A) Processing helix chain 'd' and resid 171 through 175 Processing helix chain 'd' and resid 178 through 199 Processing helix chain 'd' and resid 203 through 229 Proline residue: d 210 - end of helix removed outlier: 3.549A pdb=" N PHE d 228 " --> pdb=" O THR d 224 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N GLY d 229 " --> pdb=" O ILE d 225 " (cutoff:3.500A) Processing helix chain 'd' and resid 234 through 240 removed outlier: 3.637A pdb=" N LEU d 240 " --> pdb=" O ASP d 236 " (cutoff:3.500A) Processing helix chain 'd' and resid 252 through 257 Processing helix chain 'd' and resid 261 through 270 removed outlier: 3.990A pdb=" N TYR d 270 " --> pdb=" O ASN d 266 " (cutoff:3.500A) Processing helix chain 'd' and resid 272 through 280 removed outlier: 4.437A pdb=" N LEU d 277 " --> pdb=" O GLU d 273 " (cutoff:3.500A) Processing helix chain 'd' and resid 290 through 307 removed outlier: 4.145A pdb=" N PHE d 306 " --> pdb=" O ASN d 302 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU d 307 " --> pdb=" O LYS d 303 " (cutoff:3.500A) Processing helix chain 'd' and resid 313 through 337 Processing helix chain 'd' and resid 341 through 343 No H-bonds generated for 'chain 'd' and resid 341 through 343' Processing helix chain 'e' and resid 6 through 22 Processing helix chain 'e' and resid 24 through 26 No H-bonds generated for 'chain 'e' and resid 24 through 26' Processing helix chain 'e' and resid 34 through 57 Processing helix chain 'e' and resid 70 through 78 removed outlier: 3.575A pdb=" N ARG e 77 " --> pdb=" O ILE e 73 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N PHE e 78 " --> pdb=" O TRP e 74 " (cutoff:3.500A) Processing helix chain 'f' and resid 9 through 35 Processing helix chain 'f' and resid 55 through 89 Processing helix chain 'g' and resid 11 through 45 removed outlier: 4.138A pdb=" N GLY g 15 " --> pdb=" O SER g 11 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET g 23 " --> pdb=" O ALA g 19 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER g 26 " --> pdb=" O ALA g 22 " (cutoff:3.500A) Processing helix chain 'g' and resid 49 through 51 No H-bonds generated for 'chain 'g' and resid 49 through 51' Processing helix chain 'g' and resid 54 through 79 Proline residue: g 58 - end of helix removed outlier: 3.519A pdb=" N VAL g 74 " --> pdb=" O VAL g 71 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE g 76 " --> pdb=" O ALA g 73 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN g 78 " --> pdb=" O LEU g 75 " (cutoff:3.500A) Processing helix chain 'g' and resid 87 through 123 Processing helix chain 'g' and resid 125 through 154 removed outlier: 4.344A pdb=" N VAL g 129 " --> pdb=" O ARG g 126 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL g 148 " --> pdb=" O GLY g 145 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU g 152 " --> pdb=" O ALA g 149 " (cutoff:3.500A) Processing helix chain 'h' and resid 11 through 45 removed outlier: 3.775A pdb=" N PHE h 14 " --> pdb=" O SER h 11 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA h 22 " --> pdb=" O ALA h 19 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE h 25 " --> pdb=" O ALA h 22 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS h 36 " --> pdb=" O GLY h 33 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY h 38 " --> pdb=" O ALA h 35 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N SER h 45 " --> pdb=" O ALA h 42 " (cutoff:3.500A) Processing helix chain 'h' and resid 49 through 51 No H-bonds generated for 'chain 'h' and resid 49 through 51' Processing helix chain 'h' and resid 57 through 79 Processing helix chain 'h' and resid 87 through 123 Processing helix chain 'h' and resid 125 through 153 removed outlier: 4.163A pdb=" N VAL h 129 " --> pdb=" O ARG h 126 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER h 153 " --> pdb=" O LEU h 150 " (cutoff:3.500A) Processing helix chain 'i' and resid 11 through 47 removed outlier: 4.261A pdb=" N GLY i 15 " --> pdb=" O SER i 11 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N MET i 23 " --> pdb=" O ALA i 19 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER i 26 " --> pdb=" O ALA i 22 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N MET i 47 " --> pdb=" O ALA i 43 " (cutoff:3.500A) Processing helix chain 'i' and resid 49 through 51 No H-bonds generated for 'chain 'i' and resid 49 through 51' Processing helix chain 'i' and resid 57 through 79 Processing helix chain 'i' and resid 87 through 123 removed outlier: 3.900A pdb=" N GLN i 123 " --> pdb=" O ARG i 119 " (cutoff:3.500A) Processing helix chain 'i' and resid 125 through 153 removed outlier: 4.003A pdb=" N VAL i 129 " --> pdb=" O ARG i 126 " (cutoff:3.500A) Processing helix chain 'j' and resid 11 through 47 removed outlier: 3.659A pdb=" N PHE j 14 " --> pdb=" O SER j 11 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL j 16 " --> pdb=" O PHE j 13 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA j 22 " --> pdb=" O ALA j 19 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE j 25 " --> pdb=" O ALA j 22 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY j 38 " --> pdb=" O ALA j 35 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER j 45 " --> pdb=" O ALA j 42 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL j 46 " --> pdb=" O ALA j 43 " (cutoff:3.500A) Processing helix chain 'j' and resid 49 through 51 No H-bonds generated for 'chain 'j' and resid 49 through 51' Processing helix chain 'j' and resid 54 through 79 Proline residue: j 58 - end of helix removed outlier: 3.557A pdb=" N MET j 61 " --> pdb=" O PRO j 58 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL j 74 " --> pdb=" O VAL j 71 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE j 76 " --> pdb=" O ALA j 73 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN j 78 " --> pdb=" O LEU j 75 " (cutoff:3.500A) Processing helix chain 'j' and resid 87 through 123 Processing helix chain 'j' and resid 125 through 153 removed outlier: 3.988A pdb=" N VAL j 129 " --> pdb=" O ARG j 126 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N SER j 153 " --> pdb=" O LEU j 150 " (cutoff:3.500A) Processing helix chain 'k' and resid 11 through 47 removed outlier: 4.313A pdb=" N GLY k 15 " --> pdb=" O SER k 11 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET k 23 " --> pdb=" O ALA k 19 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL k 46 " --> pdb=" O ALA k 42 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N MET k 47 " --> pdb=" O ALA k 43 " (cutoff:3.500A) Processing