Starting phenix.real_space_refine on Thu Jan 18 20:56:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cs9_26960/01_2024/8cs9_26960_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cs9_26960/01_2024/8cs9_26960.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cs9_26960/01_2024/8cs9_26960_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cs9_26960/01_2024/8cs9_26960_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cs9_26960/01_2024/8cs9_26960_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cs9_26960/01_2024/8cs9_26960.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cs9_26960/01_2024/8cs9_26960.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cs9_26960/01_2024/8cs9_26960_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cs9_26960/01_2024/8cs9_26960_updated.pdb" } resolution = 2.74 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.012 sd= 0.101 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 18 5.49 5 S 264 5.16 5 C 39644 2.51 5 N 10069 2.21 5 O 10949 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 91": "OD1" <-> "OD2" Residue "A GLU 92": "OE1" <-> "OE2" Residue "A GLU 125": "OE1" <-> "OE2" Residue "A GLU 157": "OE1" <-> "OE2" Residue "A ASP 196": "OD1" <-> "OD2" Residue "A PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 266": "OE1" <-> "OE2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A ASP 337": "OD1" <-> "OD2" Residue "A GLU 402": "OE1" <-> "OE2" Residue "A PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 438": "OE1" <-> "OE2" Residue "A ASP 469": "OD1" <-> "OD2" Residue "A ASP 470": "OD1" <-> "OD2" Residue "A GLU 526": "OE1" <-> "OE2" Residue "A ASP 583": "OD1" <-> "OD2" Residue "A ASP 695": "OD1" <-> "OD2" Residue "A GLU 762": "OE1" <-> "OE2" Residue "A ASP 766": "OD1" <-> "OD2" Residue "A GLU 808": "OE1" <-> "OE2" Residue "A ASP 811": "OD1" <-> "OD2" Residue "K GLU 21": "OE1" <-> "OE2" Residue "K PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 164": "OD1" <-> "OD2" Residue "K GLU 340": "OE1" <-> "OE2" Residue "K TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 369": "OE1" <-> "OE2" Residue "L GLU 25": "OE1" <-> "OE2" Residue "L PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 119": "OD1" <-> "OD2" Residue "L TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 161": "OE1" <-> "OE2" Residue "L GLU 202": "OE1" <-> "OE2" Residue "L PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 56": "OD1" <-> "OD2" Residue "Q GLU 202": "OE1" <-> "OE2" Residue "Q ASP 288": "OD1" <-> "OD2" Residue "Q ASP 399": "OD1" <-> "OD2" Residue "X PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 95": "OE1" <-> "OE2" Residue "X ASP 98": "OD1" <-> "OD2" Residue "X GLU 177": "OE1" <-> "OE2" Residue "X GLU 310": "OE1" <-> "OE2" Residue "X ASP 384": "OD1" <-> "OD2" Residue "X GLU 405": "OE1" <-> "OE2" Residue "X GLU 596": "OE1" <-> "OE2" Residue "X ASP 615": "OD1" <-> "OD2" Residue "X ASP 620": "OD1" <-> "OD2" Residue "P TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 60": "OE1" <-> "OE2" Residue "V GLU 63": "OE1" <-> "OE2" Residue "V GLU 77": "OE1" <-> "OE2" Residue "V GLU 125": "OE1" <-> "OE2" Residue "V ASP 137": "OD1" <-> "OD2" Residue "V GLU 142": "OE1" <-> "OE2" Residue "V ASP 143": "OD1" <-> "OD2" Residue "V ASP 149": "OD1" <-> "OD2" Residue "V GLU 151": "OE1" <-> "OE2" Residue "V PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 297": "OD1" <-> "OD2" Residue "V GLU 312": "OE1" <-> "OE2" Residue "V GLU 341": "OE1" <-> "OE2" Residue "V ASP 399": "OD1" <-> "OD2" Residue "V PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 480": "OE1" <-> "OE2" Residue "V PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 522": "OE1" <-> "OE2" Residue "V GLU 535": "OE1" <-> "OE2" Residue "V TYR 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 607": "OD1" <-> "OD2" Residue "V GLU 681": "OE1" <-> "OE2" Residue "V GLU 693": "OE1" <-> "OE2" Residue "V ASP 705": "OD1" <-> "OD2" Residue "V GLU 755": "OE1" <-> "OE2" Residue "V TYR 818": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 871": "NH1" <-> "NH2" Residue "V ASP 887": "OD1" <-> "OD2" Residue "e GLU 60": "OE1" <-> "OE2" Residue "e GLU 63": "OE1" <-> "OE2" Residue "e GLU 125": "OE1" <-> "OE2" Residue "e PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 223": "OD1" <-> "OD2" Residue "e GLU 252": "OE1" <-> "OE2" Residue "e ASP 297": "OD1" <-> "OD2" Residue "e ASP 316": "OD1" <-> "OD2" Residue "e GLU 341": "OE1" <-> "OE2" Residue "e TYR 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 429": "OE1" <-> "OE2" Residue "e PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 472": "OE1" <-> "OE2" Residue "e TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 535": "OE1" <-> "OE2" Residue "e ASP 607": "OD1" <-> "OD2" Residue "e ASP 621": "OD1" <-> "OD2" Residue "e PHE 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 658": "OE1" <-> "OE2" Residue "e PHE 719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 758": "OE1" <-> "OE2" Residue "e PHE 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 794": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 807": "OD1" <-> "OD2" Residue "e TYR 818": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 882": "OE1" <-> "OE2" Residue "S PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 63": "OE1" <-> "OE2" Residue "Y GLU 77": "OE1" <-> "OE2" Residue "Y GLU 90": "OE1" <-> "OE2" Residue "Y PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 166": "OE1" <-> "OE2" Residue "Y GLU 312": "OE1" <-> "OE2" Residue "Y PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 340": "NH1" <-> "NH2" Residue "Y GLU 341": "OE1" <-> "OE2" Residue "Y PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 472": "OE1" <-> "OE2" Residue "Y GLU 473": "OE1" <-> "OE2" Residue "Y PHE 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 485": "OE1" <-> "OE2" Residue "Y PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 522": "OE1" <-> "OE2" Residue "Y ASP 546": "OD1" <-> "OD2" Residue "Y PHE 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 621": "OD1" <-> "OD2" Residue "Y PHE 622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 636": "OD1" <-> "OD2" Residue "Y PHE 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 755": "OE1" <-> "OE2" Residue "f GLU 63": "OE1" <-> "OE2" Residue "f ASP 67": "OD1" <-> "OD2" Residue "f GLU 68": "OE1" <-> "OE2" Residue "f GLU 90": "OE1" <-> "OE2" Residue "f PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 151": "OE1" <-> "OE2" Residue "f ASP 235": "OD1" <-> "OD2" Residue "f ASP 277": "OD1" <-> "OD2" Residue "f GLU 291": "OE1" <-> "OE2" Residue "f ASP 316": "OD1" <-> "OD2" Residue "f PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 439": "OE1" <-> "OE2" Residue "f GLU 473": "OE1" <-> "OE2" Residue "f PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 485": "OE1" <-> "OE2" Residue "f GLU 522": "OE1" <-> "OE2" Residue "f GLU 535": "OE1" <-> "OE2" Residue "f TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 597": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 681": "OE1" <-> "OE2" Residue "f GLU 693": "OE1" <-> "OE2" Residue "f TYR 818": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 821": "OD1" <-> "OD2" Residue "f TYR 824": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 878": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 887": "OD1" <-> "OD2" Residue "c GLU 89": "OE1" <-> "OE2" Residue "Z GLU 63": "OE1" <-> "OE2" Residue "Z GLU 86": "OE1" <-> "OE2" Residue "Z GLU 90": "OE1" <-> "OE2" Residue "Z GLU 125": "OE1" <-> "OE2" Residue "Z GLU 238": "OE1" <-> "OE2" Residue "Z GLU 272": "OE1" <-> "OE2" Residue "Z GLU 291": "OE1" <-> "OE2" Residue "Z ASP 316": "OD1" <-> "OD2" Residue "Z PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 429": "OE1" <-> "OE2" Residue "Z GLU 473": "OE1" <-> "OE2" Residue "Z PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 480": "OE1" <-> "OE2" Residue "Z GLU 485": "OE1" <-> "OE2" Residue "Z PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 603": "NH1" <-> "NH2" Residue "Z ASP 621": "OD1" <-> "OD2" Residue "Z ASP 626": "OD1" <-> "OD2" Residue "Z GLU 777": "OE1" <-> "OE2" Residue "Z ARG 871": "NH1" <-> "NH2" Residue "g GLU 17": "OE1" <-> "OE2" Residue "g ASP 23": "OD1" <-> "OD2" Residue "g GLU 63": "OE1" <-> "OE2" Residue "g GLU 125": "OE1" <-> "OE2" Residue "g PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 151": "OE1" <-> "OE2" Residue "g GLU 166": "OE1" <-> "OE2" Residue "g GLU 168": "OE1" <-> "OE2" Residue "g PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 238": "OE1" <-> "OE2" Residue "g GLU 249": "OE1" <-> "OE2" Residue "g GLU 252": "OE1" <-> "OE2" Residue "g GLU 272": "OE1" <-> "OE2" Residue "g GLU 306": "OE1" <-> "OE2" Residue "g PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 473": "OE1" <-> "OE2" Residue "g PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 522": "OE1" <-> "OE2" Residue "g GLU 535": "OE1" <-> "OE2" Residue "g PHE 584": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 626": "OD1" <-> "OD2" Residue "g PHE 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 702": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 882": "OE1" <-> "OE2" Residue "g ASP 887": "OD1" <-> "OD2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 60944 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 6017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 796, 6017 Classifications: {'peptide': 796} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 36, 'TRANS': 759} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 2943 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 380, 2919 Classifications: {'peptide': 380} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 365} Chain breaks: 5 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 380, 2919 Classifications: {'peptide': 380} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 365} Chain breaks: 5 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 2962 Chain: "L" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 2938 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 376} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Q" Number of atoms: 2954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2954 Classifications: {'peptide': 390} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 378} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "X" Number of atoms: 5162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 656, 5162 Classifications: {'peptide': 656} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 30, 'TRANS': 625} Chain breaks: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "P" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 248 Classifications: {'peptide': 33} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 31} Chain: "R" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 277 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 34} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "a" Number of atoms: 284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 284 Classifications: {'peptide': 37} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 35} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "V" Number of atoms: 6386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 810, 6386 Classifications: {'peptide': 810} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 764} Chain breaks: 4 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "e" Number of atoms: 6339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 804, 6339 Classifications: {'peptide': 804} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 47, 'TRANS': 755} Chain breaks: 3 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "S" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 255 Classifications: {'peptide': 33} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 31} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "b" Number of atoms: 289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 289 Classifications: {'peptide': 38} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 36} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Y" Number of atoms: 6226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 786, 6226 Classifications: {'peptide': 786} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 742} Chain breaks: 4 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "f" Number of atoms: 6331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 802, 6331 Classifications: {'peptide': 802} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 755} Chain breaks: 3 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "T" Number of atoms: 284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 284 Classifications: {'peptide': 37} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 35} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "c" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 255 Classifications: {'peptide': 33} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 31} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "Z" Number of atoms: 6226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 786, 6226 Classifications: {'peptide': 786} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 742} Chain breaks: 4 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "g" Number of atoms: 6556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 832, 6556 Classifications: {'peptide': 832} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 782} Chain breaks: 4 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 37 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'AJP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 24 Chain: "V" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 103 Unusual residues: {'CLR': 1, 'NAG': 2, 'PIO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 75 Unusual residues: {'CLR': 1, 'PIO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 103 Unusual residues: {'CLR': 1, 'NAG': 2, 'PIO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 75 Unusual residues: {'CLR': 1, 'PIO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 56 Unusual residues: {'CLR': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 94 Unusual residues: {'PIO': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "K" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "L" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "Q" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Chain: "X" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 112 Classifications: {'water': 112} Link IDs: {None: 111} Chain: "V" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "e" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "f" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "g" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ATYR K 34 " occ=0.48 ... (22 atoms not shown) pdb=" OH BTYR K 34 " occ=0.52 residue: pdb=" N ATYR K 242 " occ=0.56 ... (22 atoms not shown) pdb=" OH BTYR K 242 " occ=0.44 Time building chain proxies: 25.81, per 1000 atoms: 0.42 Number of scatterers: 60944 At special positions: 0 Unit cell: (171.81, 207.5, 277.22, 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 264 16.00 P 18 15.00 O 10949 8.00 N 10069 7.00 C 39644 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG V1002 " - " NAG V1003 " " NAG Y1002 " - " NAG Y1003 " " NAG Z1002 " - " NAG Z1003 " NAG-ASN " NAG B 1 " - " ASN e 642 " " NAG C 1 " - " ASN f 642 " " NAG D 1 " - " ASN g 642 " " NAG V1002 " - " ASN V 642 " " NAG Y1002 " - " ASN Y 642 " " NAG Z1002 " - " ASN Z 642 " Time building additional restraints: 19.43 Conformation dependent library (CDL) restraints added in 8.5 seconds 15160 Ramachandran restraints generated. 