Starting phenix.real_space_refine on Mon Mar 25 11:12:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gzh_34398/03_2024/8gzh_34398_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gzh_34398/03_2024/8gzh_34398.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gzh_34398/03_2024/8gzh_34398.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gzh_34398/03_2024/8gzh_34398.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gzh_34398/03_2024/8gzh_34398_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gzh_34398/03_2024/8gzh_34398_updated.pdb" } resolution = 2.96 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= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 18123 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 105 5.49 5 Mg 2 5.21 5 S 84 5.16 5 C 18744 2.51 5 N 5390 2.21 5 O 6012 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 10": "OE1" <-> "OE2" Residue "A ARG 30": "NH1" <-> "NH2" Residue "A ARG 57": "NH1" <-> "NH2" Residue "A ARG 72": "NH1" <-> "NH2" Residue "A ARG 144": "NH1" <-> "NH2" Residue "A ASP 171": "OD1" <-> "OD2" Residue "A ARG 197": "NH1" <-> "NH2" Residue "A ARG 211": "NH1" <-> "NH2" Residue "A PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 14": "NH1" <-> "NH2" Residue "B ASP 92": "OD1" <-> "OD2" Residue "B ASP 122": "OD1" <-> "OD2" Residue "B TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 141": "NH1" <-> "NH2" Residue "B PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 182": "OD1" <-> "OD2" Residue "B GLU 208": "OE1" <-> "OE2" Residue "C GLU 14": "OE1" <-> "OE2" Residue "C GLU 31": "OE1" <-> "OE2" Residue "C PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 53": "OD1" <-> "OD2" Residue "C GLU 65": "OE1" <-> "OE2" Residue "C ARG 82": "NH1" <-> "NH2" Residue "C TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 134": "OE1" <-> "OE2" Residue "C ARG 141": "NH1" <-> "NH2" Residue "C ASP 170": "OD1" <-> "OD2" Residue "C ASP 188": "OD1" <-> "OD2" Residue "C PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 213": "OE1" <-> "OE2" Residue "C TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 278": "OD1" <-> "OD2" Residue "C PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 480": "OD1" <-> "OD2" Residue "C GLU 497": "OE1" <-> "OE2" Residue "C GLU 504": "OE1" <-> "OE2" Residue "C GLU 552": "OE1" <-> "OE2" Residue "C GLU 561": "OE1" <-> "OE2" Residue "C ASP 567": "OD1" <-> "OD2" Residue "C GLU 587": "OE1" <-> "OE2" Residue "C TYR 628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 670": "OD1" <-> "OD2" Residue "C GLU 676": "OE1" <-> "OE2" Residue "C ARG 697": "NH1" <-> "NH2" Residue "C ARG 708": "NH1" <-> "NH2" Residue "C ARG 719": "NH1" <-> "NH2" Residue "C ARG 759": "NH1" <-> "NH2" Residue "C ARG 767": "NH1" <-> "NH2" Residue "C ARG 792": "NH1" <-> "NH2" Residue "C ASP 820": "OD1" <-> "OD2" Residue "C ARG 899": "NH1" <-> "NH2" Residue "C PHE 930": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 936": "OE1" <-> "OE2" Residue "C ASP 939": "OD1" <-> "OD2" Residue "C ASP 958": "OD1" <-> "OD2" Residue "C TYR 1002": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1013": "OD1" <-> "OD2" Residue "C ARG 1033": "NH1" <-> "NH2" Residue "C GLU 1038": "OE1" <-> "OE2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D ARG 23": "NH1" <-> "NH2" Residue "D ARG 82": "NH1" <-> "NH2" Residue "D TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 169": "OE1" <-> "OE2" Residue "D ASP 172": "OD1" <-> "OD2" Residue "D GLU 211": "OE1" <-> "OE2" Residue "D GLU 212": "OE1" <-> "OE2" Residue "D PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 296": "OE1" <-> "OE2" Residue "D ARG 319": "NH1" <-> "NH2" Residue "D GLU 339": "OE1" <-> "OE2" Residue "D TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 377": "NH1" <-> "NH2" Residue "D ARG 391": "NH1" <-> "NH2" Residue "D PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 551": "OD1" <-> "OD2" Residue "D ARG 559": "NH1" <-> "NH2" Residue "D GLU 573": "OE1" <-> "OE2" Residue "E ARG 15": "NH1" <-> "NH2" Residue "E GLU 39": "OE1" <-> "OE2" Residue "E ARG 58": "NH1" <-> "NH2" Residue "E GLU 66": "OE1" <-> "OE2" Residue "F ARG 84": "NH1" <-> "NH2" Residue "F ARG 87": "NH1" <-> "NH2" Residue "F ARG 96": "NH1" <-> "NH2" Residue "F ASP 109": "OD1" <-> "OD2" Residue "F ARG 180": "NH1" <-> "NH2" Residue "F ASP 186": "OD1" <-> "OD2" Residue "F ARG 187": "NH1" <-> "NH2" Residue "F ARG 188": "NH1" <-> "NH2" Residue "F ARG 228": "NH1" <-> "NH2" Residue "F ASP 234": "OD1" <-> "OD2" Residue "F ARG 255": "NH1" <-> "NH2" Residue "F GLU 299": "OE1" <-> "OE2" Residue "F PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 