helix chain 'k' and resid 49 through 51 No H-bonds generated for 'chain 'k' and resid 49 through 51' Processing helix chain 'k' and resid 54 through 79 Proline residue: k 58 - end of helix removed outlier: 3.518A pdb=" N ILE k 76 " --> pdb=" O ALA k 73 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN k 78 " --> pdb=" O LEU k 75 " (cutoff:3.500A) Processing helix chain 'k' and resid 87 through 123 Processing helix chain 'k' and resid 125 through 153 removed outlier: 4.215A pdb=" N VAL k 129 " --> pdb=" O ARG k 126 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER k 153 " --> pdb=" O LEU k 150 " (cutoff:3.500A) Processing helix chain 'l' and resid 11 through 47 removed outlier: 3.638A pdb=" N PHE l 14 " --> pdb=" O SER l 11 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER l 20 " --> pdb=" O MET l 17 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA l 22 " --> pdb=" O ALA l 19 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE l 25 " --> pdb=" O ALA l 22 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA l 30 " --> pdb=" O ALA l 27 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS l 36 " --> pdb=" O GLY l 33 " (cutoff:3.500A) Processing helix chain 'l' and resid 49 through 51 No H-bonds generated for 'chain 'l' and resid 49 through 51' Processing helix chain 'l' and resid 54 through 79 Proline residue: l 58 - end of helix removed outlier: 3.526A pdb=" N ILE l 76 " --> pdb=" O ALA l 73 " (cutoff:3.500A) Processing helix chain 'l' and resid 87 through 123 removed outlier: 3.737A pdb=" N GLN l 123 " --> pdb=" O ARG l 119 " (cutoff:3.500A) Processing helix chain 'l' and resid 125 through 154 removed outlier: 3.893A pdb=" N VAL l 129 " --> pdb=" O ARG l 126 " (cutoff:3.500A) Processing helix chain 'm' and resid 11 through 46 removed outlier: 3.641A pdb=" N SER m 26 " --> pdb=" O ALA m 22 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL m 46 " --> pdb=" O ALA m 42 " (cutoff:3.500A) Processing helix chain 'm' and resid 49 through 51 No H-bonds generated for 'chain 'm' and resid 49 through 51' Processing helix chain 'm' and resid 53 through 55 No H-bonds generated for 'chain 'm' and resid 53 through 55' Processing helix chain 'm' and resid 57 through 79 Processing helix chain 'm' and resid 87 through 123 removed outlier: 3.990A pdb=" N GLN m 123 " --> pdb=" O ARG m 119 " (cutoff:3.500A) Processing helix chain 'm' and resid 125 through 154 removed outlier: 3.763A pdb=" N VAL m 129 " --> pdb=" O ARG m 126 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER m 153 " --> pdb=" O LEU m 150 " (cutoff:3.500A) Processing helix chain 'n' and resid 11 through 47 removed outlier: 3.693A pdb=" N PHE n 14 " --> pdb=" O SER n 11 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER n 20 " --> pdb=" O MET n 17 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA n 22 " --> pdb=" O ALA n 19 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE n 25 " --> pdb=" O ALA n 22 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS n 36 " --> pdb=" O GLY n 33 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY n 38 " --> pdb=" O ALA n 35 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER n 45 " --> pdb=" O ALA n 42 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL n 46 " --> pdb=" O ALA n 43 " (cutoff:3.500A) Processing helix chain 'n' and resid 49 through 51 No H-bonds generated for 'chain 'n' and resid 49 through 51' Processing helix chain 'n' and resid 57 through 79 removed outlier: 3.567A pdb=" N SER n 79 " --> pdb=" O LEU n 75 " (cutoff:3.500A) Processing helix chain 'n' and resid 87 through 123 removed outlier: 3.590A pdb=" N ARG n 119 " --> pdb=" O ASP n 115 " (cutoff:3.500A) Processing helix chain 'n' and resid 125 through 154 removed outlier: 4.105A pdb=" N VAL n 129 " --> pdb=" O ARG n 126 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER n 153 " --> pdb=" O LEU n 150 " (cutoff:3.500A) Processing helix chain 'o' and resid 11 through 47 removed outlier: 4.370A pdb=" N GLY o 15 " --> pdb=" O SER o 11 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N MET o 47 " --> pdb=" O ALA o 43 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 51 No H-bonds generated for 'chain 'o' and resid 49 through 51' Processing helix chain 'o' and resid 54 through 79 removed outlier: 3.837A pdb=" N ILE o 57 " --> pdb=" O LYS o 54 " (cutoff:3.500A) Proline residue: o 58 - end of helix removed outlier: 3.509A pdb=" N VAL o 72 " --> pdb=" O GLY o 69 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL o 74 " --> pdb=" O VAL o 71 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE o 76 " --> pdb=" O ALA o 73 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASN o 78 " --> pdb=" O LEU o 75 " (cutoff:3.500A) Processing helix chain 'o' and resid 87 through 123 Processing helix chain 'o' and resid 125 through 154 removed outlier: 4.238A pdb=" N VAL o 129 " --> pdb=" O ARG o 126 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER o 153 " --> pdb=" O LEU o 150 " (cutoff:3.500A) Processing helix chain 'p' and resid 303 through 329 Processing helix chain 'p' and resid 339 through 342 No H-bonds generated for 'chain 'p' and resid 339 through 342' Processing sheet with id= A, first strand: chain 'A' and resid 78 through 80 removed outlier: 6.478A pdb=" N THR A 30 " --> pdb=" O HIS A 22 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N VAL A 24 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N VAL A 28 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG A 56 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N GLN A 65 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ILE A 54 " --> pdb=" O GLN A 65 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N GLU A 41 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N LYS A 84 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N ARG A 44 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N THR A 82 " --> pdb=" O ARG A 44 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 87 through 90 Processing sheet with id= C, first strand: chain 'A' and resid 183 through 185 Processing sheet with id= D, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.319A pdb=" N GLU A 195 " --> pdb=" O VAL A 176 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N VAL A 176 " --> pdb=" O GLU A 195 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 245 through 248 removed outlier: 8.571A pdb=" N THR A 246 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE A 406 " --> pdb=" O THR A 246 