7580 Oldfield, 0 Emsley, 7580 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14282 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 314 helices and 29 sheets defined 54.4% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.38 Creating SS restraints... Processing helix chain 'A' and resid 12 through 22 Processing helix chain 'A' and resid 25 through 34 Processing helix chain 'A' and resid 48 through 55 Processing helix chain 'A' and resid 58 through 66 Processing helix chain 'A' and resid 81 through 87 Processing helix chain 'A' and resid 91 through 99 Processing helix chain 'A' and resid 114 through 120 Processing helix chain 'A' and resid 124 through 132 Processing helix chain 'A' and resid 147 through 153 Processing helix chain 'A' and resid 157 through 166 Processing helix chain 'A' and resid 176 through 182 Processing helix chain 'A' and resid 186 through 195 Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 219 through 227 Processing helix chain 'A' and resid 242 through 249 Processing helix chain 'A' and resid 252 through 260 Processing helix chain 'A' and resid 275 through 281 Processing helix chain 'A' and resid 285 through 293 Processing helix chain 'A' and resid 308 through 314 Processing helix chain 'A' and resid 318 through 326 Processing helix chain 'A' and resid 341 through 348 Processing helix chain 'A' and resid 351 through 359 Processing helix chain 'A' and resid 374 through 380 Processing helix chain 'A' and resid 384 through 392 Processing helix chain 'A' and resid 407 through 414 Processing helix chain 'A' and resid 417 through 426 Processing helix chain 'A' and resid 440 through 445 Processing helix chain 'A' and resid 450 through 458 Processing helix chain 'A' and resid 468 through 470 No H-bonds generated for 'chain 'A' and resid 468 through 470' Processing helix chain 'A' and resid 473 through 480 removed outlier: 3.637A pdb=" N ILE A 480 " --> pdb=" O CYS A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 492 Processing helix chain 'A' and resid 506 through 513 Processing helix chain 'A' and resid 516 through 524 Processing helix chain 'A' and resid 539 through 546 Processing helix chain 'A' and resid 549 through 557 Processing helix chain 'A' and resid 572 through 578 Processing helix chain 'A' and resid 582 through 591 Proline residue: A 590 - end of helix Processing helix chain 'A' and resid 605 through 612 Processing helix chain 'A' and resid 615 through 623 Processing helix chain 'A' and resid 638 through 644 Processing helix chain 'A' and resid 648 through 657 Processing helix chain 'A' and resid 671 through 678 Processing helix chain 'A' and resid 681 through 690 Processing helix chain 'A' and resid 704 through 711 Processing helix chain 'A' and resid 714 through 723 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 747 through 756 Processing helix chain 'A' and resid 770 through 776 removed outlier: 3.727A pdb=" N ALA A 774 " --> pdb=" O PRO A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 789 removed outlier: 3.690A pdb=" N VAL A 788 " --> pdb=" O ASP A 784 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL A 789 " --> pdb=" O VAL A 785 " (cutoff:3.500A) Processing helix chain 'K' and resid 12 through 31 Processing helix chain 'K' and resid 44 through 64 removed outlier: 3.808A pdb=" N VAL K 50 " --> pdb=" O ALA K 46 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY K 51 " --> pdb=" O SER K 47 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU K 62 " --> pdb=" O ALA K 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 99 removed outlier: 3.810A pdb=" N GLN K 89 " --> pdb=" O ALA K 85 " (cutoff:3.500A) Processing helix chain 'K' and resid 110 through 129 removed outlier: 3.582A pdb=" N VAL K 123 " --> pdb=" O SER K 119 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLY K 128 " --> pdb=" O LEU K 124 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ALA K 129 " --> pdb=" O ILE K 125 " (cutoff:3.500A) Processing helix chain 'K' and resid 136 through 161 Processing helix chain 'K' and resid 167 through 186 removed outlier: 3.678A pdb=" N ARG K 170 " --> pdb=" O MET K 167 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N TYR K 173 " --> pdb=" O ARG K 170 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE K 175 " --> pdb=" O PHE K 172 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR K 178 " --> pdb=" O PHE K 175 " (cutoff:3.500A) Processing helix chain 'K' and resid 203 through 225 Proline residue: K 221 - end of helix removed outlier: 3.619A pdb=" N SER K 225 " --> pdb=" O PRO K 221 " (cutoff:3.500A) Processing helix chain 'K' and resid 231 through 255 Processing helix chain 'K' and resid 267 through 280 removed outlier: 4.954A pdb=" N LEU K 275 " --> pdb=" O HIS K 271 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ALA K 276 " --> pdb=" O SER K 272 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N GLY K 277 " --> pdb=" O ALA K 273 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N GLY K 278 " --> pdb=" O VAL K 274 " (cutoff:3.500A) Processing helix chain 'K' and resid 291 through 311 Processing helix chain 'K' and resid 327 through 349 removed outlier: 3.700A pdb=" N VAL K 348 " --> pdb=" O ILE K 344 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU K 349 " --> pdb=" O VAL K 345 " (cutoff:3.500A) Processing helix chain 'K' and resid 361 through 388 Processing helix chain 'K' and resid 391 through 393 No H-bonds generated for 'chain 'K' and resid 391 through 393' Processing helix chain 'K' and resid 398 through 400 No H-bonds generated for 'chain 'K' and resid 398 through 400' Processing helix chain 'K' and resid 404 through 406 No H-bonds generated for 'chain 'K' and resid 404 through 406' Processing helix chain 'L' and resid 4 through 23 Processing helix chain 'L' and resid 51 through 68 removed outlier: 4.132A pdb=" N PHE L 65 " --> pdb=" O ILE L 61 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLY L 66 " --> pdb=" O PHE L 62 " (cutoff:3.500A) Processing helix chain 'L' and resid 76 through 102 removed outlier: 3.740A pdb=" N GLN L 92 " --> pdb=" O ALA L 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 112 through 131 removed outlier: 3.790A pdb=" N ALA L 131 " --> pdb=" O ILE L 127 " (cutoff:3.500A) Processing helix chain 'L' and resid 138 through 161 Processing helix chain 'L' and resid 175 through 188 Processing helix chain 'L' and resid 192 through 194 No H-bonds generated for 'chain 'L' and resid 192 through 194' Processing helix chain 'L' and resid 205 through 225 removed outlier: 3.783A pdb=" N ILE L 213 " --> pdb=" O LEU L 209 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY L 214 " --> pdb=" O PHE L 210 " (cutoff:3.500A) Proline residue: L 223 - end of helix Processing helix chain 'L' and resid 234 through 261 removed outlier: 3.727A pdb=" N LEU L 252 " --> pdb=" O ALA L 248 " (cutoff:3.500A) Processing helix chain 'L' and resid 263 through 265 No H-bonds generated for 'chain 'L' and resid 263 through 265' Processing helix chain 'L' and resid 269 through 282 removed outlier: 4.303A pdb=" N THR L 276 " --> pdb=" O ILE L 272 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N LEU L 277 " --> pdb=" O GLN L 273 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA L 278 " --> pdb=" O ASN L 274 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N GLY L 279 " --> pdb=" O ALA L 275 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N GLY L 280 " --> pdb=" O THR L 276 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL L 281 " --> pdb=" O LEU L 277 " (cutoff:3.500A) Processing helix chain 'L' and resid 292 through 320 removed outlier: 4.544A pdb=" N THR L 315 " --> pdb=" O TYR L 311 " (cutoff:3.500A) Proline residue: L 316 - end of helix Processing helix chain 'L' and resid 330 through 350 removed outlier: 5.367A pdb=" N LEU L 336 " --> pdb=" O ASN L 332 " (cutoff:3.500A) Proline residue: L 337 - end of helix Processing helix chain 'L' and resid 358 through 383 Processing helix chain 'L' and resid 399 through 401 No H-bonds generated for 'chain 'L' and resid 399 through 401' Processing helix chain 'Q' and resid 4 through 23 Processing helix chain 'Q' and resid 47 through 68 Proline residue: Q 52 - end of helix removed outlier: 4.170A pdb=" N PHE Q 65 " --> pdb=" O ILE Q 61 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N GLY Q 66 " --> pdb=" O PHE Q 62 " (cutoff:3.500A) Processing helix chain 'Q' and resid 76 through 103 removed outlier: 3.869A pdb=" N GLN Q 92 " --> pdb=" O ALA Q 88 " (cutoff:3.500A) Processing helix chain 'Q' and resid 112 through 131 removed outlier: 3.812A pdb=" N ALA Q 131 " --> pdb=" O ILE Q 127 " (cutoff:3.500A) Processing helix chain 'Q' and resid 138 through 161 removed outlier: 3.633A pdb=" N VAL Q 150 " --> pdb=" O ILE Q 146 " (cutoff:3.500A) Processing helix chain 'Q' and resid 175 through 188 Processing helix chain 'Q' and resid 192 through 194 No H-bonds generated for 'chain 'Q' and resid 192 through 194' Processing helix chain 'Q' and resid 205 through 227 Proline residue: Q 223 - end of helix Processing helix chain 'Q' and resid 234 through 261 removed outlier: 3.605A pdb=" N LEU Q 252 " --> pdb=" O ALA Q 248 " (cutoff:3.500A) Processing helix chain 'Q' and resid 263 through 265 No H-bonds generated for 'chain 'Q' and resid 263 through 265' Processing helix chain 'Q' and resid 269 through 282 removed outlier: 4.294A pdb=" N THR Q 276 " --> pdb=" O ILE Q 272 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N LEU Q 277 " --> pdb=" O GLN Q 273 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA Q 278 " --> pdb=" O ASN Q 274 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N GLY Q 279 " --> pdb=" O ALA Q 275 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N GLY Q 280 " --> pdb=" O THR Q 276 " (cutoff:3.500A) Processing helix chain 'Q' and resid 292 through 320 removed outlier: 4.583A pdb=" N THR Q 315 " --> pdb=" O TYR Q 311 " (cutoff:3.500A) Proline residue: Q 316 - end of helix Processing helix chain 'Q' and resid 330 through 350 removed outlier: 5.378A pdb=" N LEU Q 336 " --> pdb=" O ASN Q 332 " (cutoff:3.500A) Proline residue: Q 337 - end of helix Processing helix chain 'Q' and resid 358 through 383 Processing helix chain 'Q' and resid 399 through 401 No H-bonds generated for 'chain 'Q' and resid 399 through 401' Processing helix chain 'X' and resid 14 through 20 Processing helix chain 'X' and resid 52 through 58 Processing helix chain 'X' and resid 152 through 159 Processing helix chain 'X' and resid 188 through 198 removed outlier: 3.788A pdb=" N LYS X 198 " --> pdb=" O ARG X 194 " (cutoff:3.500A) Processing helix chain 'X' and resid 202 through 206 removed outlier: 4.041A pdb=" N SER X 206 " --> pdb=" O GLU X 203 " (cutoff:3.500A) Processing helix chain 'X' and resid 208 through 226 Processing helix chain 'X' and resid 248 through 257 Processing helix chain 'X' and resid 265 through 282 removed outlier: 3.610A pdb=" N ALA X 268 " --> pdb=" O ASP X 265 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N TRP X 269 " --> pdb=" O GLY X 266 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU X 271 " --> pdb=" O ALA X 268 " (cutoff:3.500A) Processing helix chain 'X' and resid 368 through 373 Processing helix chain 'X' and resid 382 through 388 Processing helix chain 'X' and resid 432 through 435 No H-bonds generated for 'chain 'X' and resid 432 through 435' Processing helix chain 'X' and resid 442 through 458 Processing helix chain 'X' and resid 549 through 551 No H-bonds generated for 'chain 'X' and resid 549 through 551' Processing helix chain 'P' and resid 60 through 90 Processing helix chain 'R' and resid 89 through 113 Processing helix chain 'a' and resid 89 through 113 Processing helix chain 'V' and resid 44 through 46 No H-bonds generated for 'chain 'V' and resid 44 through 46' Processing helix chain 'V' and resid 104 through 115 Processing helix chain 'V' and resid 128 through 141 Processing helix chain 'V' and resid 147 through 157 removed outlier: 4.606A pdb=" N GLU V 151 " --> pdb=" O GLN V 148 " (cutoff:3.500A) Processing helix chain 'V' and resid 164 through 169 removed outlier: 3.923A pdb=" N GLU V 168 " --> pdb=" O GLY V 165 " (cutoff:3.500A) Processing helix chain 'V' and resid 195 through 200 Processing helix chain 'V' and resid 278 through 290 Processing helix chain 'V' and resid 292 through 299 Processing helix chain 'V' and resid 304 through 317 Processing helix chain 'V' and resid 328 through 343 removed outlier: 3.989A pdb=" N LEU V 335 " --> pdb=" O ALA V 331 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL V 336 " --> pdb=" O LEU V 332 " (cutoff:3.500A) Proline residue: V 337 - end of helix removed outlier: 3.628A pdb=" N GLU V 341 " --> pdb=" O PRO V 337 " (cutoff:3.500A) Processing helix chain 'V' and resid 380 through 393 Proline residue: V 391 - end of helix Processing helix chain 'V' and resid 395 through 400 removed outlier: 5.231A pdb=" N ALA V 400 " --> pdb=" O ASP V 396 " (cutoff:3.500A) Processing helix chain 'V' and resid 403 through 430 removed outlier: 3.744A pdb=" N PHE V 414 " --> pdb=" O ILE V 410 " (cutoff:3.500A) Proline residue: V 419 - end of helix Processing helix chain 'V' and resid 437 through 454 Processing helix chain 'V' and resid 466 through 482 Processing helix chain 'V' and resid 486 through 506 Processing helix chain 'V' and resid 509 through 515 removed outlier: 3.546A pdb=" N LEU V 512 " --> pdb=" O GLY V 509 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL V 513 " --> pdb=" O SER V 510 " (cutoff:3.500A) Processing helix chain 'V' and resid 518 through 546 removed outlier: 3.635A pdb=" N LEU V 540 " --> pdb=" O THR V 536 " (cutoff:3.500A) Processing helix chain 'V' and resid 570 through 592 Processing helix chain 'V' and resid 599 through 607 Processing helix chain 'V' and resid 609 through 622 Processing helix chain 'V' and resid 661 through 689 removed outlier: 3.687A pdb=" N PHE V 665 " --> pdb=" O ILE V 661 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ALA V 668 " --> pdb=" O MET V 664 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N LEU V 669 " --> pdb=" O PHE V 665 " (cutoff:3.500A) Proline residue: V 670 - end of helix Processing helix chain 'V' and resid 692 through 694 No H-bonds generated for 'chain 'V' and resid 692 through 694' Processing helix chain 'V' and resid 702 through 718 removed outlier: 3.660A pdb=" N LEU V 718 " --> pdb=" O GLY V 714 " (cutoff:3.500A) Processing helix chain 'V' and resid 728 through 737 Processing helix chain 'V' and resid 761 through 773 Processing helix chain 'V' and resid 777 through 780 No H-bonds generated for 'chain 'V' and resid 777 through 780' Processing helix chain 'V' and resid 785 through 800 removed outlier: 3.876A pdb=" N LEU V 800 " --> pdb=" O GLY V 796 " (cutoff:3.500A) Processing helix chain 'V' and resid 804 through 812 Processing helix chain 'V' and resid 823 through 826 No H-bonds generated for 'chain 'V' and resid 823 through 826' Processing helix chain 'V' and resid 830 through 851 Processing helix chain 'V' and resid 856 through 877 Proline residue: V 860 - end of helix removed outlier: 3.740A pdb=" N THR V 866 " --> pdb=" O LEU V 863 " (cutoff:3.500A) Proline residue: V 868 - end of helix removed outlier: 4.864A pdb=" N LEU V 873 " --> pdb=" O ARG V 870 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N LEU V 874 " --> pdb=" O ARG V 871 " (cutoff:3.500A) Proline residue: V 875 - end of helix Processing helix chain 'V' and resid 880 through 886 Processing helix chain 'e' and resid 104 through 115 Processing helix chain 'e' and resid 128 through 141 Processing helix chain 'e' and resid 147 through 157 removed outlier: 4.331A pdb=" N GLU e 151 " --> pdb=" O GLN e 148 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU e 153 " --> pdb=" O ARG e 150 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU e 154 " --> pdb=" O GLU e 151 " (cutoff:3.500A) Processing helix chain 'e' and resid 164 through 166 No H-bonds generated for 'chain 'e' and resid 164 through 166' Processing helix chain 'e' and resid 278 through 290 Processing helix chain 'e' and resid 292 through 299 Processing helix chain 'e' and resid 304 through 316 Processing helix chain 'e' and resid 329 through 348 removed outlier: 4.037A pdb=" N LEU e 335 " --> pdb=" O ALA e 331 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N VAL e 336 " --> pdb=" O LEU e 332 " (cutoff:3.500A) Proline residue: e 337 - end of helix Processing helix chain 'e' and resid 380 through 393 Proline residue: e 391 - end of helix Processing helix chain 'e' and resid 395 through 400 removed outlier: 5.253A pdb=" N ALA e 400 " --> pdb=" O ASP e 396 " (cutoff:3.500A) Processing helix chain 'e' and resid 403 through 430 removed outlier: 3.634A pdb=" N PHE e 414 " --> pdb=" O ILE e 410 " (cutoff:3.500A) Proline residue: e 419 - end of helix Processing helix chain 'e' and resid 437 through 454 Processing helix chain 'e' and resid 466 through 482 Processing helix chain 'e' and resid 486 through 506 removed outlier: 3.529A pdb=" N LEU e 499 " --> pdb=" O PHE e 495 " (cutoff:3.500A) Processing helix chain 'e' and resid 509 through 514 removed outlier: 3.576A pdb=" N LEU e 512 " --> pdb=" O GLY e 509 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL e 513 " --> pdb=" O SER e 510 " (cutoff:3.500A) Processing helix chain 'e' and resid 518 through 546 removed outlier: 3.572A pdb=" N LEU e 540 " --> pdb=" O THR e 536 " (cutoff:3.500A) Processing helix chain 'e' and resid 570 through 592 Processing helix chain 'e' and resid 599 through 607 Processing helix chain 'e' and resid 609 through 622 Processing helix chain 'e' and resid 663 through 689 removed outlier: 6.171A pdb=" N ALA e 668 " --> pdb=" O MET e 664 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N LEU e 669 " --> pdb=" O PHE e 665 " (cutoff:3.500A) Proline residue: e 670 - end of helix Processing helix chain 'e' and resid 692 through 694 No H-bonds generated for 'chain 'e' and resid 692 through 694' Processing helix chain 'e' and resid 702 through 719 removed outlier: 4.071A pdb=" N PHE e 719 " --> pdb=" O VAL e 715 " (cutoff:3.500A) Processing helix chain 'e' and resid 728 through 737 Processing helix chain 'e' and resid 761 through 774 removed outlier: 4.889A pdb=" N ILE e 774 " --> pdb=" O VAL e 770 " (cutoff:3.500A) Processing helix chain 'e' and resid 777 through 782 removed outlier: 4.107A pdb=" N ARG e 782 " --> pdb=" O PRO e 778 " (cutoff:3.500A) Processing helix chain 'e' and resid 785 through 800 removed outlier: 4.173A pdb=" N LEU e 800 " --> pdb=" O GLY e 796 " (cutoff:3.500A) Processing helix chain 'e' and resid 804 through 812 removed outlier: 3.749A pdb=" N LEU e 812 " --> pdb=" O ARG e 808 " (cutoff:3.500A) Processing helix chain 'e' and resid 823 through 826 No H-bonds generated for 'chain 'e' and resid 823 through 826' Processing helix chain 'e' and resid 830 through 851 Processing helix chain 'e' and resid 856 through 871 removed outlier: 3.660A pdb=" N LEU e 859 " --> pdb=" O SER e 856 " (cutoff:3.500A) Proline residue: e 860 - end of helix removed outlier: 4.261A pdb=" N VAL e 867 " --> pdb=" O ILE e 864 " (cutoff:3.500A) Proline residue: e 868 - end of helix Processing helix chain 'e' and resid 874 through 876 No H-bonds generated for 'chain 'e' and resid 874 through 876' Processing helix chain 'e' and resid 880 through 886 Processing helix chain 'S' and resid 89 through 113 Processing helix chain 'b' and resid 89 through 113 Processing helix chain 'Y' and resid 90 through 92 No H-bonds generated for 'chain 'Y' and resid 90 through 92' Processing helix chain 'Y' and resid 104 through 115 Processing helix chain 'Y' and resid 128 through 141 Processing helix chain 'Y' and resid 150 through 157 Processing helix chain 'Y' and resid 164 through 170 removed outlier: 3.757A pdb=" N GLU Y 168 " --> pdb=" O GLY Y 165 " (cutoff:3.500A) Processing helix chain 'Y' and resid 278 through 290 Processing helix chain 'Y' and resid 292 through 299 Processing helix chain 'Y' and resid 304 through 316 Processing helix chain 'Y' and resid 328 through 334 Processing helix chain 'Y' and resid 336 through 346 Processing helix chain 'Y' and resid 380 through 393 Proline residue: Y 391 - end of helix Processing helix chain 'Y' and resid 395 through 400 removed outlier: 5.283A pdb=" N ALA Y 400 " --> pdb=" O ASP Y 396 " (cutoff:3.500A) Processing helix chain 'Y' and resid 403 through 430 removed outlier: 3.847A pdb=" N PHE Y 414 " --> pdb=" O ILE Y 410 " (cutoff:3.500A) Proline residue: Y 419 - end of helix Processing helix chain 'Y' and resid 437 through 454 Processing helix chain 'Y' and resid 467 through 482 removed outlier: 3.761A pdb=" N GLU Y 472 " --> pdb=" O LEU Y 468 " (cutoff:3.500A) Processing helix chain 'Y' and resid 486 through 506 Processing helix chain 'Y' and resid 509 through 515 removed outlier: 3.618A pdb=" N LEU Y 512 " --> pdb=" O GLY Y 509 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL Y 513 " --> pdb=" O SER Y 510 " (cutoff:3.500A) Processing helix chain 'Y' and resid 518 through 546 Processing helix chain 'Y' and resid 570 through 592 Processing helix chain 'Y' and resid 599 through 607 Processing helix chain 'Y' and resid 609 through 622 Processing helix chain 'Y' and resid 661 through 689 removed outlier: 3.759A pdb=" N PHE Y 665 " --> pdb=" O ILE Y 661 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ALA Y 668 " --> pdb=" O MET Y 664 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N LEU Y 669 " --> pdb=" O PHE Y 665 " (cutoff:3.500A) Proline residue: Y 670 - end of helix Processing helix chain 'Y' and resid 692 through 694 No H-bonds generated for 'chain 'Y' and resid 692 through 694' Processing helix chain 'Y' and resid 704 through 718 removed outlier: 3.953A pdb=" N MET Y 712 " --> pdb=" O LEU Y 708 " (cutoff:3.500A) Processing helix chain 'Y' and resid 728 through 738 Processing helix chain 'Y' and resid 761 through 773 Processing helix chain 'Y' and resid 777 through 782 removed outlier: 4.190A pdb=" N ARG Y 782 " --> pdb=" O PRO Y 778 " (cutoff:3.500A) Processing helix chain 'Y' and resid 785 through 800 removed outlier: 4.204A pdb=" N LEU Y 800 " --> pdb=" O GLY Y 796 " (cutoff:3.500A) Processing helix chain 'Y' and resid 804 through 812 Processing helix chain 'Y' and resid 830 through 851 Processing helix chain 'Y' and resid 859 through 877 removed outlier: 3.816A pdb=" N THR Y 866 " --> pdb=" O VAL Y 862 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL Y 867 " --> pdb=" O LEU Y 863 " (cutoff:3.500A) Proline residue: Y 868 - end of helix removed outlier: 4.248A pdb=" N LEU Y 874 " --> pdb=" O ARG Y 870 " (cutoff:3.500A) Proline residue: Y 875 - end of helix Processing helix chain 'Y' and resid 880 through 886 removed outlier: 3.646A pdb=" N CYS Y 885 " --> pdb=" O VAL Y 881 " (cutoff:3.500A) Processing helix chain 'f' and resid 104 through 115 Processing helix chain 'f' and resid 128 through 142 Processing helix chain 'f' and resid 147 through 157 removed outlier: 4.713A pdb=" N GLU f 151 " --> pdb=" O GLN f 148 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU f 157 " --> pdb=" O LEU f 154 " (cutoff:3.500A) Processing helix chain 'f' and resid 164 through 166 No H-bonds generated for 'chain 'f' and resid 164 through 166' Processing helix chain 'f' and resid 195 through 200 Processing helix chain 'f' and resid 278 through 290 Processing helix chain 'f' and resid 292 through 300 Processing helix chain 'f' and resid 304 through 316 Processing helix chain 'f' and resid 332 through 344 Proline residue: f 337 - end of helix removed outlier: 3.550A pdb=" N ARG f 340 " --> pdb=" O PRO f 337 " (cutoff:3.500A) Processing helix chain 'f' and resid 380 through 393 Proline residue: f 391 - end of helix Processing helix chain 'f' and resid 395 through 398 No H-bonds generated for 'chain 'f' and resid 395 through 398' Processing helix chain 'f' and resid 403 through 430 removed outlier: 3.711A pdb=" N PHE f 414 " --> pdb=" O ILE f 410 " (cutoff:3.500A) Proline residue: f 419 - end of helix Processing helix chain 'f' and resid 437 through 454 Processing helix chain 'f' and resid 466 through 479 Processing helix chain 'f' and resid 486 through 506 removed outlier: 3.568A pdb=" N ARG f 490 " --> pdb=" O TYR f 486 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE f 495 " --> pdb=" O VAL f 491 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU f 499 " --> pdb=" O PHE f 495 " (cutoff:3.500A) Processing helix chain 'f' and resid 509 through 515 removed outlier: 3.559A pdb=" N LEU f 512 " --> pdb=" O GLY f 509 " (cutoff:3.500A) Processing helix chain 'f' and resid 518 through 546 Processing helix chain 'f' and resid 570 through 592 removed outlier: 3.874A pdb=" N LEU f 588 " --> pdb=" O PHE f 584 " (cutoff:3.500A) Processing helix chain 'f' and resid 599 through 607 removed outlier: 3.697A pdb=" N ILE f 605 " --> pdb=" O LEU f 601 " (cutoff:3.500A) Processing helix chain 'f' and resid 609 through 622 Processing helix chain 'f' and resid 661 through 664 No H-bonds generated for 'chain 'f' and resid 661 through 664' Processing helix chain 'f' and resid 669 through 689 Processing helix chain 'f' and resid 692 through 694 No H-bonds generated for 'chain 'f' and resid 692 through 694' Processing helix chain 'f' and resid 702 through 718 removed outlier: 3.708A pdb=" N LEU f 718 " --> pdb=" O GLY f 714 " (cutoff:3.500A) Processing helix chain 'f' and resid 728 through 738 Processing helix chain 'f' and resid 761 through 774 removed outlier: 4.721A pdb=" N ILE f 774 " --> pdb=" O VAL f 770 " (cutoff:3.500A) Processing helix chain 'f' and resid 777 through 782 removed outlier: 4.046A pdb=" N ARG f 782 " --> pdb=" O PRO f 778 " (cutoff:3.500A) Processing helix chain 'f' and resid 785 through 800 removed outlier: 4.019A pdb=" N LEU f 800 " --> pdb=" O GLY f 796 " (cutoff:3.500A) Processing helix chain 'f' and resid 804 through 812 removed outlier: 3.580A pdb=" N LEU f 812 " --> pdb=" O ARG f 808 " (cutoff:3.500A) Processing helix chain 'f' and resid 823 through 826 No H-bonds generated for 'chain 'f' and resid 823 through 826' Processing helix chain 'f' and resid 830 through 851 Processing helix chain 'f' and resid 856 through 872 Proline residue: f 860 - end of helix Proline residue: f 868 - end of helix Processing helix chain 'f' and resid 874 through 876 No H-bonds generated for 'chain 'f' and resid 874 through 876' Processing helix chain 'f' and resid 880 through 886 Processing helix chain 'T' and resid 89 through 113 removed outlier: 3.569A pdb=" N GLY T 102 " --> pdb=" O GLY T 98 " (cutoff:3.500A) Processing helix chain 'c' and resid 89 through 116 removed outlier: 3.644A pdb=" N ARG c 116 " --> pdb=" O TYR c 112 " (cutoff:3.500A) Processing helix chain 'Z' and resid 104 through 115 Processing helix chain 'Z' and resid 128 through 141 Processing helix chain 'Z' and resid 147 through 157 removed outlier: 4.048A pdb=" N GLU Z 151 " --> pdb=" O GLN Z 148 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLU Z 152 " --> pdb=" O ASP Z 149 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU Z 157 " --> pdb=" O LEU Z 154 " (cutoff:3.500A) Processing helix chain 'Z' and resid 164 through 166 No H-bonds generated for 'chain 'Z' and resid 164 through 166' Processing helix chain 'Z' and resid 168 through 170 No H-bonds generated for 'chain 'Z' and resid 168 through 170' Processing helix chain 'Z' and resid 195 through 200 Processing helix chain 'Z' and resid 278 through 290 Processing helix chain 'Z' and resid 292 through 299 Processing helix chain 'Z' and resid 304 through 316 Processing helix chain 'Z' and resid 328 through 342 removed outlier: 4.154A pdb=" N LEU Z 335 " --> pdb=" O ALA Z 331 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL Z 336 " --> pdb=" O LEU Z 332 " (cutoff:3.500A) Proline residue: Z 337 - end of helix Processing helix chain 'Z' and resid 380 through 393 Proline residue: Z 391 - end of helix Processing helix chain 'Z' and resid 395 through 398 No H-bonds generated for 'chain 'Z' and resid 395 through 398' Processing helix chain 'Z' and resid 403 through 431 removed outlier: 3.726A pdb=" N PHE Z 414 " --> pdb=" O ILE Z 410 " (cutoff:3.500A) Proline residue: Z 419 - end of helix Processing helix chain 'Z' and resid 437 through 454 Processing helix chain 'Z' and resid 466 through 481 Processing helix chain 'Z' and resid 486 through 506 Processing helix chain 'Z' and resid 509 through 515 removed outlier: 3.745A pdb=" N VAL Z 513 " --> pdb=" O SER Z 510 " (cutoff:3.500A) Processing helix chain 'Z' and resid 518 through 546 removed outlier: 3.560A pdb=" N LEU Z 540 " --> pdb=" O THR Z 536 " (cutoff:3.500A) Processing helix chain 'Z' and resid 570 through 593 removed outlier: 3.682A pdb=" N ASN Z 593 " --> pdb=" O ARG Z 589 " (cutoff:3.500A) Processing helix chain 'Z' and resid 599 through 607 Processing helix chain 'Z' and resid 609 through 622 Processing helix chain 'Z' and resid 661 through 689 removed outlier: 3.733A pdb=" N PHE Z 665 " --> pdb=" O ILE Z 661 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N ALA Z 668 " --> pdb=" O MET Z 664 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LEU Z 669 " --> pdb=" O PHE Z 665 " (cutoff:3.500A) Proline residue: Z 670 - end of helix Processing helix chain 'Z' and resid 692 through 694 No H-bonds generated for 'chain 'Z' and resid 692 through 694' Processing helix chain 'Z' and resid 703 through 718 removed outlier: 3.701A pdb=" N LEU Z 718 " --> pdb=" O GLY Z 714 " (cutoff:3.500A) Processing helix chain 'Z' and resid 728 through 737 Processing helix chain 'Z' and resid 761 through 774 removed outlier: 4.730A pdb=" N ILE Z 774 " --> pdb=" O VAL Z 770 " (cutoff:3.500A) Processing helix chain 'Z' and resid 777 through 782 removed outlier: 4.432A pdb=" N ARG Z 782 " --> pdb=" O PRO Z 778 " (cutoff:3.500A) Processing helix chain 'Z' and resid 785 through 800 removed outlier: 4.062A pdb=" N LEU Z 800 " --> pdb=" O GLY Z 796 " (cutoff:3.500A) Processing helix chain 'Z' and resid 804 through 813 removed outlier: 4.040A pdb=" N PHE Z 813 " --> pdb=" O ILE Z 809 " (cutoff:3.500A) Processing helix chain 'Z' and resid 823 through 826 No H-bonds generated for 'chain 'Z' and resid 823 through 826' Processing helix chain 'Z' and resid 830 through 852 Processing helix chain 'Z' and resid 856 through 872 Proline residue: Z 860 - end of helix Proline residue: Z 868 - end of helix Processing helix chain 'Z' and resid 874 through 877 No H-bonds generated for 'chain 'Z' and resid 874 through 877' Processing helix chain 'Z' and resid 880 through 886 Processing helix chain 'g' and resid 5 through 7 No H-bonds generated for 'chain 'g' and resid 5 through 7' Processing helix chain 'g' and resid 9 through 16 Processing helix chain 'g' and resid 18 through 21 Processing helix chain 'g' and resid 104 through 115 Processing helix chain 'g' and resid 128 through 141 Processing helix chain 'g' and resid 147 through 157 removed outlier: 4.158A pdb=" N GLU g 151 " --> pdb=" O GLN g 148 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU g 154 " --> pdb=" O GLU g 151 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG g 155 " --> pdb=" O GLU g 152 " (cutoff:3.500A) Processing helix chain 'g' and resid 168 through 170 No H-bonds generated for 'chain 'g' and resid 168 through 170' Processing helix chain 'g' and resid 195 through 199 Processing helix chain 'g' and resid 278 through 290 Processing helix chain 'g' and resid 292 through 299 Processing helix chain 'g' and resid 304 through 316 Processing helix chain 'g' and resid 332 through 334 No H-bonds generated for 'chain 'g' and resid 332 through 334' Processing helix chain 'g' and resid 336 through 347 Processing helix chain 'g' and resid 380 through 393 Proline residue: g 391 - end of helix Processing helix chain 'g' and resid 395 through 398 No H-bonds generated for 'chain 'g' and resid 395 through 398' Processing helix chain 'g' and resid 403 through 430 removed outlier: 3.762A pdb=" N PHE g 414 " --> pdb=" O ILE g 410 " (cutoff:3.500A) Proline residue: g 419 - end of helix Processing helix chain 'g' and resid 437 through 454 Processing helix chain 'g' and resid 466 through 482 Processing helix chain 'g' and resid 486 through 506 removed outlier: 3.525A pdb=" N LEU g 499 " --> pdb=" O PHE g 495 " (cutoff:3.500A) Processing helix chain 'g' and resid 509 through 515 removed outlier: 3.632A pdb=" N LEU g 512 " --> pdb=" O GLY g 509 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL g 513 " --> pdb=" O SER g 510 " (cutoff:3.500A) Processing helix chain 'g' and resid 518 through 546 removed outlier: 3.629A pdb=" N LEU g 540 " --> pdb=" O THR g 536 " (cutoff:3.500A) Processing helix chain 'g' and resid 570 through 592 Processing helix chain 'g' and resid 599 through 607 Processing helix chain 'g' and resid 609 through 622 Processing helix chain 'g' and resid 661 through 689 removed outlier: 3.758A pdb=" N PHE g 665 " --> pdb=" O ILE g 661 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ALA g 668 " --> pdb=" O MET g 664 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N LEU g 669 " --> pdb=" O PHE g 665 " (cutoff:3.500A) Proline residue: g 670 - end of helix Processing helix chain 'g' and resid 692 through 694 No H-bonds generated for 'chain 'g' and resid 692 through 694' Processing helix chain 'g' and resid 704 through 718 removed outlier: 3.719A pdb=" N LEU g 718 " --> pdb=" O GLY g 714 " (cutoff:3.500A) Processing helix chain 'g' and resid 728 through 737 Processing helix chain 'g' and resid 761 through 773 Processing helix chain 'g' and resid 777 through 782 removed outlier: 