346": "OD1" <-> "OD2" Residue "F GLU 358": "OE1" <-> "OE2" Residue "F ASP 362": "OD1" <-> "OD2" Residue "F ASP 370": "OD1" <-> "OD2" Residue "F ASP 379": "OD1" <-> "OD2" Residue "F ASP 380": "OD1" <-> "OD2" Residue "F GLU 387": "OE1" <-> "OE2" Residue "F GLU 388": "OE1" <-> "OE2" Residue "F PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 412": "NH1" <-> "NH2" Residue "F TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 23": "NH1" <-> "NH2" Residue "Z GLU 61": "OE1" <-> "OE2" Residue "Z TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 84": "OE1" <-> "OE2" Residue "Z GLU 89": "OE1" <-> "OE2" Residue "Z ASP 96": "OD1" <-> "OD2" Residue "Z ARG 138": "NH1" <-> "NH2" Residue "Z ASP 185": "OD1" <-> "OD2" Residue "Z ARG 189": "NH1" <-> "NH2" Residue "Z ASP 192": "OD1" <-> "OD2" Residue "Z GLU 217": "OE1" <-> "OE2" Residue "Z ARG 218": "NH1" <-> "NH2" Residue "Z ARG 221": "NH1" <-> "NH2" Residue "Z ARG 270": "NH1" <-> "NH2" Residue "Z ARG 331": "NH1" <-> "NH2" Residue "Z PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 345": "NH1" <-> "NH2" Residue "Z GLU 351": "OE1" <-> "OE2" Residue "Z GLU 372": "OE1" <-> "OE2" Residue "Z GLU 388": "OE1" <-> "OE2" Residue "Z GLU 455": "OE1" <-> "OE2" Residue "Z ASP 512": "OD1" <-> "OD2" Residue "Z TYR 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 580": "OD1" <-> "OD2" Residue "Z TYR 583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 592": "NH1" <-> "NH2" Residue "Z TYR 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 620": "OE1" <-> "OE2" Residue "Z GLU 621": "OE1" <-> "OE2" Residue "Z ASP 636": "OD1" <-> "OD2" Residue "Z TYR 639": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 668": "NH1" <-> "NH2" Residue "Z ASP 676": "OD1" <-> "OD2" Residue "Z PHE 734": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 756": "NH1" <-> "NH2" Residue "Z ARG 760": "NH1" <-> "NH2" Residue "Z ARG 768": "NH1" <-> "NH2" Residue "Z GLU 820": "OE1" <-> "OE2" Residue "Z ASP 827": "OD1" <-> "OD2" Residue "Z ARG 857": "NH1" <-> "NH2" Residue "Z ARG 869": "NH1" <-> "NH2" Residue "Z ARG 885": "NH1" <-> "NH2" Residue "Z ASP 893": "OD1" <-> "OD2" Residue "Z GLU 920": "OE1" <-> "OE2" Residue "Z TYR 934": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 942": "NH1" <-> "NH2" Residue "Z ASP 958": "OD1" <-> "OD2" Residue "Z ARG 973": "NH1" <-> "NH2" Residue "Z ASP 1019": "OD1" <-> "OD2" Residue "Z ASP 1026": "OD1" <-> "OD2" Residue "Z ARG 1047": "NH1" <-> "NH2" Residue "Z PHE 1068": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 1084": "NH1" <-> "NH2" Residue "Z ASP 1107": "OD1" <-> "OD2" Residue "Z ASP 1128": "OD1" <-> "OD2" Residue "Z ARG 1143": "NH1" <-> "NH2" Residue "Z TYR 1162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 1179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 1187": "OE1" <-> "OE2" Residue "Z ASP 1202": "OD1" <-> "OD2" Residue "Z ARG 1215": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 30339 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1675 Classifications: {'peptide': 219} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 208} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1673 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 206} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 8171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1052, 8171 Classifications: {'peptide': 1052} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PCIS': 1, 'PTRANS': 60, 'TRANS': 990} Chain breaks: 2 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 4, 'GLU:plan': 9, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 79 Chain: "D" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4862 Classifications: {'peptide': 615} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 585} Chain breaks: 1 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 31 Chain: "E" Number of atoms: 450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 450 Classifications: {'peptide': 59} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 56} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "F" Number of atoms: 2474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2474 Classifications: {'peptide': 314} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 8, 'TRANS': 305} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 164 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 8, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 93 Chain: "Z" Number of atoms: 8860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1217, 8860 Classifications: {'peptide': 1217} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'PTRANS': 