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ILE A 248 " --> pdb=" O ILE A 406 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N GLY A 408 " --> pdb=" O ILE A 248 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 272 through 277 Processing sheet with id= G, first strand: chain 'A' and resid 390 through 393 Processing sheet with id= H, first strand: chain 'B' and resid 18 through 20 removed outlier: 6.881A pdb=" N THR B 63 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N LEU B 57 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N MET B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N CYS B 32 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N VAL B 21 " --> pdb=" O CYS B 32 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 87 through 90 Processing sheet with id= J, first strand: chain 'B' and resid 183 through 185 removed outlier: 6.909A pdb=" N ILE B 166 " --> pdb=" O TYR B 153 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ILE B 155 " --> pdb=" O HIS B 164 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N HIS B 164 " --> pdb=" O ILE B 155 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 199 through 203 removed outlier: 6.175A pdb=" N GLU B 195 " --> pdb=" O VAL B 176 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N VAL B 176 " --> pdb=" O GLU B 195 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 219 through 221 removed outlier: 4.066A pdb=" N ARG B 391 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 245 through 247 removed outlier: 8.414A pdb=" N THR B 246 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ILE B 406 " --> pdb=" O THR B 246 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL B 271 " --> pdb=" O SER B 345 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N MET B 347 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE B 273 " --> pdb=" O MET B 347 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 295 through 297 Processing sheet with id= O, first strand: chain 'C' and resid 18 through 20 removed outlier: 3.557A pdb=" N LEU C 42 " --> pdb=" O THR C 82 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N CYS C 32 " --> pdb=" O VAL C 21 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N VAL C 21 " --> pdb=" O CYS C 32 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 87 through 90 Processing sheet with id= Q, first strand: chain 'C' and resid 183 through 185 removed outlier: 4.721A pdb=" N GLU C 134 " --> pdb=" O ASN C 157 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ILE C 166 " --> pdb=" O TYR C 153 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N ILE C 155 " --> pdb=" O HIS C 164 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N HIS C 164 " --> pdb=" O ILE C 155 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 199 through 203 removed outlier: 6.263A pdb=" N GLU C 195 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N VAL C 176 " --> pdb=" O GLU C 195 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 309 through 312 removed outlier: 6.306A pdb=" N ILE C 272 " --> pdb=" O ALA C 310 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N VAL C 312 " --> pdb=" O ILE C 272 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TYR C 274 " --> pdb=" O VAL C 312 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N VAL C 344 " --> pdb=" O GLU C 401 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N SER C 403 " --> pdb=" O VAL C 344 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N MET C 346 " --> pdb=" O SER C 403 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N SER C 405 " --> pdb=" O MET C 346 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N ALA C 348 " --> pdb=" O SER C 405 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 295 through 297 Processing sheet with id= U, first strand: chain 'D' and resid 50 through 54 removed outlier: 6.807A pdb=" N ILE D 59 " --> pdb=" O SER D 51 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N VAL D 53 " --> pdb=" O LEU D 57 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LEU D 57 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU D 88 " --> pdb=" O VAL D 95 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLN D 97 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N VAL D 86 " --> pdb=" O GLN D 97 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 120 through 123 Processing sheet with id= W, first strand: chain 'D' and resid 131 through 133 removed outlier: 7.955A pdb=" N PHE D 132 " --> pdb=" O VAL D 257 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N LEU D 259 " --> pdb=" O PHE D 132 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE D 229 " --> pdb=" O CYS D 258 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N PHE D 260 " --> pdb=" O ILE D 229 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N PHE D 231 " --> pdb=" O PHE D 260 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ASN D 262 " --> pdb=" O PHE D 231 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALA D 233 " --> pdb=" O ASN D 262 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N SER D 347 " --> pdb=" O VAL D 293 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N VAL D 295 " --> pdb=" O SER D 347 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N THR D 349 " --> pdb=" O VAL D 295 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N LEU D 297 " --> pdb=" O THR D 349 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE D 351 " --> pdb=" O LEU D 297 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 50 through 54 removed outlier: 6.724A pdb=" N ILE E 59 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N VAL E 53 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU E 57 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU E 88 " --> pdb=" O VAL E 95 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N GLN E 97 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N VAL E 86 " --> pdb=" O GLN E 97 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 120 through 123 Processing sheet with id= Z, first strand: chain 'E' and resid 130 through 133 removed outlier: 3.642A pdb=" N ARG E 130 " --> pdb=" O VAL E 257 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE E 229 " --> pdb=" O CYS E 258 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N PHE E 260 " --> pdb=" O ILE E 229 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N PHE E 231 " --> pdb=" O PHE E 260 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ASN E 262 " --> pdb=" O PHE E 231 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N