4.136A pdb=" N ARG g 782 " --> pdb=" O PRO g 778 " (cutoff:3.500A) Processing helix chain 'g' and resid 785 through 800 removed outlier: 4.138A pdb=" N LEU g 800 " --> pdb=" O GLY g 796 " (cutoff:3.500A) Processing helix chain 'g' and resid 804 through 812 Processing helix chain 'g' and resid 830 through 852 Processing helix chain 'g' and resid 856 through 877 Proline residue: g 860 - end of helix Proline residue: g 868 - end of helix removed outlier: 4.878A pdb=" N LEU g 873 " --> pdb=" O ARG g 870 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LEU g 874 " --> pdb=" O ARG g 871 " (cutoff:3.500A) Proline residue: g 875 - end of helix Processing helix chain 'g' and resid 880 through 886 Processing sheet with id= A, first strand: chain 'X' and resid 31 through 34 removed outlier: 4.667A pdb=" N LEU X 31 " --> pdb=" O GLN X 133 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU X 119 " --> pdb=" O LEU X 131 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLN X 133 " --> pdb=" O TYR X 117 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N TYR X 117 " --> pdb=" O GLN X 133 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N THR X 135 " --> pdb=" O GLY X 115 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLY X 115 " --> pdb=" O THR X 135 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'X' and resid 7 through 11 removed outlier: 6.858A pdb=" N TYR X 44 " --> pdb=" O LYS X 8 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N CYS X 10 " --> pdb=" O ILE X 42 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ILE X 42 " --> pdb=" O CYS X 10 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N SER X 105 " --> pdb=" O VAL X 94 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N VAL X 94 " --> pdb=" O SER X 105 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N THR X 107 " --> pdb=" O ALA X 92 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ALA X 92 " --> pdb=" O THR X 107 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'X' and resid 163 through 169 Processing sheet with id= D, first strand: chain 'X' and resid 286 through 292 removed outlier: 12.036A pdb=" N THR X 328 " --> pdb=" O PRO X 351 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N THR X 330 " --> pdb=" O LEU X 349 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N SER X 362 " --> pdb=" O SER X 352 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'X' and resid 294 through 296 Processing sheet with id= F, first strand: chain 'X' and resid 303 through 309 removed outlier: 6.517A pdb=" N SER X 392 " --> pdb=" O ILE X 304 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N GLU X 306 " --> pdb=" O SER X 392 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL X 394 " --> pdb=" O GLU X 306 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N TYR X 308 " --> pdb=" O VAL X 394 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N TRP X 396 " --> pdb=" O TYR X 308 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'X' and resid 419 through 421 Processing sheet with id= H, first strand: chain 'X' and resid 475 through 480 Processing sheet with id= I, first strand: chain 'X' and resid 484 through 486 removed outlier: 6.360A pdb=" N ALA X 584 " --> pdb=" O LEU X 485 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'X' and resid 576 through 583 removed outlier: 6.462A pdb=" N ALA X 515 " --> pdb=" O LYS X 525 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N LYS X 525 " --> pdb=" O ALA X 515 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'X' and resid 590 through 593 Processing sheet with id= L, first strand: chain 'X' and resid 597 through 599 removed outlier: 8.172A pdb=" N ALA X 598 " --> pdb=" O SER X 681 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N THR X 683 " --> pdb=" O ALA X 598 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'V' and resid 85 through 87 removed outlier: 3.870A pdb=" N GLU V 72 " --> pdb=" O ASP V 67 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP V 67 " --> pdb=" O GLU V 72 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU V 61 " --> pdb=" O ALA V 78 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ARG V 80 " --> pdb=" O VAL V 59 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL V 59 " --> pdb=" O ARG V 80 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ARG V 233 " --> pdb=" O LEU V 64 " (cutoff:3.500A) removed outlier: 10.183A pdb=" N MET V 66 " --> pdb=" O ARG V 233 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N LEU V 228 " --> pdb=" O ARG V 263 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LEU V 265 " --> pdb=" O LEU V 228 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LEU V 230 " --> pdb=" O LEU V 265 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N VAL V 267 " --> pdb=" O LEU V 230 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N GLY V 232 " --> pdb=" O VAL V 267 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LEU V 269 " --> pdb=" O GLY V 232 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N THR V 118 " --> pdb=" O PHE V 244 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ARG V 246 " --> pdb=" O THR V 118 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU V 120 " --> pdb=" O ARG V 246 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'V' and resid 739 through 741 Processing sheet with id= O, first strand: chain 'e' and resid 84 through 87 removed outlier: 6.784A pdb=" N LEU e 61 " --> pdb=" O ALA e 78 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ARG e 80 " --> pdb=" O VAL e 59 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL e 59 " --> pdb=" O ARG e 80 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N THR e 227 " --> pdb=" O GLU e 60 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N GLN e 62 " --> pdb=" O THR e 227 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL e 229 " --> pdb=" O GLN e 62 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N LEU e 64 " --> pdb=" O VAL e 229 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N VAL e 231 " --> pdb=" O LEU e 64 " (cutoff:3.500A) removed outlier: 9.864A pdb=" N MET e 66 " --> pdb=" O VAL e 231 " (cutoff:3.500A) removed outlier: 12.513A pdb=" N ARG e 233 " --> pdb=" O MET e 66 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N LEU e 228 " --> pdb=" O ARG e 263 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LEU e 265 " --> pdb=" O LEU e 228 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LEU e 230 " --> pdb=" O LEU e 265 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N VAL e 267 " --> pdb=" O LEU e 230 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N GLY e 232 " --> pdb=" O VAL e 267 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU e 269 " --> pdb=" O GLY e 232 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N THR e 118 " --> pdb=" O PHE e 244 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N ARG e 246 " --> pdb=" O THR e 118 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LEU e 120 " --> pdb=" O ARG e 246 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'e' and resid 65 through 67 Processing sheet with id= Q, first strand: chain 'e' and resid 739 through 741 removed outlier: 3.903A pdb=" N GLU e 755 " --> pdb=" O VAL e 740 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'Y' and resid 85 through 87 removed outlier: 6.875A pdb=" N LEU Y 61 " --> pdb=" O ALA Y 78 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ARG Y 80 " --> pdb=" O VAL Y 59 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL Y 59 " --> pdb=" O ARG Y 80 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ARG Y 233 " --> pdb=" O LEU Y 64 " (cutoff:3.500A) removed outlier: 10.474A pdb=" N MET Y 66 " --> pdb=" O ARG Y 233 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N LEU Y 228 " --> pdb=" O ARG Y 263 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LEU Y 265 " --> pdb=" O LEU Y 228 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU Y 230 " --> pdb=" O LEU Y 265 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL Y 267 " --> pdb=" O LEU Y 230 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N GLY Y 232 " --> pdb=" O VAL Y 267 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU Y 269 " --> pdb=" O GLY Y 232 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N THR Y 118 " --> pdb=" O PHE Y 244 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N ARG Y 246 " --> pdb=" O THR Y 118 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU Y 120 " --> pdb=" O ARG Y 246 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'Y' and resid 65 through 67 Processing sheet with id= T, first strand: chain 'Y' and resid 739 through 741 Processing sheet with id= U, first strand: chain 'f' and resid 85 through 87 removed outlier: 6.955A pdb=" N LEU f 61 " --> pdb=" O ALA f 78 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ARG f 80 " --> pdb=" O VAL f 59 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL f 59 " --> pdb=" O ARG f 80 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N THR f 227 " --> pdb=" O GLU f 60 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N GLN f 62 " --> pdb=" O THR f 227 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL f 229 " --> pdb=" O GLN f 62 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N LEU f 64 " --> pdb=" O VAL f 229 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N VAL f 231 " --> pdb=" O LEU f 64 " (cutoff:3.500A) removed outlier: 9.632A pdb=" N MET f 66 " --> pdb=" O VAL f 231 " (cutoff:3.500A) removed outlier: 12.299A pdb=" N ARG f 233 " --> pdb=" O MET f 66 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N LEU f 228 " --> pdb=" O ARG f 263 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU f 265 " --> pdb=" O LEU f 228 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LEU f 230 " --> pdb=" O LEU f 265 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL f 267 " --> pdb=" O LEU f 230 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N GLY f 232 " --> pdb=" O VAL f 267 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LEU f 269 " --> pdb=" O GLY f 232 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ARG f 263 " --> pdb=" O LEU f 247 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N THR f 118 " --> pdb=" O PHE f 244 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ARG f 246 " --> pdb=" O THR f 118 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU f 120 " --> pdb=" O ARG f 246 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'f' and resid 65 through 67 Processing sheet with id= W, first strand: chain 'f' and resid 739 through 741 Processing sheet with id= X, first strand: chain 'Z' and resid 85 through 87 removed outlier: 6.798A pdb=" N LEU Z 61 " --> pdb=" O ALA Z 78 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ARG Z 80 " --> pdb=" O VAL Z 59 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL Z 59 " --> pdb=" O ARG Z 80 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LEU Z 228 " --> pdb=" O ARG Z 263 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LEU Z 265 " --> pdb=" O LEU Z 228 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU Z 230 " --> pdb=" O LEU Z 265 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL Z 267 " --> pdb=" O LEU Z 230 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N THR Z 118 " --> pdb=" O PHE Z 244 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ARG Z 246 " --> pdb=" O THR Z 118 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU Z 120 " --> pdb=" O ARG Z 246 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'Z' and resid 65 through 67 Processing sheet with id= Z, first strand: chain 'Z' and resid 461 through 463 removed outlier: 4.951A pdb=" N VAL Z 461 " --> pdb=" O THR Z 727 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'Z' and resid 739 through 741 Processing sheet with id= AB, first strand: chain 'g' and resid 84 through 87 removed outlier: 6.670A pdb=" N LEU g 61 " --> pdb=" O ALA g 78 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ARG g 80 " --> pdb=" O VAL g 59 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL g 59 " --> pdb=" O ARG g 80 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N VAL g 82 " --> pdb=" O VAL g 57 " (cutoff:3.500A) removed outlier: 9.334A pdb=" N VAL g 57 " --> pdb=" O VAL g 82 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLU g 225 " --> pdb=" O TYR g 58 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N GLU g 60 " --> pdb=" O GLU g 225 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR g 227 " --> pdb=" O GLU g 60 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N GLN g 62 " --> pdb=" O THR g 227 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL g 229 " --> pdb=" O GLN g 62 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N LEU g 64 " --> pdb=" O VAL g 229 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N VAL g 231 " --> pdb=" O LEU g 64 " (cutoff:3.500A) removed outlier: 9.824A pdb=" N MET g 66 " --> pdb=" O VAL g 231 " (cutoff:3.500A) removed outlier: 12.579A pdb=" N ARG g 233 " --> pdb=" O MET g 66 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N LEU g 228 " --> pdb=" O PRO g 261 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N ARG g 263 " --> pdb=" O LEU g 228 " (cutoff:3.500A) removed outlier: 12.171A pdb=" N LEU g 230 " --> pdb=" O ARG g 263 " (cutoff:3.500A) removed outlier: 9.731A pdb=" N LEU g 265 " --> pdb=" O LEU g 230 " (cutoff:3.500A) removed outlier: 12.365A pdb=" N GLY g 232 " --> pdb=" O LEU g 265 " (cutoff:3.500A) removed outlier: 9.740A pdb=" N VAL g 267 " --> pdb=" O GLY g 232 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ARG g 263 " --> pdb=" O LEU g 247 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N THR g 118 " --> pdb=" O PHE g 244 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ARG g 246 " --> pdb=" O THR g 118 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU g 120 " --> pdb=" O ARG g 246 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'g' and resid 739 through 741 2944 hydrogen bonds defined for protein. 8431 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: 18.99 Time building geometry restraints manager: 21.