ALA E 233 " --> pdb=" O ASN E 262 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N SER E 347 " --> pdb=" O VAL E 293 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N VAL E 295 " --> pdb=" O SER E 347 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N THR E 349 " --> pdb=" O VAL E 295 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N LEU E 297 " --> pdb=" O THR E 349 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 191 through 193 Processing sheet with id= AB, first strand: chain 'F' and resid 50 through 54 removed outlier: 6.651A pdb=" N ILE F 59 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N VAL F 53 " --> pdb=" O LEU F 57 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU F 57 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA F 94 " --> pdb=" O LEU F 60 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLN F 97 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL F 86 " --> pdb=" O GLN F 97 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 120 through 123 Processing sheet with id= AD, first strand: chain 'F' and resid 131 through 133 removed outlier: 8.181A pdb=" N PHE F 132 " --> pdb=" O VAL F 257 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU F 259 " --> pdb=" O PHE F 132 " (cutoff:3.500A) removed outlier: 8.750A pdb=" N CYS F 258 " --> pdb=" O PHE F 227 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE F 229 " --> pdb=" O CYS F 258 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N PHE F 260 " --> pdb=" O ILE F 229 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N PHE F 231 " --> pdb=" O PHE F 260 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ASN F 262 " --> pdb=" O PHE F 231 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ALA F 233 " --> pdb=" O ASN F 262 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N HIS F 292 " --> pdb=" O ALA F 228 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL F 230 " --> pdb=" O HIS F 292 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LEU F 294 " --> pdb=" O VAL F 230 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ALA F 232 " --> pdb=" O LEU F 294 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE F 296 " --> pdb=" O ALA F 232 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N MET F 234 " --> pdb=" O ILE F 296 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N THR F 298 " --> pdb=" O MET F 234 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL F 236 " --> pdb=" O THR F 298 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N SER F 347 " --> pdb=" O VAL F 293 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N VAL F 295 " --> pdb=" O SER F 347 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N THR F 349 " --> pdb=" O VAL F 295 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N LEU F 297 " --> pdb=" O THR F 349 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain 'F' and resid 191 through 194 Processing sheet with id= AF, first strand: chain 'G' and resid 370 through 374 Processing sheet with id= AG, first strand: chain 'G' and resid 247 through 249 removed outlier: 6.399A pdb=" N ASN G 226 " --> pdb=" O VAL G 215 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N VAL G 215 " --> pdb=" O ASN G 226 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'H' and resid 93 through 99 Processing sheet with id= AI, first strand: chain 'I' and resid 164 through 167 removed outlier: 4.056A pdb=" N VAL I 181 " --> pdb=" O ASN I 194 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'J' and resid 164 through 167 removed outlier: 3.506A pdb=" N VAL J 181 " --> pdb=" O ASN J 194 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'K' and resid 164 through 167 Processing sheet with id= AL, first strand: chain 'L' and resid 36 through 38 removed outlier: 8.550A pdb=" N LEU L 37 " --> pdb=" O ILE L 8 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL L 10 " --> pdb=" O LEU L 37 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE L 63 " --> pdb=" O ALA L 9 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N ILE L 11 " --> pdb=" O ILE L 63 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU L 65 " --> pdb=" O ILE L 11 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'a' and resid 351 through 353 removed outlier: 3.512A pdb=" N ILE a 351 " --> pdb=" O PHE a 16 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLU a 322 " --> pdb=" O ARG a 38 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLN a 36 " --> pdb=" O TRP a 324 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'a' and resid 198 through 202 removed outlier: 4.519A pdb=" N LYS a 217 " --> pdb=" O ILE a 202 " (cutoff:3.500A) 3920 hydrogen bonds defined for protein. 9894 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: 19.79 Time building geometry restraints manager: 22.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 10391 1.30 - 1.43: 14561 1.43 - 1.56: 36122 1.56 - 1.69: 3 1.69 - 1.81: 561 Bond restraints: 61638 Sorted by residual: bond pdb=" C ASP B 290 " pdb=" N PHE B 291 " ideal model delta sigma weight residual 1.334 1.216 0.118 1.26e-02 6.30e+03 8.76e+01 bond pdb=" N PRO F 391 " pdb=" CA PRO F 391 " ideal model delta sigma weight residual 1.469 1.531 -0.063 7.40e-03 1.83e+04 7.16e+01 bond pdb=" C TYR E 504 " pdb=" N PRO E 505 " ideal model delta sigma weight residual 1.337 1.407 -0.070 1.06e-02 8.90e+03 4.38e+01 bond pdb=" N PRO E 352 " pdb=" CA PRO E 352 " ideal model delta sigma weight residual 1.466 1.537 -0.071 1.24e-02 6.50e+03 3.29e+01 bond pdb=" C ASN A 397 " pdb=" N PRO A 398 " ideal model delta sigma weight residual 1.336 1.397 -0.061 1.08e-02 8.57e+03 3.19e+01 ... (remaining 61633 not shown) Histogram of bond angle deviations from ideal: 99.58 - 106.50: 1655 106.50 - 113.43: 33819 113.43 - 120.35: 25449 120.35 - 127.28: 22372 127.28 - 134.20: 378 Bond angle restraints: 83673 Sorted by residual: angle pdb=" C ILE F 189 " pdb=" N PRO F 190 " pdb=" CA PRO F 190 " ideal model delta sigma weight residual 119.85 129.35 -9.50 1.01e+00 9.80e-01 8.85e+01 angle pdb=" C ARG A 215 " pdb=" N PRO A 216 " pdb=" CA PRO A 216 " ideal model delta sigma weight residual 119.76 129.35 -9.59 1.03e+00 9.43e-01 8.66e+01 angle pdb=" C SER B 411 " pdb=" N PRO B 412 " pdb=" CA PRO B 412 " ideal model delta sigma weight residual 120.38 129.06 -8.68 1.03e+00 9.43e-01 7.10e+01 angle pdb=" C ILE L 91 " pdb=" N PRO L 92 " pdb=" CA PRO L 92 " ideal model delta sigma weight residual 119.76 127.77 -8.01 1.00e+00 1.00e+00 6.42e+01 angle pdb=" C LEU F 395 " pdb=" N PRO F 396 " pdb=" CA PRO F 396 " ideal model delta sigma weight residual 120.04 128.50 -8.46 1.08e+00 8.57e-01 6.14e+01 ... (remaining 83668 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.67: 36325 23.67 - 47.34: 640 47.34 - 71.01: 143 71.01 - 94.68: 57 94.68 - 118.35: 2 Dihedral angle restraints: 37167 sinusoidal: 12878 harmonic: 24289 Sorted by residual: dihedral pdb=" C5' ADP A 701 " pdb=" O5' ADP A 701 " pdb=" PA ADP A 701 " pdb=" O2A ADP A 701 " ideal model delta sinusoidal sigma weight residual -60.00 -178.35 118.35 1 2.00e+01 2.50e-03 3.54e+01 dihedral pdb=" CA GLY O 64 " pdb=" C GLY O 64 " pdb=" N SER O 65 " pdb=" CA SER O 65 " ideal model delta harmonic sigma weight residual 180.00 -152.25 -27.75 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" O2A ADP A 701 " pdb=" O3A ADP A 701 " pdb=" PA ADP A 701 " pdb=" PB ADP A 701 " ideal model delta sinusoidal sigma weight residual -60.00 38.47 -98.47 1 2.00e+01 2.50e-03 2.75e+01 ... (remaining 37164 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 7026 0.063 - 0.125: 2278 0.125 - 0.188: 413 0.188 - 0.250: 145 0.250 - 0.313: 9 Chirality restraints: 9871 Sorted by residual: chirality pdb=" CA TYR o 68 " pdb=" N TYR o 68 " pdb=" C TYR o 68 " pdb=" CB TYR o 68 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" CA TYR l 68 " pdb=" N TYR l 68 " pdb=" C TYR l 68 " pdb=" CB TYR l 68 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CA MET a 10 " pdb=" N MET a 10 " pdb=" C MET a 10 " pdb=" CB MET a 10 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 9868 not shown) Planarity restraints: 10900 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU o 86 " -0.023 2.00e-02 2.50e+03 4.57e-02 2.09e+01 pdb=" C LEU o 86 " 0.079 2.00e-02 2.50e+03 pdb=" O LEU o 86 " -0.029 2.00e-02 2.50e+03 pdb=" N TYR o 87 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR a 113 " 0.021 2.00e-02 2.50e+03 4.32e-02 1.87e+01 pdb=" C THR a 113 " -0.075 2.00e-02 2.50e+03 pdb=" O THR a 113 " 0.028 2.00e-02 2.50e+03 pdb=" N ASN a 114 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN k 7 " -0.022 2.00e-02 2.50e+03 4.30e-02 1.85e+01 pdb=" C ASN k 7 " 0.074 2.00e-02 2.50e+03 pdb=" O ASN k 7 " -0.028 2.00e-02 2.50e+03 pdb=" N PRO k 8 " -0.025 2.00e-02 2.50e+03 ... (remaining 10897 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 9672 2.76 - 3.29: 65171 3.29 - 3.83: 102023 3.83 - 4.36: 123320 4.36 - 4.90: 202631 Nonbonded interactions: 502817 Sorted by model distance: nonbonded pdb=" N ASP a 208 " pdb=" O ASP a 213 " model vdw 2.220 2.520 nonbonded pdb=" OH TYR Q 126 " pdb=" OG1 THR Q 169 " model vdw 2.221 2.440 nonbonded pdb=" OD1 ASP D 266 " pdb=" NZ LYS S 9 " model vdw 2.305 2.520 nonbonded pdb=" CB ALA B 499 " pdb=" CA GLY H 103 " model vdw 2.331 3.860 nonbonded pdb=" O THR G 18 " pdb=" N LEU G 22 " model vdw 2.332 2.520 ... (remaining 502812 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' and resid 17 through 616) selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = (chain 'I' and resid 3 through 226) selection = chain 'J' selection = (chain 'K' and resid 3 through 226) } ncs_group { reference = (chain 'M' and resid 4 through 116) selection = (chain 'N' and resid 4 through 116) selection = chain 'O' } ncs_group { reference = (chain 'Q' and resid 12 through 218) selection = (chain 'R' and resid 12 through 218) selection = (chain 'S' and resid 12 through 218) } ncs_group { reference = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 311 5.16 5 C 38448 2.51 5 N 10527 2.21 5 O 11426 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.520 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: 0.050 Extract box with map and model: 12.080 Check model and map are aligned: 0.700 Convert atoms to be neutral: 0.400 Process input model: 124.280 Find NCS groups from input model: 2.750 Set up NCS constraints: 0.390 Set refine NCS operators: 0.000 Set scattering table: 0.030 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 144.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 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 : 0.009 0.118 61638 Z= 0.612 Angle : 0.975 10.874 83673 Z= 0.721 Chirality : 0.064 0.313 9871 Planarity : 0.005 0.046 10900 Dihedral : 10.703 118.352 21549 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.52 % Favored : 97.29 % Rotamer Outliers : 0.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.09), residues: 8369 helix: 0.90 (0.07), residues: 4959 sheet: -0.12 (0.18), residues: 703 loop : -0.18 (0.12), residues: 2707 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16738 Ramachandran restraints generated. 8369 Oldfield, 0 Emsley, 8369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16738 Ramachandran restraints generated. 8369 Oldfield, 0 Emsley, 8369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1996 residues out of total 7117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 1952 time to evaluate : 5.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 13 residues processed: 1974 average time/residue: 0.5795 time to fit residues: 1915.9624 Evaluate side-chains 1107 residues out of total 7117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 1094 time to evaluate : 5.600 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.4795 time to fit residues: 18.6466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 836 random chunks: chunk 705 optimal weight: 30.0000 chunk 633 optimal weight: 7.9990 chunk 351 optimal weight: 9.9990 chunk 216 optimal weight: 8.9990 chunk 427 optimal weight: 3.9990 chunk 338 optimal weight: 40.0000 chunk 655 optimal weight: 6.9990 chunk 253 optimal weight: 0.7980 chunk 398 optimal weight: 6.9990 chunk 487 optimal weight: 6.9990 chunk 759 optimal weight: 20.0000 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 GLN A 397 ASN ** A 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 GLN B 146 HIS B 314 ASN B 573 HIS ** C 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 181 ASN H 88 ASN H 137 ASN ** I 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 77 ASN ** J 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 34 GLN Q 207 GLN R 50 GLN R 207 GLN ** h 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 92 GLN ** j 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.110 61638 Z= 0.373 Angle : 0.744 13.412 83673 Z= 0.392 Chirality : 0.046 0.330 9871 Planarity : 0.006 0.105 10900 Dihedral : 4.657 109.727 9018 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.17 % Favored : 97.81 % Rotamer Outliers : 3.