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 9498 1.31 - 1.44: 16145 1.44 - 1.56: 35932 1.56 - 1.69: 27 1.69 - 1.82: 460 Bond restraints: 62062 Sorted by residual: bond pdb=" C1B PIO e1002 " pdb=" O3C PIO e1002 " ideal model delta sigma weight residual 1.419 1.326 0.093 2.00e-02 2.50e+03 2.18e+01 bond pdb=" C1B PIO Y1004 " pdb=" O3C PIO Y1004 " ideal model delta sigma weight residual 1.419 1.326 0.093 2.00e-02 2.50e+03 2.16e+01 bond pdb=" C1B PIO g1001 " pdb=" O3C PIO g1001 " ideal model delta sigma weight residual 1.419 1.327 0.092 2.00e-02 2.50e+03 2.10e+01 bond pdb=" C1B PIO V1004 " pdb=" O3C PIO V1004 " ideal model delta sigma weight residual 1.419 1.328 0.091 2.00e-02 2.50e+03 2.07e+01 bond pdb=" C1B PIO f1002 " pdb=" O3C PIO f1002 " ideal model delta sigma weight residual 1.419 1.328 0.091 2.00e-02 2.50e+03 2.05e+01 ... (remaining 62057 not shown) Histogram of bond angle deviations from ideal: 95.78 - 103.50: 932 103.50 - 111.22: 25640 111.22 - 118.94: 25912 118.94 - 126.65: 31020 126.65 - 134.37: 874 Bond angle restraints: 84378 Sorted by residual: angle pdb=" N PRO e 97 " pdb=" CA PRO e 97 " pdb=" CB PRO e 97 " ideal model delta sigma weight residual 103.23 97.18 6.05 6.70e-01 2.23e+00 8.15e+01 angle pdb=" C PRO e 97 " pdb=" CA PRO e 97 " pdb=" CB PRO e 97 " ideal model delta sigma weight residual 111.40 118.15 -6.75 9.10e-01 1.21e+00 5.50e+01 angle pdb=" N GLU g 218 " pdb=" CA GLU g 218 " pdb=" C GLU g 218 " ideal model delta sigma weight residual 113.15 104.60 8.55 1.19e+00 7.06e-01 5.16e+01 angle pdb=" N PRO f 548 " pdb=" CA PRO f 548 " pdb=" C PRO f 548 " ideal model delta sigma weight residual 111.13 121.44 -10.31 1.49e+00 4.50e-01 4.79e+01 angle pdb=" N LYS A 436 " pdb=" CA LYS A 436 " pdb=" C LYS A 436 " ideal model delta sigma weight residual 110.30 100.47 9.83 1.50e+00 4.44e-01 4.30e+01 ... (remaining 84373 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.29: 35327 31.29 - 62.59: 1979 62.59 - 93.88: 234 93.88 - 125.18: 27 125.18 - 156.47: 4 Dihedral angle restraints: 37571 sinusoidal: 15474 harmonic: 22097 Sorted by residual: dihedral pdb=" CA TRP e 81 " pdb=" C TRP e 81 " pdb=" N VAL e 82 " pdb=" CA VAL e 82 " ideal model delta harmonic sigma weight residual 180.00 157.23 22.77 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" C1A PIO V1004 " pdb=" C2C PIO V1004 " pdb=" O2C PIO V1004 " pdb=" C1C PIO V1004 " ideal model delta sinusoidal sigma weight residual -111.77 44.70 -156.47 1 3.00e+01 1.11e-03 2.04e+01 dihedral pdb=" C1A PIO V1004 " pdb=" C2C PIO V1004 " pdb=" O2C PIO V1004 " pdb=" C3C PIO V1004 " ideal model delta sinusoidal sigma weight residual 128.15 -80.17 -151.68 1 3.00e+01 1.11e-03 2.01e+01 ... (remaining 37568 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 7919 0.058 - 0.117: 1648 0.117 - 0.175: 291 0.175 - 0.233: 62 0.233 - 0.292: 7 Chirality restraints: 9927 Sorted by residual: chirality pdb=" C1 NAG Z1003 " pdb=" O4 NAG Z1002 " pdb=" C2 NAG Z1003 " pdb=" O5 NAG Z1003 " both_signs ideal model delta sigma weight residual False -2.40 -2.46 0.06 2.00e-02 2.50e+03 9.16e+00 chirality pdb=" CG LEU K 386 " pdb=" CB LEU K 386 " pdb=" CD1 LEU K 386 " pdb=" CD2 LEU K 386 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CB VAL g 697 " pdb=" CA VAL g 697 " pdb=" CG1 VAL g 697 " pdb=" CG2 VAL g 697 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 9924 not shown) Planarity restraints: 10492 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 PIO g1002 " -0.557 2.00e-02 2.50e+03 4.96e-01 7.38e+03 pdb=" C2 PIO g1002 " -0.161 2.00e-02 2.50e+03 pdb=" C3 PIO g1002 " -0.503 2.00e-02 2.50e+03 pdb=" C4 PIO g1002 " 0.174 2.00e-02 2.50e+03 pdb=" C5 PIO g1002 " -0.154 2.00e-02 2.50e+03 pdb=" C6 PIO g1002 " 0.131 2.00e-02 2.50e+03 pdb=" O1 PIO g1002 " -0.109 2.00e-02 2.50e+03 pdb=" O2 PIO g1002 " 1.233 2.00e-02 2.50e+03 pdb=" O3 PIO g1002 " -0.098 2.00e-02 2.50e+03 pdb=" O4 PIO g1002 " -0.360 2.00e-02 2.50e+03 pdb=" O5 PIO g1002 " 0.721 2.00e-02 2.50e+03 pdb=" O6 PIO g1002 " -0.316 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 PIO e1002 " 0.562 2.00e-02 2.50e+03 4.92e-01 7.25e+03 pdb=" C2 PIO e1002 " 0.143 2.00e-02 2.50e+03 pdb=" C3 PIO e1002 " 0.496 2.00e-02 2.50e+03 pdb=" C4 PIO e1002 " -0.173 2.00e-02 2.50e+03 pdb=" C5 PIO e1002 " 0.173 2.00e-02 2.50e+03 pdb=" C6 PIO e1002 " -0.142 2.00e-02 2.50e+03 pdb=" O1 PIO e1002 " 0.160 2.00e-02 2.50e+03 pdb=" O2 PIO e1002 " -1.260 2.00e-02 2.50e+03 pdb=" O3 PIO e1002 " 0.091 2.00e-02 2.50e+03 pdb=" O4 PIO e1002 " 0.349 2.00e-02 2.50e+03 pdb=" O5 PIO e1002 " -0.655 2.00e-02 2.50e+03 pdb=" O6 PIO e1002 " 0.256 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 PIO f1002 " 0.556 2.00e-02 2.50e+03 4.83e-01 7.00e+03 pdb=" C2 PIO f1002 " 0.151 2.00e-02 2.50e+03 pdb=" C3 PIO f1002 " 0.501 2.00e-02 2.50e+03 pdb=" C4 PIO f1002 " -0.177 2.00e-02 2.50e+03 pdb=" C5 PIO f1002 " 0.185 2.00e-02 2.50e+03 pdb=" C6 PIO f1002 " -0.150 2.00e-02 2.50e+03 pdb=" O1 PIO f1002 " 0.155 2.00e-02 2.50e+03 pdb=" O2 PIO f1002 " -1.249 2.00e-02 2.50e+03 pdb=" O3 PIO f1002 " 0.106 2.00e-02 2.50e+03 pdb=" O4 PIO f1002 " 0.306 2.00e-02 2.50e+03 pdb=" O5 PIO f1002 " -0.619 2.00e-02 2.50e+03 pdb=" O6 PIO f1002 " 0.235 2.00e-02 2.50e+03 ... (remaining 10489 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 8486 2.75 - 3.29: 59612 3.29 - 3.83: 108683 3.83 - 4.36: 130792 4.36 - 4.90: 216789 Nonbonded interactions: 524362 Sorted by model distance: nonbonded pdb=" OE2 GLU Z 472 " pdb=" OH TYR Z 486 " model vdw 2.218 2.440 nonbonded pdb=" OE2 GLU X 331 " pdb=" OH TYR X 435 " model vdw 2.224 2.440 nonbonded pdb=" O LEU Z 863 " pdb=" OG1 THR Z 866 " model vdw 2.224 2.440 nonbonded pdb=" OE1 GLU g 472 " pdb=" OH TYR g 486 " model vdw 2.227 2.440 nonbonded pdb=" O PRO Q 316 " pdb=" OG1 THR Q 320 " model vdw 2.241 2.440 ... (remaining 524357 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 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = (chain 'L' and resid 1 through 409) selection = (chain 'Q' and (resid 1 through 26 or resid 48 through 409)) } ncs_group { reference = (chain 'R' and resid 85 through 117) selection = chain 'S' selection = (chain 'T' and resid 85 through 117) selection = (chain 'a' and resid 85 through 117) selection = (chain 'b' and resid 85 through 117) selection = (chain 'c' and resid 85 through 117) } ncs_group { reference = (chain 'V' and (resid 56 through 203 or resid 217 through 890)) selection = (chain 'Y' and (resid 56 through 203 or resid 217 through 890)) selection = (chain 'Z' and (resid 56 through 203 or resid 217 through 890)) selection = (chain 'e' and ((resid 56 and (name N or name CA or name C or name O or name CB \ )) or resid 57 through 181 or resid 192 through 348 or resid 371 through 890)) selection = (chain 'f' and ((resid 56 and (name N or name CA or name C or name O or name CB \ )) or resid 57 through 181 or resid 192 through 348 or resid 371 through 890)) selection = (chain 'g' and ((resid 56 and (name N or name CA or name C or name O or name CB \ )) or resid 57 through 181 or resid 192 through 348 or resid 371 through 890)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.44 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.410 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: 0.060 Extract box with map and model: 19.160 Check model and map are aligned: 0.690 Set scattering table: 0.410 Process input model: 128.900 Find NCS groups from input model: 3.910 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 169.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 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 : 0.006 0.093 62062 Z= 0.380 Angle : 0.845 10.315 84378 Z= 0.530 Chirality : 0.051 0.292 9927 Planarity : 0.013 0.496 10486 Dihedral : 18.626 156.470 23289 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.29 % Allowed : 2.20 % Favored : 97.50 % Rotamer: Outliers : 3.66 % Allowed : 22.39 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.60 % 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: 0.33 (0.09), residues: 7580 helix: 0.56 (0.08), residues: 4366 sheet: 1.14 (0.22), residues: 547 loop : -0.37 (0.11), residues: 2667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP g 75 HIS 0.016 0.001 HIS A 739 PHE 0.030 0.002 PHE Y 314 TYR 0.025 0.002 TYR g 824 ARG 0.025 0.001 ARG A 550 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15160 Ramachandran restraints generated. 7580 Oldfield, 0 Emsley, 7580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15160 Ramachandran restraints generated. 7580 Oldfield, 0 Emsley, 7580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1334 residues out of total 6541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 1098 time to evaluate : 5.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 600 TRP cc_start: 0.8056 (p-90) cc_final: 0.7458 (p-90) REVERT: K 21 GLU cc_start: 0.8607 (tp30) cc_final: 0.8365 (tp30) REVERT: Q 231 GLU cc_start: 0.7035 (mp0) cc_final: 0.6534 (mp0) REVERT: Q 294 PHE cc_start: 0.8853 (OUTLIER) cc_final: 0.7750 (p90) REVERT: X 123 VAL cc_start: 0.8461 (t) cc_final: 0.8101 (m) REVERT: V 330 GLN cc_start: 0.7578 (tt0) cc_final: 0.6690 (mp-120) REVERT: V 343 LEU cc_start: 0.7844 (mt) cc_final: 0.7602 (mt) REVERT: e 118 THR cc_start: 0.8039 (m) cc_final: 0.7791 (p) REVERT: e 133 ASN cc_start: 0.7751 (m-40) cc_final: 0.7469 (m-40) REVERT: e 511 PHE cc_start: 0.7862 (OUTLIER) cc_final: 0.7641 (p90) REVERT: e 535 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7534 (mp0) REVERT: e 663 MET cc_start: 0.5378 (OUTLIER) cc_final: 0.4121 (tpp) REVERT: e 664 MET cc_start: 0.7265 (mtm) cc_final: 0.7041 (mtt) REVERT: e 721 MET cc_start: 0.8205 (mmm) cc_final: 0.7961 (mmm) REVERT: e 871 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7620 (mtp-110) REVERT: Y 289 MET cc_start: 0.8899 (tpt) cc_final: 0.8685 (tpt) REVERT: Y 308 LEU cc_start: 0.8669 (mm) cc_final: 0.8379 (mp) REVERT: Y 430 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7724 (mtpm) REVERT: Y 469 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8114 (tp) REVERT: Y 514 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7614 (ptm160) REVERT: f 116 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.7775 (pttp) REVERT: f 191 GLN cc_start: 0.7073 (mm110) cc_final: 0.6835 (pp30) REVERT: f 337 PRO cc_start: 0.7930 (Cg_exo) cc_final: 0.7631 (Cg_endo) REVERT: f 621 ASP cc_start: 0.7341 (OUTLIER) cc_final: 0.7110 (t0) REVERT: Z 141 PHE cc_start: 0.7801 (t80) cc_final: 0.7588 (t80) REVERT: Z 197 THR cc_start: 0.8620 (m) cc_final: 0.8385 (p) REVERT: g 67 ASP cc_start: 0.6266 (OUTLIER) cc_final: 0.5551 (p0) REVERT: g 68 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.6252 (mm-30) REVERT: g 166 GLU cc_start: 0.6770 (OUTLIER) cc_final: 0.6457 (mt-10) REVERT: g 198 GLN cc_start: 0.7133 (tp40) cc_final: 0.6425 (tp-100) REVERT: g 333 LEU cc_start: 0.7765 (mt) cc_final: 0.7436 (tt) REVERT: g 473 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7487 (mt-10) REVERT: g 519 TYR cc_start: 0.8615 (t80) cc_final: 0.8364 (t80) REVERT: g 649 VAL cc_start: 0.8726 (t) cc_final: 0.8496 (p) REVERT: g 871 ARG cc_start: 0.7325 (ttp80) cc_final: 0.6833 (mtt90) outliers start: 236 outliers final: 139 residues processed: 1278 average time/residue: 1.3149 time to fit residues: 2176.1651 Evaluate side-chains 1172 residues out of total 6541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 1020 time to evaluate : 5.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 667 SER Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 66 THR Chi-restraints excluded: chain K residue 99 SER Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 200 GLN Chi-restraints excluded: chain K residue 230 SER Chi-restraints excluded: chain K residue 248 SER Chi-restraints excluded: chain K residue 268 THR Chi-restraints excluded: chain K residue 311 CYS Chi-restraints excluded: chain K residue 330 SER Chi-restraints excluded: chain L residue 387 LEU Chi-restraints excluded: chain Q residue 294 PHE Chi-restraints excluded: chain X residue 88 LYS Chi-restraints excluded: chain X residue 118 SER Chi-restraints excluded: chain X residue 407 THR Chi-restraints excluded: chain X residue 533 LEU Chi-restraints excluded: chain X residue 648 MET Chi-restraints excluded: chain X residue 659 VAL Chi-restraints excluded: chain P residue 61 VAL Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain P residue 75 ILE Chi-restraints excluded: chain R residue 91 GLU Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain a residue 87 PHE Chi-restraints excluded: chain V residue 126 THR Chi-restraints excluded: chain V residue 173 VAL Chi-restraints excluded: chain V residue 194 SER Chi-restraints excluded: chain V residue 265 LEU Chi-restraints excluded: chain V residue 334 SER Chi-restraints excluded: chain V residue 338 VAL Chi-restraints excluded: chain V residue 339 GLN Chi-restraints excluded: chain V residue 340 ARG Chi-restraints excluded: chain V residue 437 VAL Chi-restraints excluded: chain V residue 497 LEU Chi-restraints excluded: chain V residue 552 THR Chi-restraints excluded: chain V residue 604 VAL Chi-restraints excluded: chain V residue 773 SER Chi-restraints excluded: chain V residue 863 LEU Chi-restraints excluded: chain V residue 864 ILE Chi-restraints excluded: chain e residue 68 GLU Chi-restraints excluded: chain e residue 82 VAL Chi-restraints excluded: chain e residue 223 ASP Chi-restraints excluded: chain e residue 237 LEU Chi-restraints excluded: chain e residue 372 LEU Chi-restraints excluded: chain e residue 426 LEU Chi-restraints excluded: chain e residue 438 SER Chi-restraints excluded: chain e residue 462 VAL Chi-restraints excluded: chain e residue 487 ILE Chi-restraints excluded: chain e residue 510 SER Chi-restraints excluded: chain e residue 511 PHE Chi-restraints excluded: chain e residue 535 GLU Chi-restraints excluded: chain e residue 560 VAL Chi-restraints excluded: chain e residue 643 SER Chi-restraints excluded: chain e residue 663 MET Chi-restraints excluded: chain e residue 822 VAL Chi-restraints excluded: chain e residue 871 ARG Chi-restraints excluded: chain e residue 881 VAL Chi-restraints excluded: chain Y residue 217 LEU Chi-restraints excluded: chain Y residue 249 GLU Chi-restraints excluded: chain Y residue 372 LEU Chi-restraints excluded: chain Y residue 426 LEU Chi-restraints excluded: chain Y residue 430 LYS Chi-restraints excluded: chain Y residue 469 LEU Chi-restraints excluded: chain Y residue 477 SER Chi-restraints excluded: chain Y residue 486 TYR Chi-restraints excluded: chain Y residue 499 LEU Chi-restraints excluded: chain Y residue 505 VAL Chi-restraints excluded: chain Y residue 514 ARG Chi-restraints excluded: chain Y residue 633 SER Chi-restraints excluded: chain Y residue 672 LEU Chi-restraints excluded: chain Y residue 682 SER Chi-restraints excluded: chain Y residue 774 ILE Chi-restraints excluded: chain Y residue 797 VAL Chi-restraints excluded: chain Y residue 812 LEU Chi-restraints excluded: chain Y residue 851 LYS Chi-restraints excluded: chain Y residue 856 SER Chi-restraints excluded: chain Y residue 877 ILE Chi-restraints excluded: chain f residue 116 LYS Chi-restraints excluded: chain f residue 135 LEU Chi-restraints excluded: chain f residue 219 LYS Chi-restraints excluded: chain f residue 281 LEU Chi-restraints excluded: chain f residue 289 MET Chi-restraints excluded: chain f residue 426 LEU Chi-restraints excluded: chain f residue 558 LEU Chi-restraints excluded: chain f residue 576 VAL Chi-restraints excluded: chain f residue 601 LEU Chi-restraints excluded: chain f residue 621 ASP Chi-restraints excluded: chain f residue 634 VAL Chi-restraints excluded: chain f residue 662 TRP Chi-restraints excluded: chain f residue 663 MET Chi-restraints excluded: chain f residue 667 SER Chi-restraints excluded: chain f residue 704 LEU Chi-restraints excluded: chain f residue 779 ILE Chi-restraints excluded: chain f residue 825 VAL Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain Z residue 59 VAL Chi-restraints excluded: chain Z residue 106 SER Chi-restraints excluded: chain Z residue 108 LEU Chi-restraints excluded: chain Z residue 126 THR Chi-restraints excluded: chain Z residue 217 LEU Chi-restraints excluded: chain Z residue 231 VAL Chi-restraints excluded: chain Z residue 290 SER Chi-restraints excluded: chain Z residue 502 VAL Chi-restraints excluded: chain Z residue 546 ASP Chi-restraints excluded: chain Z residue 557 VAL Chi-restraints excluded: chain Z residue 604 VAL Chi-restraints excluded: chain Z residue 658 GLU Chi-restraints excluded: chain g residue 66 MET Chi-restraints excluded: chain g residue 67 ASP Chi-restraints excluded: chain g residue 68 GLU Chi-restraints excluded: chain g residue 82 VAL Chi-restraints excluded: chain g residue 119 VAL Chi-restraints excluded: chain g residue 166 GLU Chi-restraints excluded: chain g residue 167 LEU Chi-restraints excluded: chain g residue 173 VAL Chi-restraints excluded: chain g residue 197 THR Chi-restraints excluded: chain g residue 262 ILE Chi-restraints excluded: chain g residue 345 ARG Chi-restraints excluded: chain g residue 462 VAL Chi-restraints excluded: chain g residue 485 GLU Chi-restraints excluded: chain g residue 528 ILE Chi-restraints excluded: chain g residue 595 SER Chi-restraints excluded: chain g residue 601 LEU Chi-restraints excluded: chain g residue 646 ARG Chi-restraints excluded: chain g residue 657 SER Chi-restraints excluded: chain g residue 673 LEU Chi-restraints excluded: chain g residue 680 LEU Chi-restraints excluded: chain g residue 681 GLU Chi-restraints excluded: chain g residue 718 LEU Chi-restraints excluded: chain g residue 814 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 641 optimal weight: 4.9990 chunk 576 optimal weight: 1.9990 chunk 319 optimal weight: 1.9990 chunk 196 optimal weight: 2.9990 chunk 388 optimal weight: 0.8980 chunk 307 optimal weight: 0.5980 chunk 595 optimal weight: 5.9990 chunk 230 optimal weight: 0.0980 chunk 362 optimal weight: 20.0000 chunk 443 optimal weight: 3.9990 chunk 690 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 66 HIS ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 162 HIS A 194 GLN A 350 HIS A 442 HIS A 459 ASN ** A 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 HIS K 200 GLN L 98 GLN L 102 GLN Q 83 ASN X 73 ASN X 492 GLN X 499 ASN X 551 ASN ** V 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 198 GLN V 545 GLN V 630 GLN V 834 HIS e 302 GLN e 564 GLN Y 71 GLN Y 683 GLN f 564 GLN f 569 ASN ** f 819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 377 GLN Z 433 ASN Z 593 ASN ** Z 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 62 GLN g 70 ASN g 101 HIS g 203 GLN g 433 ASN g 880 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.0810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 62062 Z= 0.210 Angle : 0.675 17.248 84378 Z= 0.305 Chirality : 0.041 0.251 9927 Planarity : 0.005 0.058 10486 Dihedral : 11.415 147.794 9600 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.78 % Favored : 98.20 % Rotamer: Outliers : 4.13 % Allowed : 21.29 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.60 % 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: 0.96 (0.09), residues: 7580 helix: 1.12 (0.08), residues: 4359 sheet: 1.27 (0.22), residues: 531 loop : -0.15 (0.12), residues: 2690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP V 492 HIS 0.007 0.001 HIS A 607 PHE 0.021 0.001 PHE V 314 TYR 0.017 0.002 TYR X 167 ARG 0.010 0.000 ARG g 74 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15160 Ramachandran restraints generated. 7580 Oldfield, 0 Emsley, 7580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15160 Ramachandran restraints generated. 7580 Oldfield, 0 Emsley, 7580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1316 residues out of total 6541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 266 poor density : 1050 time to evaluate : 5.139 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 ASP cc_start: 0.7652 (t0) cc_final: 0.7296 (t0) REVERT: A 66 HIS cc_start: 0.8287 (m170) cc_final: 0.7924 (m-70) REVERT: A 187 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.7372 (mtp85) REVERT: A 600 TRP cc_start: 0.8072 (p-90) cc_final: 0.7500 (p-90) REVERT: A 700 MET cc_start: 0.7844 (OUTLIER) cc_final: 0.7425 (mtp) REVERT: A 730 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8547 (mtmm) REVERT: A 776 ARG cc_start: 0.7763 (ttp80) cc_final: 0.7473 (mtm110) REVERT: K 21 GLU cc_start: 0.8669 (tp30) cc_final: 0.8267 (tp30) REVERT: K 262 GLN cc_start: 0.7966 (OUTLIER) cc_final: 0.7736 (mp10) REVERT: Q 231 GLU cc_start: 0.6996 (mp0) cc_final: 0.6486 (mp0) REVERT: X 128 GLN cc_start: 0.7291 (tt0) cc_final: 0.7074 (tt0) REVERT: X 549 PHE cc_start: 0.8166 (OUTLIER) cc_final: 0.7155 (t80) REVERT: P 75 ILE cc_start: 0.6877 (OUTLIER) cc_final: 0.6404 (mt) REVERT: V 272 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7476 (mp0) REVERT: V 330 GLN cc_start: 0.7587 (tt0) cc_final: 0.6725 (mp-120) REVERT: V 343 LEU cc_start: 0.7870 (mt) cc_final: 0.7670 (mt) REVERT: e 118 THR cc_start: 0.8069 (m) cc_final: 0.7859 (p) REVERT: e 128 LEU cc_start: 0.6301 (OUTLIER) cc_final: 0.6074 (tp) REVERT: e 133 ASN cc_start: 0.7739 (m-40) cc_final: 0.7415 (m110) REVERT: e 535 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7536 (mp0) REVERT: S 87 PHE cc_start: 0.5674 (OUTLIER) cc_final: 0.5315 (m-80) REVERT: Y 248 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.7754 (tm-30) REVERT: Y 291 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7479 (tt0) REVERT: Y 308 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8376 (mp) REVERT: Y 544 PHE cc_start: 0.7770 (OUTLIER) cc_final: 0.7357 (t80) REVERT: f 191 GLN cc_start: 0.7040 (mm110) cc_final: 0.6819 (pp30) REVERT: f 291 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8238 (tt0) REVERT: f 535 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.7073 (mt-10) REVERT: Z 60 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7764 (tp30) REVERT: Z 141 PHE cc_start: 0.7791 (t80) cc_final: 0.7534 (t80) REVERT: Z 197 THR cc_start: 0.8636 (m) cc_final: 0.8393 (p) REVERT: Z 291 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7354 (tm-30) REVERT: Z 480 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7491 (mp0) REVERT: Z 650 ILE cc_start: 0.8478 (OUTLIER) cc_final: 0.8277 (mm) REVERT: Z 696 MET cc_start: 0.8276 (mmt) cc_final: 0.7735 (mmt) REVERT: g 151 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7635 (tm-30) REVERT: g 166 GLU cc_start: 0.6681 (OUTLIER) cc_final: 0.6422 (mt-10) REVERT: g 198 GLN cc_start: 0.7011 (tp40) cc_final: 0.6767 (tp-100) REVERT: g 333 LEU cc_start: 0.7868 (mt) cc_final: 0.7501 (tt) REVERT: g 644 SER cc_start: 0.8053 (OUTLIER) cc_final: 0.7799 (t) REVERT: g 649 VAL cc_start: 0.8744 (t) cc_final: 0.8523 (p) REVERT: g 871 ARG cc_start: 0.7205 (ttp80) cc_final: 0.6711 (mtt90) outliers start: 266 outliers final: 116 residues processed: 1227 average time/residue: 1.3528 time to fit residues: 2157.4016 Evaluate side-chains 1147 residues out of total 6541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 1009 time to evaluate : 5.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 484 ASN Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 667 SER Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 700 MET Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 730 LYS Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 793 THR Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 248 SER Chi-restraints excluded: chain K residue 262 GLN Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 220 MET Chi-restraints excluded: chain L residue 394 GLN Chi-restraints excluded: chain Q residue 10 ILE Chi-restraints excluded: chain Q residue 192 SER Chi-restraints excluded: chain X residue 68 GLN Chi-restraints excluded: chain X residue 83 SER Chi-restraints excluded: chain X residue 298 THR Chi-restraints excluded: chain X residue 407 THR Chi-restraints excluded: chain X residue 549 PHE Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain P residue 75 ILE Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain a residue 87 PHE Chi-restraints excluded: chain V residue 100 SER Chi-restraints excluded: chain V residue 124 GLN Chi-restraints excluded: chain V residue 126 THR Chi-restraints excluded: chain V residue 137 ASP Chi-restraints excluded: chain V residue 149 ASP Chi-restraints excluded: chain V residue 155 ARG Chi-restraints excluded: chain V residue 173 VAL Chi-restraints excluded: chain V residue 231 VAL Chi-restraints excluded: chain V residue 257 GLU Chi-restraints excluded: chain V residue 272 GLU Chi-restraints excluded: chain V residue 338 VAL Chi-restraints excluded: chain V residue 604 VAL Chi-restraints excluded: chain V residue 727 THR Chi-restraints excluded: chain V residue 822 VAL Chi-restraints excluded: chain V residue 837 THR Chi-restraints excluded: chain V residue 839 ILE Chi-restraints excluded: chain V residue 863 LEU Chi-restraints excluded: chain V residue 881 VAL Chi-restraints excluded: chain e residue 128 LEU Chi-restraints excluded: chain e residue 223 ASP Chi-restraints excluded: chain e residue 237 LEU Chi-restraints excluded: chain e residue 372 LEU Chi-restraints excluded: chain e residue 426 LEU Chi-restraints excluded: chain e residue 438 SER Chi-restraints excluded: chain e residue 450 LEU Chi-restraints excluded: chain e residue 462 VAL Chi-restraints excluded: chain e residue 535 GLU Chi-restraints excluded: chain e residue 560 VAL Chi-restraints excluded: chain e residue 696 MET Chi-restraints excluded: chain e residue 732 VAL Chi-restraints excluded: chain e residue 822 VAL Chi-restraints excluded: chain S residue 87 PHE Chi-restraints excluded: chain b residue 112 TYR Chi-restraints excluded: chain Y residue 108 LEU Chi-restraints excluded: chain Y residue 224 SER Chi-restraints excluded: chain Y residue 248 GLN Chi-restraints excluded: chain Y residue 249 GLU Chi-restraints excluded: chain Y residue 291 GLU Chi-restraints excluded: chain Y residue 308 LEU Chi-restraints excluded: chain Y residue 440 LEU Chi-restraints excluded: chain Y residue 486 TYR Chi-restraints excluded: chain Y residue 511 PHE Chi-restraints excluded: chain Y residue 544 PHE Chi-restraints excluded: chain Y residue 672 LEU Chi-restraints excluded: chain f residue 116 LYS Chi-restraints excluded: chain f residue 149 ASP Chi-restraints excluded: chain f residue 173 VAL Chi-restraints excluded: chain f residue 242 LEU Chi-restraints excluded: chain f residue 260 VAL Chi-restraints excluded: chain f residue 281 LEU Chi-restraints excluded: chain f residue 291 GLU Chi-restraints excluded: chain f residue 426 LEU Chi-restraints excluded: chain f residue 477 SER Chi-restraints excluded: chain f residue 535 GLU Chi-restraints excluded: chain f residue 558 LEU Chi-restraints excluded: chain f residue 560 VAL Chi-restraints excluded: chain f residue 594 SER Chi-restraints excluded: chain f residue 662 TRP Chi-restraints excluded: chain f residue 673 LEU Chi-restraints excluded: chain f residue 704 LEU Chi-restraints excluded: chain f residue 741 MET Chi-restraints excluded: chain f residue 755 GLU Chi-restraints excluded: chain f residue 779 ILE Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain c residue 94 LEU Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain Z residue 60 GLU Chi-restraints excluded: chain Z residue 108 LEU Chi-restraints excluded: chain Z residue 177 VAL Chi-restraints excluded: chain Z residue 291 GLU Chi-restraints excluded: chain Z residue 333 LEU Chi-restraints excluded: chain Z residue 480 GLU Chi-restraints excluded: chain Z residue 546 ASP Chi-restraints excluded: chain Z residue 604 VAL Chi-restraints excluded: chain Z residue 650 ILE Chi-restraints excluded: chain Z residue 669 LEU Chi-restraints excluded: chain Z residue 779 ILE Chi-restraints excluded: chain Z residue 880 ASN Chi-restraints excluded: chain Z residue 881 VAL Chi-restraints excluded: chain g residue 82 VAL Chi-restraints excluded: chain g residue 99 LEU Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 119 VAL Chi-restraints excluded: chain g residue 166 GLU Chi-restraints excluded: chain g residue 197 THR Chi-restraints excluded: chain g residue 201 CYS Chi-restraints excluded: chain g residue 348 GLN Chi-restraints excluded: chain g residue 375 THR Chi-restraints excluded: chain g residue 462 VAL Chi-restraints excluded: chain g residue 485 GLU Chi-restraints excluded: chain g residue 514 ARG Chi-restraints excluded: chain g residue 581 THR Chi-restraints excluded: chain g residue 594 SER Chi-restraints excluded: chain g residue 595 SER Chi-restraints excluded: chain g residue 644 SER Chi-restraints excluded: chain g residue 646 ARG Chi-restraints excluded: chain g residue 673 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 383 optimal weight: 7.9990 chunk 214 optimal weight: 0.6980 chunk 574 optimal weight: 10.0000 chunk 469 optimal weight: 4.9990 chunk 190 optimal weight: 0.8980 chunk 691 optimal weight: 8.9990 chunk 746 optimal weight: 6.9990 chunk 615 optimal weight: 0.5980 chunk 685 optimal weight: 0.9980 chunk 235 optimal weight: 1.9990 chunk 554 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 162 HIS A 194 GLN ** A 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 HIS L 102 GLN X 73 ASN X 492 GLN X 499 ASN X 551 ASN ** V 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 198 GLN V 545 GLN V 564 GLN V 630 GLN e 302 GLN f 521 GLN f 569 ASN Z 198 GLN Z 593 ASN ** Z 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 70 ASN g 880 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 62062 Z= 0.221 Angle : 0.655 15.775 84378 Z= 0.296 Chirality : 0.041 0.226 9927 Planarity : 0.005 0.060 10486 Dihedral : 9.585 138.260 9425 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 4.30 % Allowed : 21.25 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.60 % 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: 1.18 (0.10), residues: 7580 helix: 1.30 (0.08), residues: 4367 sheet: 1.21 (0.22), residues: 532 loop : -0.04 (0.12), residues: 2681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP e 662 HIS 0.010 0.001 HIS V 163 PHE 0.022 0.001 PHE V 314 TYR 0.017 0.002 TYR V 519 ARG 0.010 0.000 ARG Z 514 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15160 Ramachandran restraints generated. 7580 Oldfield, 0 Emsley, 7580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15160 Ramachandran restraints generated. 7580 Oldfield, 0 Emsley, 7580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1313 residues out of total 6541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 277 poor density : 1036 time to evaluate : 5.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ASP cc_start: 0.7672 (t0) cc_final: 0.7314 (t0) REVERT: A 66 HIS cc_start: 0.8351 (m170) cc_final: 0.7931 (m-70) REVERT: A 187 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.7357 (mtp85) REVERT: A 454 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7530 (ttmp) REVERT: A 600 TRP cc_start: 0.8081 (p-90) cc_final: 0.7545 (p-90) REVERT: A 700 MET cc_start: 0.7837 (OUTLIER) cc_final: 0.7433 (mtp) REVERT: A 730 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8578 (mtmm) REVERT: A 787 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.8018 (ttpt) REVERT: K 262 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7770 (mp10) REVERT: L 323 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7354 (mtp85) REVERT: Q 83 ASN cc_start: 0.8655 (t0) cc_final: 0.8451 (t0) REVERT: Q 231 GLU cc_start: 0.7030 (mp0) cc_final: 0.6423 (mp0) REVERT: X 133 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.7768 (mp10) REVERT: X 549 PHE cc_start: 0.8190 (OUTLIER) cc_final: 0.7027 (t80) REVERT: R 83 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7566 (tt) REVERT: V 272 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7503 (mp0) REVERT: V 343 LEU cc_start: 0.7821 (mt) cc_final: 0.7603 (mt) REVERT: V 395 SER cc_start: 0.8179 (p) cc_final: 0.7865 (m) REVERT: V 551 LYS cc_start: 0.6376 (OUTLIER) cc_final: 0.5491 (mtmt) REVERT: e 118 THR cc_start: 0.8093 (m) cc_final: 0.7859 (p) REVERT: e 128 LEU cc_start: 0.6244 (OUTLIER) cc_final: 0.5904 (tp) REVERT: e 535 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7544 (mp0) REVERT: Y 86 GLU cc_start: 0.7519 (mt-10) cc_final: 0.7277 (mp0) REVERT: Y 248 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.7733 (tm-30) REVERT: Y 291 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7466 (tt0) REVERT: Y 544 PHE cc_start: 0.7785 (OUTLIER) cc_final: 0.7344 (t80) REVERT: Y 759 GLN cc_start: 0.8121 (pm20) cc_final: 0.7764 (pm20) REVERT: f 191 GLN cc_start: 0.7014 (mm110) cc_final: 0.6500 (pm20) REVERT: f 291 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8307 (tm-30) REVERT: f 535 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.7069 (mt-10) REVERT: f 700 SER cc_start: 0.8381 (p) cc_final: 0.8166 (p) REVERT: Z 141 PHE cc_start: 0.7796 (t80) cc_final: 0.7543 (t80) REVERT: Z 476 PHE cc_start: 0.8116 (t80) cc_final: 0.7887 (t80) REVERT: Z 480 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7497 (mp0) REVERT: Z 551 LYS cc_start: 0.8351 (ttmm) cc_final: 0.7986 (ttmm) REVERT: Z 696 MET cc_start: 0.8366 (mmt) cc_final: 0.7795 (mmt) REVERT: g 166 GLU cc_start: 0.6639 (OUTLIER) cc_final: 0.6429 (mt-10) REVERT: g 333 LEU cc_start: 0.7890 (mt) cc_final: 0.7513 (tt) REVERT: g 430 LYS cc_start: 0.7642 (OUTLIER) cc_final: 0.7346 (ttmm) REVERT: g 535 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7897 (mp0) REVERT: g 644 SER cc_start: 0.8112 (OUTLIER) cc_final: 0.7849 (t) REVERT: g 649 VAL cc_start: 0.8737 (t) cc_final: 0.8524 (p) REVERT: g 650 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.8284 (mp) REVERT: g 721 MET cc_start: 0.8563 (OUTLIER) cc_final: 0.7922 (mtm) REVERT: g 871 ARG cc_start: 0.7207 (ttp80) cc_final: 0.6734 (mtt90) outliers start: 277 outliers final: 140 residues processed: 1225 average time/residue: 1.3393 time to fit residues: 2124.2446 Evaluate side-chains 1178 residues out of total 6541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 1013 time to evaluate : 5.