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % 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: 1.38 (0.09), residues: 8369 helix: 1.66 (0.07), residues: 4881 sheet: -0.13 (0.19), residues: 726 loop : -0.00 (0.12), residues: 2762 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16738 Ramachandran restraints generated. 8369 Oldfield, 0 Emsley, 8369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16738 Ramachandran restraints generated. 8369 Oldfield, 0 Emsley, 8369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1311 residues out of total 7117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 1107 time to evaluate : 5.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 204 outliers final: 110 residues processed: 1221 average time/residue: 0.5305 time to fit residues: 1107.5011 Evaluate side-chains 1036 residues out of total 7117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 926 time to evaluate : 5.602 Switching outliers to nearest non-outliers outliers start: 110 outliers final: 0 residues processed: 110 average time/residue: 0.4228 time to fit residues: 94.3426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 836 random chunks: chunk 421 optimal weight: 20.0000 chunk 235 optimal weight: 3.9990 chunk 631 optimal weight: 0.9990 chunk 516 optimal weight: 9.9990 chunk 209 optimal weight: 6.9990 chunk 760 optimal weight: 30.0000 chunk 821 optimal weight: 6.9990 chunk 677 optimal weight: 9.9990 chunk 754 optimal weight: 5.9990 chunk 259 optimal weight: 4.9990 chunk 610 optimal weight: 30.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 146 HIS ** A 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 GLN C 468 HIS ** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 187 GLN ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 160 GLN R 150 ASN S 198 HIS ** b 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 197 GLN d 10 ASN d 30 GLN ** d 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 123 GLN ** h 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 300 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.4090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.091 61638 Z= 0.326 Angle : 0.693 13.793 83673 Z= 0.359 Chirality : 0.044 0.460 9871 Planarity : 0.005 0.091 10900 Dihedral : 4.615 113.993 9018 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.87 % Favored : 97.12 % Rotamer Outliers : 1.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % 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: 1.29 (0.09), residues: 8369 helix: 1.63 (0.07), residues: 4898 sheet: -0.08 (0.19), residues: 710 loop : -0.18 (0.12), residues: 2761 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16738 Ramachandran restraints generated. 8369 Oldfield, 0 Emsley, 8369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16738 Ramachandran restraints generated. 8369 Oldfield, 0 Emsley, 8369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1091 residues out of total 7117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 979 time to evaluate : 5.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 112 outliers final: 49 residues processed: 1047 average time/residue: 0.5497 time to fit residues: 991.7458 Evaluate side-chains 901 residues out of total 7117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 852 time to evaluate : 5.620 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 0 residues processed: 49 average time/residue: 0.4528 time to fit residues: 48.8427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 836 random chunks: chunk 751 optimal weight: 30.0000 chunk 571 optimal weight: 30.0000 chunk 394 optimal weight: 40.0000 chunk 84 optimal weight: 4.9990 chunk 362 optimal weight: 5.9990 chunk 510 optimal weight: 1.9990 chunk 763 optimal weight: 40.0000 chunk 808 optimal weight: 20.0000 chunk 398 optimal weight: 10.0000 chunk 723 optimal weight: 20.0000 chunk 217 optimal weight: 4.9990 overall best weight: 5.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN A 573 HIS B 543 ASN ** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 ASN ** L 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 50 GLN S 50 GLN ** b 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.4678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.095 61638 Z= 0.369 Angle : 0.712 17.669 83673 Z= 0.367 Chirality : 0.044 0.258 9871 Planarity : 0.005 0.092 10900 Dihedral : 4.700 120.492 9018 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 19.02 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.36 % Favored : 96.63 % Rotamer Outliers : 2.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.09), residues: 8369 helix: 1.42 (0.07), residues: 4970 sheet: -0.17 (0.19), residues: 692 loop : -0.38 (0.12), residues: 2707 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16738 Ramachandran restraints generated. 8369 Oldfield, 0 Emsley, 8369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16738 Ramachandran restraints generated. 8369 Oldfield, 0 Emsley, 8369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1010 residues out of total 7117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 895 time to evaluate : 5.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 115 outliers final: 62 residues processed: 962 average time/residue: 0.5260 time to fit residues: 877.8299 Evaluate side-chains 888 residues out of total 7117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 826 time to evaluate : 5.592 Switching outliers to nearest non-outliers outliers start: 62 outliers final: 0 residues processed: 62 average time/residue: 0.4319 time to fit residues: 57.4736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 836 random chunks: chunk 673 optimal weight: 3.9990 chunk 458 optimal weight: 5.9990 chunk 11 optimal weight: 8.9990 chunk 601 optimal weight: 30.0000 chunk 333 optimal weight: 20.0000 chunk 689 optimal weight: 50.0000 chunk 558 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 412 optimal weight: 3.9990 chunk 725 optimal weight: 0.0870 chunk 203 optimal weight: 3.9990 overall best weight: 3.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 ASN B 543 ASN ** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 251 ASN ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 113 HIS ** I 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 198 HIS ** b 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 48 HIS d 340 HIS ** g 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 123 GLN j 123 GLN ** l 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.4958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.104 61638 Z= 0.275 Angle : 0.679 14.058 83673 Z= 0.345 Chirality : 0.044 0.260 9871 Planarity : 0.005 0.099 10900 Dihedral : 4.616 122.350 9018 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 17.73 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.31 % Favored : 96.68 % Rotamer Outliers : 1.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 1.10 (0.09), residues: 8369 helix: 1.51 (0.07), residues: 4971 sheet: -0.14 (0.20), residues: 663 loop : -0.38 (0.12), residues: 2735 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16738 Ramachandran restraints generated. 8369 Oldfield, 0 Emsley, 8369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16738 Ramachandran restraints generated. 8369 Oldfield, 0 Emsley, 8369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 975 residues out of total 7117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 912 time to evaluate : 5.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 27 residues processed: 943 average time/residue: 0.5430 time to fit residues: 889.5544 Evaluate side-chains 852 residues out of total 7117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 825 time to evaluate : 5.647 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.4584 time to fit residues: 30.2571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 836 random chunks: chunk 271 optimal weight: 4.9990 chunk 727 optimal weight: 20.0000 chunk 159 optimal weight: 8.9990 chunk 474 optimal weight: 20.0000 chunk 199 optimal weight: 6.9990 chunk 808 optimal weight: 40.0000 chunk 671 optimal weight: 0.8980 chunk 374 optimal weight: 50.0000 chunk 67 optimal weight: 4.9990 chunk 267 optimal weight: 3.9990 chunk 424 optimal weight: 9.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 ASN B 521 GLN ** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 91 GLN I 66 GLN ** I 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 177 GLN R 207 GLN S 19 HIS ** b 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 297 HIS d 340 HIS ** l 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.5273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.094 61638 Z= 0.311 Angle : 0.704 19.325 83673 Z= 0.358 Chirality : 0.044 0.261 9871 Planarity : 0.005 0.097 10900 Dihedral : 4.616 120.231 9018 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 18.80 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.84 % Favored : 96.15 % Rotamer Outliers : 1.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % 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: 1.03 (0.09), residues: 8369 helix: 1.47 (0.07), residues: 4949 sheet: -0.20 (0.20), residues: 655 loop : -0.45 (0.12), residues: 2765 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16738 Ramachandran restraints generated. 8369 Oldfield, 0 Emsley, 8369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16738 Ramachandran restraints generated. 8369 Oldfield, 0 Emsley, 8369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 960 residues out of total 7117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 869 time to evaluate : 5.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 91 outliers final: 43 residues processed: 917 average time/residue: 0.5316 time to fit residues: 850.7522 Evaluate side-chains 859 residues out of total 7117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 816 time to evaluate : 5.778 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.4398 time to fit residues: 42.9141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 836 random chunks: chunk 779 optimal weight: 40.0000 chunk 91 optimal weight: 0.7980 chunk 460 optimal weight: 40.0000 chunk 590 optimal weight: 40.0000 chunk 457 optimal weight: 6.9990 chunk 680 optimal weight: 5.9990 chunk 451 optimal weight: 30.0000 chunk 805 optimal weight: 4.9990 chunk 504 optimal weight: 10.0000 chunk 491 optimal weight: 2.9990 chunk 372 optimal weight: 7.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 ASN ** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 19 HIS ** b 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 123 GLN ** j 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.5517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.107 61638 Z= 0.311 Angle : 0.718 15.054 83673 Z= 0.363 Chirality : 0.044 0.331 9871 Planarity : 0.005 0.104 10900 Dihedral : 4.631 118.651 9018 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 19.63 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.85 % Favored : 96.14 % Rotamer Outliers : 1.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.09), residues: 8369 helix: 1.45 (0.07), residues: 4952 sheet: -0.23 (0.20), residues: 664 loop : -0.49 (0.12), residues: 2753 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16738 Ramachandran restraints generated. 8369 Oldfield, 0 Emsley, 8369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16738 Ramachandran restraints generated. 8369 Oldfield, 0 Emsley, 8369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 944 residues out of total 7117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 869 time to evaluate : 5.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 75 outliers final: 35 residues processed: 906 average time/residue: 0.5478 time to fit residues: 871.0309 Evaluate side-chains 843 residues out of total 7117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 808 time to evaluate : 5.678 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.4644 time to fit residues: 37.5757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 836 random chunks: chunk 498 optimal weight: 0.4980 chunk 321 optimal weight: 10.0000 chunk 481 optimal weight: 3.9990 chunk 242 optimal weight: 9.9990 chunk 158 optimal weight: 0.8980 chunk 156 optimal weight: 1.9990 chunk 512 optimal weight: 9.9990 chunk 548 optimal weight: 50.0000 chunk 398 optimal weight: 7.9990 chunk 75 optimal weight: 0.9980 chunk 633 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 ASN ** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 197 GLN ** g 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.5619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.162 61638 Z= 0.220 Angle : 0.735 18.776 83673 Z= 0.363 Chirality : 0.045 0.303 9871 Planarity : 0.005 0.115 10900 Dihedral : 4.545 118.412 9018 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.31 % Favored : 96.68 % Rotamer Outliers : 0.