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 381 LYS Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 454 LYS Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 484 ASN Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 700 MET Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 730 LYS Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 784 ASP Chi-restraints excluded: chain A residue 787 LYS Chi-restraints excluded: chain A residue 793 THR Chi-restraints excluded: chain K residue 19 THR Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 248 SER Chi-restraints excluded: chain K residue 262 GLN Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 220 MET Chi-restraints excluded: chain L residue 323 ARG Chi-restraints excluded: chain Q residue 10 ILE Chi-restraints excluded: chain Q residue 192 SER Chi-restraints excluded: chain Q residue 199 GLU Chi-restraints excluded: chain X residue 68 GLN Chi-restraints excluded: chain X residue 83 SER Chi-restraints excluded: chain X residue 88 LYS Chi-restraints excluded: chain X residue 133 GLN Chi-restraints excluded: chain X residue 298 THR Chi-restraints excluded: chain X residue 407 THR Chi-restraints excluded: chain X residue 533 LEU Chi-restraints excluded: chain X residue 549 PHE Chi-restraints excluded: chain X residue 649 CYS Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain P residue 75 ILE Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain a residue 87 PHE Chi-restraints excluded: chain V residue 100 SER Chi-restraints excluded: chain V residue 124 GLN Chi-restraints excluded: chain V residue 126 THR Chi-restraints excluded: chain V residue 149 ASP Chi-restraints excluded: chain V residue 155 ARG Chi-restraints excluded: chain V residue 173 VAL Chi-restraints excluded: chain V residue 231 VAL Chi-restraints excluded: chain V residue 265 LEU Chi-restraints excluded: chain V residue 272 GLU Chi-restraints excluded: chain V residue 338 VAL Chi-restraints excluded: chain V residue 340 ARG Chi-restraints excluded: chain V residue 437 VAL Chi-restraints excluded: chain V residue 551 LYS Chi-restraints excluded: chain V residue 727 THR Chi-restraints excluded: chain V residue 822 VAL Chi-restraints excluded: chain V residue 837 THR Chi-restraints excluded: chain V residue 839 ILE Chi-restraints excluded: chain V residue 863 LEU Chi-restraints excluded: chain V residue 864 ILE Chi-restraints excluded: chain V residue 873 LEU Chi-restraints excluded: chain V residue 881 VAL Chi-restraints excluded: chain e residue 73 LEU Chi-restraints excluded: chain e residue 128 LEU Chi-restraints excluded: chain e residue 223 ASP Chi-restraints excluded: chain e residue 237 LEU Chi-restraints excluded: chain e residue 281 LEU Chi-restraints excluded: chain e residue 372 LEU Chi-restraints excluded: chain e residue 426 LEU Chi-restraints excluded: chain e residue 450 LEU Chi-restraints excluded: chain e residue 462 VAL Chi-restraints excluded: chain e residue 495 PHE Chi-restraints excluded: chain e residue 535 GLU Chi-restraints excluded: chain e residue 560 VAL Chi-restraints excluded: chain e residue 672 LEU Chi-restraints excluded: chain e residue 696 MET Chi-restraints excluded: chain e residue 732 VAL Chi-restraints excluded: chain e residue 822 VAL Chi-restraints excluded: chain b residue 112 TYR Chi-restraints excluded: chain Y residue 100 SER Chi-restraints excluded: chain Y residue 108 LEU Chi-restraints excluded: chain Y residue 197 THR Chi-restraints excluded: chain Y residue 224 SER Chi-restraints excluded: chain Y residue 248 GLN Chi-restraints excluded: chain Y residue 249 GLU Chi-restraints excluded: chain Y residue 276 ILE Chi-restraints excluded: chain Y residue 291 GLU Chi-restraints excluded: chain Y residue 308 LEU Chi-restraints excluded: chain Y residue 440 LEU Chi-restraints excluded: chain Y residue 486 TYR Chi-restraints excluded: chain Y residue 511 PHE Chi-restraints excluded: chain Y residue 544 PHE Chi-restraints excluded: chain Y residue 552 THR Chi-restraints excluded: chain Y residue 672 LEU Chi-restraints excluded: chain Y residue 877 ILE Chi-restraints excluded: chain f residue 116 LYS Chi-restraints excluded: chain f residue 173 VAL Chi-restraints excluded: chain f residue 242 LEU Chi-restraints excluded: chain f residue 260 VAL Chi-restraints excluded: chain f residue 281 LEU Chi-restraints excluded: chain f residue 291 GLU Chi-restraints excluded: chain f residue 426 LEU Chi-restraints excluded: chain f residue 477 SER Chi-restraints excluded: chain f residue 535 GLU Chi-restraints excluded: chain f residue 558 LEU Chi-restraints excluded: chain f residue 560 VAL Chi-restraints excluded: chain f residue 662 TRP Chi-restraints excluded: chain f residue 673 LEU Chi-restraints excluded: chain f residue 704 LEU Chi-restraints excluded: chain f residue 718 LEU Chi-restraints excluded: chain f residue 779 ILE Chi-restraints excluded: chain f residue 889 ASP Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain c residue 112 TYR Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain Z residue 108 LEU Chi-restraints excluded: chain Z residue 177 VAL Chi-restraints excluded: chain Z residue 217 LEU Chi-restraints excluded: chain Z residue 333 LEU Chi-restraints excluded: chain Z residue 334 SER Chi-restraints excluded: chain Z residue 480 GLU Chi-restraints excluded: chain Z residue 500 LEU Chi-restraints excluded: chain Z residue 528 ILE Chi-restraints excluded: chain Z residue 546 ASP Chi-restraints excluded: chain Z residue 604 VAL Chi-restraints excluded: chain Z residue 613 SER Chi-restraints excluded: chain Z residue 676 ILE Chi-restraints excluded: chain Z residue 740 VAL Chi-restraints excluded: chain Z residue 775 LEU Chi-restraints excluded: chain Z residue 779 ILE Chi-restraints excluded: chain Z residue 864 ILE Chi-restraints excluded: chain Z residue 881 VAL Chi-restraints excluded: chain g residue 82 VAL Chi-restraints excluded: chain g residue 99 LEU Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 166 GLU Chi-restraints excluded: chain g residue 173 VAL Chi-restraints excluded: chain g residue 197 THR Chi-restraints excluded: chain g residue 201 CYS Chi-restraints excluded: chain g residue 266 PHE Chi-restraints excluded: chain g residue 348 GLN Chi-restraints excluded: chain g residue 375 THR Chi-restraints excluded: chain g residue 430 LYS Chi-restraints excluded: chain g residue 485 GLU Chi-restraints excluded: chain g residue 514 ARG Chi-restraints excluded: chain g residue 581 THR Chi-restraints excluded: chain g residue 593 ASN Chi-restraints excluded: chain g residue 594 SER Chi-restraints excluded: chain g residue 595 SER Chi-restraints excluded: chain g residue 644 SER Chi-restraints excluded: chain g residue 646 ARG Chi-restraints excluded: chain g residue 650 ILE Chi-restraints excluded: chain g residue 673 LEU Chi-restraints excluded: chain g residue 680 LEU Chi-restraints excluded: chain g residue 721 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 683 optimal weight: 0.6980 chunk 519 optimal weight: 0.3980 chunk 358 optimal weight: 0.0870 chunk 76 optimal weight: 1.9990 chunk 329 optimal weight: 0.6980 chunk 464 optimal weight: 4.9990 chunk 693 optimal weight: 2.9990 chunk 734 optimal weight: 0.0470 chunk 362 optimal weight: 20.0000 chunk 657 optimal weight: 4.9990 chunk 197 optimal weight: 0.5980 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 162 HIS A 194 GLN A 471 GLN ** A 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 HIS ** K 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 73 ASN ** X 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 492 GLN X 499 ASN X 551 ASN V 564 GLN V 630 GLN V 683 GLN e 302 GLN e 564 GLN f 569 ASN ** f 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 198 GLN Z 374 GLN Z 593 ASN ** Z 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 70 ASN g 198 GLN g 880 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 62062 Z= 0.138 Angle : 0.609 15.622 84378 Z= 0.271 Chirality : 0.039 0.201 9927 Planarity : 0.004 0.060 10486 Dihedral : 8.676 132.721 9415 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.63 % Allowed : 22.30 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.60 % 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: 1.46 (0.10), residues: 7580 helix: 1.54 (0.08), residues: 4373 sheet: 1.25 (0.23), residues: 521 loop : 0.09 (0.12), residues: 2686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP V 492 HIS 0.006 0.001 HIS Y 101 PHE 0.021 0.001 PHE Z 524 TYR 0.017 0.001 TYR Y 413 ARG 0.011 0.000 ARG K 201 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15160 Ramachandran restraints generated. 7580 Oldfield, 0 Emsley, 7580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15160 Ramachandran restraints generated. 7580 Oldfield, 0 Emsley, 7580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1288 residues out of total 6541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 1054 time to evaluate : 5.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ASP cc_start: 0.7639 (t0) cc_final: 0.7325 (t0) REVERT: A 60 MET cc_start: 0.8850 (tpp) cc_final: 0.8455 (ttt) REVERT: A 66 HIS cc_start: 0.8354 (m170) cc_final: 0.7795 (m-70) REVERT: A 187 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7226 (mtp85) REVERT: A 454 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7444 (ttmp) REVERT: A 455 TYR cc_start: 0.7711 (t80) cc_final: 0.7427 (t80) REVERT: A 600 TRP cc_start: 0.8086 (p-90) cc_final: 0.7480 (p-90) REVERT: A 700 MET cc_start: 0.7750 (OUTLIER) cc_final: 0.7354 (mtm) REVERT: A 776 ARG cc_start: 0.7724 (ttp80) cc_final: 0.7415 (mtm110) REVERT: A 787 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7981 (tttp) REVERT: K 262 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7744 (mp10) REVERT: Q 231 GLU cc_start: 0.6929 (mp0) cc_final: 0.6339 (mp0) REVERT: Q 326 ASP cc_start: 0.8192 (t0) cc_final: 0.7984 (t0) REVERT: X 123 VAL cc_start: 0.8302 (t) cc_final: 0.8101 (m) REVERT: X 133 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7705 (mp10) REVERT: X 445 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.8050 (ttmt) REVERT: X 549 PHE cc_start: 0.8171 (OUTLIER) cc_final: 0.7025 (t80) REVERT: P 75 ILE cc_start: 0.6776 (OUTLIER) cc_final: 0.6296 (mt) REVERT: R 83 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7580 (tt) REVERT: R 115 ARG cc_start: 0.3574 (OUTLIER) cc_final: 0.2965 (mtt90) REVERT: V 289 MET cc_start: 0.8702 (mmt) cc_final: 0.8311 (mmt) REVERT: V 343 LEU cc_start: 0.7741 (mt) cc_final: 0.7499 (mt) REVERT: e 535 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7491 (mp0) REVERT: S 100 MET cc_start: 0.3641 (OUTLIER) cc_final: 0.3390 (ttm) REVERT: Y 86 GLU cc_start: 0.7476 (mt-10) cc_final: 0.7213 (mp0) REVERT: Y 139 PHE cc_start: 0.8185 (OUTLIER) cc_final: 0.7321 (m-10) REVERT: Y 248 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.7744 (tm-30) REVERT: Y 291 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7473 (tt0) REVERT: Y 396 ASP cc_start: 0.7686 (t0) cc_final: 0.7411 (t0) REVERT: Y 544 PHE cc_start: 0.7687 (OUTLIER) cc_final: 0.7413 (t80) REVERT: Y 651 HIS cc_start: 0.5704 (OUTLIER) cc_final: 0.5460 (t-170) REVERT: Y 759 GLN cc_start: 0.8035 (pm20) cc_final: 0.7734 (pm20) REVERT: Y 760 ARG cc_start: 0.8191 (mtt90) cc_final: 0.7755 (mtt90) REVERT: Y 817 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.8231 (ttmt) REVERT: Y 842 ILE cc_start: 0.8424 (OUTLIER) cc_final: 0.8220 (mp) REVERT: f 86 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7237 (mt-10) REVERT: f 116 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.8023 (ptmm) REVERT: f 191 GLN cc_start: 0.6999 (mm110) cc_final: 0.6504 (pm20) REVERT: f 262 ILE cc_start: 0.9013 (OUTLIER) cc_final: 0.8064 (tp) REVERT: f 535 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.7044 (mt-10) REVERT: f 700 SER cc_start: 0.8350 (p) cc_final: 0.8128 (p) REVERT: Z 141 PHE cc_start: 0.7803 (t80) cc_final: 0.7534 (t80) REVERT: Z 197 THR cc_start: 0.8635 (m) cc_final: 0.8380 (p) REVERT: Z 480 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7515 (mp0) REVERT: Z 551 LYS cc_start: 0.8315 (ttmm) cc_final: 0.7974 (ttmm) REVERT: Z 650 ILE cc_start: 0.8437 (OUTLIER) cc_final: 0.8212 (mm) REVERT: Z 696 MET cc_start: 0.8342 (mmt) cc_final: 0.7713 (mmt) REVERT: g 66 MET cc_start: 0.7432 (ttp) cc_final: 0.7187 (ttm) REVERT: g 198 GLN cc_start: 0.6816 (tp40) cc_final: 0.6413 (tp-100) REVERT: g 333 LEU cc_start: 0.7901 (mt) cc_final: 0.7556 (tt) REVERT: g 646 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.5792 (ppp80) REVERT: g 649 VAL cc_start: 0.8629 (t) cc_final: 0.8393 (p) REVERT: g 650 ILE cc_start: 0.8357 (OUTLIER) cc_final: 0.7400 (mt) REVERT: g 721 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.7717 (mtm) REVERT: g 871 ARG cc_start: 0.7253 (ttp80) cc_final: 0.6768 (mtt90) outliers start: 234 outliers final: 105 residues processed: 1202 average time/residue: 1.3630 time to fit residues: 2123.6969 Evaluate side-chains 1154 residues out of total 6541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 1020 time to evaluate : 5.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 381 LYS Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 454 LYS Chi-restraints excluded: chain A residue 484 ASN Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 700 MET Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 787 LYS Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 60 LEU Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 248 SER Chi-restraints excluded: chain K residue 262 GLN Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 220 MET Chi-restraints excluded: chain L residue 394 GLN Chi-restraints excluded: chain Q residue 10 ILE Chi-restraints excluded: chain Q residue 119 ASP Chi-restraints excluded: chain X residue 68 GLN Chi-restraints excluded: chain X residue 88 LYS Chi-restraints excluded: chain X residue 133 GLN Chi-restraints excluded: chain X residue 298 THR Chi-restraints excluded: chain X residue 445 LYS Chi-restraints excluded: chain X residue 456 MET Chi-restraints excluded: chain X residue 533 LEU Chi-restraints excluded: chain X residue 549 PHE Chi-restraints excluded: chain X residue 555 ASN Chi-restraints excluded: chain X residue 649 CYS Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain P residue 75 ILE Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 115 ARG Chi-restraints excluded: chain a residue 87 PHE Chi-restraints excluded: chain V residue 99 LEU Chi-restraints excluded: chain V residue 114 PHE Chi-restraints excluded: chain V residue 124 GLN Chi-restraints excluded: chain V residue 126 THR Chi-restraints excluded: chain V residue 155 ARG Chi-restraints excluded: chain V residue 173 VAL Chi-restraints excluded: chain V residue 231 VAL Chi-restraints excluded: chain V residue 338 VAL Chi-restraints excluded: chain V residue 541 ILE Chi-restraints excluded: chain V residue 822 VAL Chi-restraints excluded: chain V residue 864 ILE Chi-restraints excluded: chain e residue 73 LEU Chi-restraints excluded: chain e residue 145 ILE Chi-restraints excluded: chain e residue 237 LEU Chi-restraints excluded: chain e residue 281 LEU Chi-restraints excluded: chain e residue 372 LEU Chi-restraints excluded: chain e residue 450 LEU Chi-restraints excluded: chain e residue 462 VAL Chi-restraints excluded: chain e residue 495 PHE Chi-restraints excluded: chain e residue 535 GLU Chi-restraints excluded: chain e residue 672 LEU Chi-restraints excluded: chain e residue 727 THR Chi-restraints excluded: chain e residue 822 VAL Chi-restraints excluded: chain S residue 100 MET Chi-restraints excluded: chain b residue 112 TYR Chi-restraints excluded: chain Y residue 100 SER Chi-restraints excluded: chain Y residue 108 LEU Chi-restraints excluded: chain Y residue 139 PHE Chi-restraints excluded: chain Y residue 224 SER Chi-restraints excluded: chain Y residue 248 GLN Chi-restraints excluded: chain Y residue 276 ILE Chi-restraints excluded: chain Y residue 291 GLU Chi-restraints excluded: chain Y residue 377 GLN Chi-restraints excluded: chain Y residue 486 TYR Chi-restraints excluded: chain Y residue 511 PHE Chi-restraints excluded: chain Y residue 544 PHE Chi-restraints excluded: chain Y residue 552 THR Chi-restraints excluded: chain Y residue 651 HIS Chi-restraints excluded: chain Y residue 672 LEU Chi-restraints excluded: chain Y residue 817 LYS Chi-restraints excluded: chain Y residue 842 ILE Chi-restraints excluded: chain f residue 86 GLU Chi-restraints excluded: chain f residue 116 LYS Chi-restraints excluded: chain f residue 173 VAL Chi-restraints excluded: chain f residue 219 LYS Chi-restraints excluded: chain f residue 242 LEU Chi-restraints excluded: chain f residue 262 ILE Chi-restraints excluded: chain f residue 281 LEU Chi-restraints excluded: chain f residue 426 LEU Chi-restraints excluded: chain f residue 535 GLU Chi-restraints excluded: chain f residue 558 LEU Chi-restraints excluded: chain f residue 560 VAL Chi-restraints excluded: chain f residue 581 THR Chi-restraints excluded: chain f residue 594 SER Chi-restraints excluded: chain f residue 634 VAL Chi-restraints excluded: chain f residue 662 TRP Chi-restraints excluded: chain f residue 673 LEU Chi-restraints excluded: chain f residue 681 GLU Chi-restraints excluded: chain f residue 704 LEU Chi-restraints excluded: chain f residue 779 ILE Chi-restraints excluded: chain f residue 864 ILE Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain c residue 112 TYR Chi-restraints excluded: chain Z residue 177 VAL Chi-restraints excluded: chain Z residue 231 VAL Chi-restraints excluded: chain Z residue 235 ASP Chi-restraints excluded: chain Z residue 480 GLU Chi-restraints excluded: chain Z residue 546 ASP Chi-restraints excluded: chain Z residue 560 VAL Chi-restraints excluded: chain Z residue 650 ILE Chi-restraints excluded: chain Z residue 669 LEU Chi-restraints excluded: chain Z residue 676 ILE Chi-restraints excluded: chain Z residue 740 VAL Chi-restraints excluded: chain Z residue 775 LEU Chi-restraints excluded: chain g residue 82 VAL Chi-restraints excluded: chain g residue 99 LEU Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 197 THR Chi-restraints excluded: chain g residue 201 CYS Chi-restraints excluded: chain g residue 375 THR Chi-restraints excluded: chain g residue 485 GLU Chi-restraints excluded: chain g residue 514 ARG Chi-restraints excluded: chain g residue 528 ILE Chi-restraints excluded: chain g residue 593 ASN Chi-restraints excluded: chain g residue 646 ARG Chi-restraints excluded: chain g residue 650 ILE Chi-restraints excluded: chain g residue 673 LEU Chi-restraints excluded: chain g residue 721 MET Chi-restraints excluded: chain g residue 812 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 611 optimal weight: 0.9990 chunk 417 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 546 optimal weight: 4.9990 chunk 303 optimal weight: 5.9990 chunk 626 optimal weight: 0.8980 chunk 507 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 375 optimal weight: 0.0970 chunk 659 optimal weight: 6.9990 chunk 185 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 162 HIS A 194 GLN ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 102 GLN Q 83 ASN X 73 ASN X 128 GLN X 492 GLN X 499 ASN X 551 ASN X 559 ASN ** V 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 198 GLN V 630 GLN V 884 GLN e 302 GLN f 569 ASN ** f 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 804 GLN Z 374 GLN Z 550 GLN Z 593 ASN ** Z 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 70 ASN g 880 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 62062 Z= 0.179 Angle : 0.619 15.685 84378 Z= 0.277 Chirality : 0.039 0.269 9927 Planarity : 0.004 0.060 10486 Dihedral : 8.377 125.144 9391 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.69 % Allowed : 22.53 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.60 % 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: 1.54 (0.10), residues: 7580 helix: 1.59 (0.08), residues: 4363 sheet: 1.25 (0.23), residues: 524 loop : 0.14 (0.12), residues: 2693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP e 492 HIS 0.006 0.001 HIS A 607 PHE 0.019 0.001 PHE Z 524 TYR 0.016 0.001 TYR g 824 ARG 0.007 0.000 ARG g 387 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15160 Ramachandran restraints generated. 7580 Oldfield, 0 Emsley, 7580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15160 Ramachandran restraints generated. 7580 Oldfield, 0 Emsley, 7580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1271 residues out of total 6541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 1033 time to evaluate : 5.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ASP cc_start: 0.7690 (t0) cc_final: 0.7341 (t0) REVERT: A 187 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.7196 (mtp85) REVERT: A 360 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8057 (mppt) REVERT: A 434 ASN cc_start: 0.8202 (OUTLIER) cc_final: 0.7982 (p0) REVERT: A 454 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7353 (ttmp) REVERT: A 458 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7266 (mt0) REVERT: A 524 GLU cc_start: 0.6993 (OUTLIER) cc_final: 0.6570 (mp0) REVERT: A 600 TRP cc_start: 0.8097 (p-90) cc_final: 0.7495 (p-90) REVERT: A 700 MET cc_start: 0.7813 (OUTLIER) cc_final: 0.7403 (mtm) REVERT: A 730 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8582 (mtmm) REVERT: A 768 THR cc_start: 0.8047 (p) cc_final: 0.7760 (t) REVERT: A 776 ARG cc_start: 0.7734 (ttp80) cc_final: 0.7449 (mtm110) REVERT: A 787 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.8081 (ttpt) REVERT: K 262 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7737 (mp10) REVERT: Q 231 GLU cc_start: 0.6985 (mp0) cc_final: 0.6397 (mp0) REVERT: Q 326 ASP cc_start: 0.8201 (t0) cc_final: 0.7989 (t0) REVERT: X 133 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7701 (mp10) REVERT: X 310 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7295 (mt-10) REVERT: X 445 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.8085 (ttmt) REVERT: X 549 PHE cc_start: 0.8170 (OUTLIER) cc_final: 0.7005 (t80) REVERT: P 75 ILE cc_start: 0.6772 (OUTLIER) cc_final: 0.6266 (mt) REVERT: R 83 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7582 (tt) REVERT: R 115 ARG cc_start: 0.3602 (OUTLIER) cc_final: 0.3003 (mtt90) REVERT: V 343 LEU cc_start: 0.7745 (mt) cc_final: 0.7511 (mt) REVERT: V 395 SER cc_start: 0.8161 (p) cc_final: 0.7880 (m) REVERT: V 551 LYS cc_start: 0.6400 (OUTLIER) cc_final: 0.5501 (mtmt) REVERT: e 535 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7537 (mp0) REVERT: S 100 MET cc_start: 0.3546 (OUTLIER) cc_final: 0.3023 (ttm) REVERT: Y 86 GLU cc_start: 0.7506 (mt-10) cc_final: 0.7237 (mp0) REVERT: Y 139 PHE cc_start: 0.8197 (OUTLIER) cc_final: 0.7295 (m-10) REVERT: Y 248 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.7755 (tm-30) REVERT: Y 289 MET cc_start: 0.8699 (tpt) cc_final: 0.8125 (tpt) REVERT: Y 291 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7451 (tt0) REVERT: Y 308 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8372 (mp) REVERT: Y 544 PHE cc_start: 0.7716 (OUTLIER) cc_final: 0.7396 (t80) REVERT: Y 759 GLN cc_start: 0.8060 (pm20) cc_final: 0.7782 (pm20) REVERT: f 116 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.8058 (ptmm) REVERT: f 191 GLN cc_start: 0.7063 (mm110) cc_final: 0.6500 (pm20) REVERT: f 262 ILE cc_start: 0.9019 (OUTLIER) cc_final: 0.8050 (tp) REVERT: f 291 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8278 (tm-30) REVERT: f 535 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.7034 (mt-10) REVERT: f 700 SER cc_start: 0.8367 (p) cc_final: 0.8147 (p) REVERT: Z 141 PHE cc_start: 0.7826 (t80) cc_final: 0.7538 (t80) REVERT: Z 476 PHE cc_start: 0.8105 (t80) cc_final: 0.7870 (t80) REVERT: Z 480 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7516 (mp0) REVERT: Z 485 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7803 (mt-10) REVERT: Z 551 LYS cc_start: 0.8338 (ttmm) cc_final: 0.7999 (ttmm) REVERT: Z 696 MET cc_start: 0.8365 (mmt) cc_final: 0.7782 (mmt) REVERT: g 198 GLN cc_start: 0.6827 (tp40) cc_final: 0.6405 (tp-100) REVERT: g 333 LEU cc_start: 0.7917 (mt) cc_final: 0.7568 (tt) REVERT: g 430 LYS cc_start: 0.7702 (OUTLIER) cc_final: 0.7340 (ttpt) REVERT: g 646 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.5681 (ppp80) REVERT: g 649 VAL cc_start: 0.8679 (t) cc_final: 0.8444 (p) REVERT: g 721 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.7807 (mtm) REVERT: g 871 ARG cc_start: 0.7260 (ttp80) cc_final: 0.6742 (mtt90) outliers start: 238 outliers final: 115 residues processed: 1189 average time/residue: 1.3496 time to fit residues: 2084.5672 Evaluate side-chains 1158 residues out of total 6541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 1009 time to evaluate : 5.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 360 LYS Chi-restraints excluded: chain A residue 381 LYS Chi-restraints excluded: chain A residue 434 ASN Chi-restraints excluded: chain A residue 454 LYS Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 484 ASN Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 700 MET Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 730 LYS Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain A residue 787 LYS Chi-restraints excluded: chain A residue 793 THR Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 60 LEU Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 248 SER Chi-restraints excluded: chain K residue 262 GLN Chi-restraints excluded: chain K residue 290 SER Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 220 MET Chi-restraints excluded: chain X residue 68 GLN Chi-restraints excluded: chain X residue 88 LYS Chi-restraints excluded: chain X residue 133 GLN Chi-restraints excluded: chain X residue 159 LEU Chi-restraints excluded: chain X residue 298 THR Chi-restraints excluded: chain X residue 310 GLU Chi-restraints excluded: chain X residue 445 LYS Chi-restraints excluded: chain X residue 453 LYS Chi-restraints excluded: chain X residue 456 MET Chi-restraints excluded: chain X residue 533 LEU Chi-restraints excluded: chain X residue 549 PHE Chi-restraints excluded: chain X residue 649 CYS Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain P residue 75 ILE Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 115 ARG Chi-restraints excluded: chain V residue 99 LEU Chi-restraints excluded: chain V residue 124 GLN Chi-restraints excluded: chain V residue 126 THR Chi-restraints excluded: chain V residue 149 ASP Chi-restraints excluded: chain V residue 155 ARG Chi-restraints excluded: chain V residue 173 VAL Chi-restraints excluded: chain V residue 216 ILE Chi-restraints excluded: chain V residue 231 VAL Chi-restraints excluded: chain V residue 265 LEU Chi-restraints excluded: chain V residue 340 ARG Chi-restraints excluded: chain V residue 437 VAL Chi-restraints excluded: chain V residue 551 LYS Chi-restraints excluded: chain V residue 727 THR Chi-restraints excluded: chain V residue 741 MET Chi-restraints excluded: chain V residue 822 VAL Chi-restraints excluded: chain V residue 839 ILE Chi-restraints excluded: chain V residue 864 ILE Chi-restraints excluded: chain e residue 73 LEU Chi-restraints excluded: chain e residue 145 ILE Chi-restraints excluded: chain e residue 199 LEU Chi-restraints excluded: chain e residue 237 LEU Chi-restraints excluded: chain e residue 281 LEU Chi-restraints excluded: chain e residue 372 LEU Chi-restraints excluded: chain e residue 450 LEU Chi-restraints excluded: chain e residue 462 VAL Chi-restraints excluded: chain e residue 495 PHE Chi-restraints excluded: chain e residue 535 GLU Chi-restraints excluded: chain e residue 672 LEU Chi-restraints excluded: chain e residue 727 THR Chi-restraints excluded: chain S residue 100 MET Chi-restraints excluded: chain b residue 112 TYR Chi-restraints excluded: chain Y residue 108 LEU Chi-restraints excluded: chain Y residue 139 PHE Chi-restraints excluded: chain Y residue 224 SER Chi-restraints excluded: chain Y residue 248 GLN Chi-restraints excluded: chain Y residue 276 ILE Chi-restraints excluded: chain Y residue 291 GLU Chi-restraints excluded: chain Y residue 308 LEU Chi-restraints excluded: chain Y residue 440 LEU Chi-restraints excluded: chain Y residue 486 TYR Chi-restraints excluded: chain Y residue 511 PHE Chi-restraints excluded: chain Y residue 544 PHE Chi-restraints excluded: chain Y residue 552 THR Chi-restraints excluded: chain Y residue 672 LEU Chi-restraints excluded: chain Y residue 740 VAL Chi-restraints excluded: chain Y residue 877 ILE Chi-restraints excluded: chain f residue 116 LYS Chi-restraints excluded: chain f residue 173 VAL Chi-restraints excluded: chain f residue 219 LYS Chi-restraints excluded: chain f residue 242 LEU Chi-restraints excluded: chain f residue 260 VAL Chi-restraints excluded: chain f residue 262 ILE Chi-restraints excluded: chain f residue 281 LEU Chi-restraints excluded: chain f residue 291 GLU Chi-restraints excluded: chain f residue 343 LEU Chi-restraints excluded: chain f residue 535 GLU Chi-restraints excluded: chain f residue 558 LEU Chi-restraints excluded: chain f residue 560 VAL Chi-restraints excluded: chain f residue 581 THR Chi-restraints excluded: chain f residue 662 TRP Chi-restraints excluded: chain f residue 667 SER Chi-restraints excluded: chain f residue 673 LEU Chi-restraints excluded: chain f residue 681 GLU Chi-restraints excluded: chain f residue 704 LEU Chi-restraints excluded: chain f residue 741 MET Chi-restraints excluded: chain f residue 864 ILE Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain c residue 112 TYR Chi-restraints excluded: chain Z residue 108 LEU Chi-restraints excluded: chain Z residue 177 VAL Chi-restraints excluded: chain Z residue 217 LEU Chi-restraints excluded: chain Z residue 231 VAL Chi-restraints excluded: chain Z residue 235 ASP Chi-restraints excluded: chain Z residue 333 LEU Chi-restraints excluded: chain Z residue 334 SER Chi-restraints excluded: chain Z residue 480 GLU Chi-restraints excluded: chain Z residue 485 GLU Chi-restraints excluded: chain Z residue 546 ASP Chi-restraints excluded: chain Z residue 560 VAL Chi-restraints excluded: chain Z residue 613 SER Chi-restraints excluded: chain Z residue 669 LEU Chi-restraints excluded: chain Z residue 676 ILE Chi-restraints excluded: chain Z residue 740 VAL Chi-restraints excluded: chain Z residue 775 LEU Chi-restraints excluded: chain Z residue 881 VAL Chi-restraints excluded: chain g residue 82 VAL Chi-restraints excluded: chain g residue 99 LEU Chi-restraints excluded: chain g residue 109 GLU Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 173 VAL Chi-restraints excluded: chain g residue 197 THR Chi-restraints excluded: chain g residue 201 CYS Chi-restraints excluded: chain g residue 375 THR Chi-restraints excluded: chain g residue 430 LYS Chi-restraints excluded: chain g residue 528 ILE Chi-restraints excluded: chain g residue 581 THR Chi-restraints excluded: chain g residue 593 ASN Chi-restraints excluded: chain g residue 595 SER Chi-restraints excluded: chain g residue 644 SER Chi-restraints excluded: chain g residue 646 ARG Chi-restraints excluded: chain g residue 650 ILE Chi-restraints excluded: chain g residue 673 LEU Chi-restraints excluded: chain g residue 721 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.146 > 50: distance: 47 - 51: 23.988 distance: 51 - 52: 49.666 distance: 52 - 53: 45.075 distance: 52 - 55: 37.504 distance: 53 - 54: 38.188 distance: 53 - 59: 23.910 distance: 55 - 56: 55.117 distance: 56 - 57: 60.489 distance: 56 - 58: 32.792 distance: 59 - 60: 35.629 distance: 60 - 61: 40.359 distance: 60 - 63: 27.928 distance: 61 - 62: 50.217 distance: 61 - 65: 15.896 distance: 63 - 64: 63.495 distance: 65 - 66: 56.571 distance: 66 - 67: 35.186 distance: 67 - 68: 69.708 distance: 67 - 69: 56.391 distance: 69 - 70: 41.078 distance: 70 - 71: 39.040 distance: 70 - 73: 22.698 distance: 71 - 72: 40.295 distance: 71 - 77: 64.104 distance: 73 - 74: 29.971 distance: 73 - 75: 47.112 distance: 74 - 76: 41.167 distance: 77 - 78: 44.783 distance: 78 - 79: 24.946 distance: 78 - 81: 25.160 distance: 79 - 80: 45.544 distance: 79 - 86: 35.021 distance: 80 - 113: 7.932 distance: 81 - 82: 23.691 distance: 82 - 83: 28.552 distance: 83 - 84: 48.849 distance: 83 - 85: 49.122 distance: 86 - 87: 16.506 distance: 87 - 88: 36.657 distance: 87 - 90: 46.852 distance: 88 - 89: 49.210 distance: 88 - 94: 62.227 distance: 89 - 124: 40.806 distance: 90 - 91: 57.687 distance: 91 - 92: 46.516 distance: 91 - 93: 49.689 distance: 94 - 95: 12.684 distance: 95 - 96: 27.805 distance: 95 - 98: 24.667 distance: 96 - 97: 45.843 distance: 96 - 105: 16.138 distance: 97 - 132: 36.876 distance: 98 - 99: 51.879 distance: 99 - 100: 49.456 distance: 99 - 101: 30.900 distance: 100 - 102: 37.607 distance: 101 - 103: 19.176 distance: 102 - 104: 17.722 distance: 103 - 104: 16.131 distance: 105 - 106: 37.337 distance: 106 - 107: 24.096 distance: 106 - 109: 15.482 distance: 107 - 108: 43.574 distance: 107 - 113: 41.867 distance: 108 - 140: 31.650 distance: 109 - 110: 47.791 distance: 110 - 111: 45.982 distance: 110 - 112: 38.489 distance: 113 - 114: 3.789 distance: 114 - 115: 59.868 distance: 114 - 117: 22.175 distance: 115 - 116: 31.966 distance: 115 - 124: 18.295 distance: 116 - 148: 28.940 distance: 117 - 118: 58.246 distance: 118 - 119: 41.583 distance: 119 - 120: 50.235 distance: 120 - 121: 29.252 distance: 121 - 122: 12.319 distance: 121 - 123: 4.546 distance: 124 - 125: 55.655 distance: 125 - 126: 57.909 distance: 125 - 128: 18.136 distance: 126 - 127: 28.876 distance: 126 - 132: 34.162 distance: 128 - 129: 58.522 distance: 128 - 130: 39.943 distance: 129 - 131: 53.348