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 1.10 (0.09), residues: 8369 helix: 1.54 (0.07), residues: 4956 sheet: 0.00 (0.21), residues: 605 loop : -0.50 (0.12), residues: 2808 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16738 Ramachandran restraints generated. 8369 Oldfield, 0 Emsley, 8369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16738 Ramachandran restraints generated. 8369 Oldfield, 0 Emsley, 8369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 966 residues out of total 7117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 923 time to evaluate : 5.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 23 residues processed: 943 average time/residue: 0.5426 time to fit residues: 891.4252 Evaluate side-chains 855 residues out of total 7117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 832 time to evaluate : 5.635 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.4680 time to fit residues: 27.0518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 836 random chunks: chunk 732 optimal weight: 6.9990 chunk 771 optimal weight: 40.0000 chunk 704 optimal weight: 7.9990 chunk 750 optimal weight: 6.9990 chunk 451 optimal weight: 9.9990 chunk 327 optimal weight: 30.0000 chunk 589 optimal weight: 50.0000 chunk 230 optimal weight: 8.9990 chunk 678 optimal weight: 20.0000 chunk 710 optimal weight: 20.0000 chunk 748 optimal weight: 0.0770 overall best weight: 6.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 HIS ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 345 ASN ** E 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 71 GLN ** J 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 89 GLN ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 117 GLN S 177 GLN ** b 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.5893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.277 61638 Z= 0.415 Angle : 0.800 16.286 83673 Z= 0.407 Chirality : 0.046 0.312 9871 Planarity : 0.005 0.113 10900 Dihedral : 4.719 117.204 9018 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 22.15 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.19 % Favored : 95.79 % Rotamer Outliers : 0.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.09), residues: 8369 helix: 1.41 (0.07), residues: 4978 sheet: -0.16 (0.20), residues: 672 loop : -0.66 (0.12), residues: 2719 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16738 Ramachandran restraints generated. 8369 Oldfield, 0 Emsley, 8369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16738 Ramachandran restraints generated. 8369 Oldfield, 0 Emsley, 8369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 849 residues out of total 7117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 808 time to evaluate : 5.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 30 residues processed: 827 average time/residue: 0.5606 time to fit residues: 809.4479 Evaluate side-chains 800 residues out of total 7117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 770 time to evaluate : 5.765 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.4768 time to fit residues: 33.8075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 836 random chunks: chunk 493 optimal weight: 3.9990 chunk 794 optimal weight: 30.0000 chunk 484 optimal weight: 0.9980 chunk 376 optimal weight: 10.0000 chunk 551 optimal weight: 30.0000 chunk 832 optimal weight: 0.0970 chunk 766 optimal weight: 9.9990 chunk 663 optimal weight: 10.0000 chunk 68 optimal weight: 0.1980 chunk 512 optimal weight: 8.9990 chunk 406 optimal weight: 10.0000 overall best weight: 2.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 GLN ** E 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 89 GLN ** b 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.5992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.476 61638 Z= 0.309 Angle : 0.798 23.162 83673 Z= 0.399 Chirality : 0.046 0.393 9871 Planarity : 0.005 0.131 10900 Dihedral : 4.678 117.240 9018 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 19.87 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.67 % Favored : 96.32 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.09), residues: 8369 helix: 1.42 (0.07), residues: 4973 sheet: -0.22 (0.20), residues: 677 loop : -0.56 (0.12), residues: 2719 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16738 Ramachandran restraints generated. 8369 Oldfield, 0 Emsley, 8369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16738 Ramachandran restraints generated. 8369 Oldfield, 0 Emsley, 8369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 850 residues out of total 7117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 827 time to evaluate : 5.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 12 residues processed: 837 average time/residue: 0.5359 time to fit residues: 781.1636 Evaluate side-chains 803 residues out of total 7117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 791 time to evaluate : 5.604 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.4597 time to fit residues: 17.4539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 836 random chunks: chunk 526 optimal weight: 9.9990 chunk 706 optimal weight: 20.0000 chunk 203 optimal weight: 10.0000 chunk 611 optimal weight: 50.0000 chunk 97 optimal weight: 5.9990 chunk 184 optimal weight: 6.9990 chunk 664 optimal weight: 10.0000 chunk 278 optimal weight: 0.9990 chunk 682 optimal weight: 40.0000 chunk 84 optimal weight: 6.9990 chunk 122 optimal weight: 0.8980 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.083287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.056484 restraints weight = 281208.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.057957 restraints weight = 147673.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.058738 restraints weight = 90204.004| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.6160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.185 61638 Z= 0.334 Angle : 0.806 23.900 83673 Z= 0.404 Chirality : 0.047 0.407 9871 Planarity : 0.005 0.118 10900 Dihedral : 4.736 116.511 9018 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 21.51 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.23 % Favored : 95.76 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.09), residues: 8369 helix: 1.33 (0.07), residues: 4986 sheet: -0.20 (0.20), residues: 669 loop : -0.64 (0.12), residues: 2714 =============================================================================== Job complete usr+sys time: 14733.09 seconds wall clock time: 258 minutes 46.86 seconds (15526.86 seconds total)