44, 'TRANS': 1172} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 537 Unresolved non-hydrogen angles: 663 Unresolved non-hydrogen dihedrals: 435 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 20, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 17, 'PHE:plan': 1, 'GLU:plan': 25, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 369 Chain: "1" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1029 Classifications: {'DNA': 50} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 49} Chain: "2" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1031 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "3" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 81 Classifications: {'RNA': 4} Modifications used: {'5*END': 1, 'rna3p_pur': 1, 'rna3p_pyr': 2} Link IDs: {'rna3p': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "2" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'CTP': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12047 SG CYS D 71 117.205 56.559 69.453 1.00 19.83 S ATOM 12067 SG CYS D 73 118.776 56.116 65.335 1.00 22.80 S ATOM 12170 SG CYS D 86 121.000 55.682 69.194 1.00 25.00 S ATOM 20997 SG CYS Z 214 86.351 75.790 126.040 1.00 18.67 S ATOM 21530 SG CYS Z 286 85.589 76.041 122.144 1.00 18.67 S ATOM 21579 SG CYS Z 293 84.540 72.699 124.196 1.00 18.67 S ATOM 21602 SG CYS Z 296 82.454 75.901 125.023 1.00 18.67 S Time building chain proxies: 15.41, per 1000 atoms: 0.51 Number of scatterers: 30339 At special positions: 0 Unit cell: (157.3, 155.1, 159.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 84 16.00 P 105 15.00 Mg 2 11.99 O 6012 8.00 N 5390 7.00 C 18744 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.83 Conformation dependent library (CDL) restraints added in 5.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2002 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 71 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 73 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 86 " pdb=" ZN Z2001 " pdb="ZN ZN Z2001 " - pdb=" SG CYS Z 293 " pdb="ZN ZN Z2001 " - pdb=" SG CYS Z 296 " pdb="ZN ZN Z2001 " - pdb=" SG CYS Z 214 " pdb="ZN ZN Z2001 " - pdb=" SG CYS Z 286 " Number of angles added : 6 7330 Ramachandran restraints generated. 3665 Oldfield, 0 Emsley, 3665 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6810 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 108 helices and 39 sheets defined 30.7% alpha, 12.5% beta 39 base pairs and 79 stacking pairs defined. Time for finding SS restraints: 13.73 Creating SS restraints... Processing helix chain 'A' and resid 32 through 46 Processing helix chain 'A' and resid 75 through 83 Processing helix chain 'A' and resid 109 through 111 No H-bonds generated for 'chain 'A' and resid 109 through 111' Processing helix chain 'A' and resid 210 through 230 Proline residue: A 227 - end of helix Processing helix chain 'B' and resid 32 through 46 Processing helix chain 'B' and resid 75 through 83 Processing helix chain 'B' and resid 109 through 111 No H-bonds generated for 'chain 'B' and resid 109 through 111' Processing helix chain 'B' and resid 206 through 225 removed outlier: 3.627A pdb=" N SER B 211 " --> pdb=" O ARG B 207 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'C' and resid 14 through 25 Processing helix chain 'C' and resid 27 through 35 removed outlier: 3.717A pdb=" N GLU C 31 " --> pdb=" O GLY C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 67 Processing helix chain 'C' and resid 177 through 184 Processing helix chain 'C' and resid 188 through 194 removed outlier: 3.721A pdb=" N LEU C 192 " --> pdb=" O ASP C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 208 removed outlier: 3.583A pdb=" N LYS C 203 " --> pdb=" O GLU C 199 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N THR C 204 " --> pdb=" O PHE C 200 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP C 206 " --> pdb=" O GLN C 202 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LYS C 207 " --> pdb=" O LYS C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 224 removed outlier: 3.640A pdb=" N LEU C 217 " --> pdb=" O GLU C 213 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL C 218 " --> pdb=" O GLU C 214 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU C 219 " --> pdb=" O GLU C 215 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU C 220 " --> pdb=" O ALA C 216 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N TYR C 221 " --> pdb=" O LEU C 217 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS C 223 " --> pdb=" O GLU C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 242 Processing helix chain 'C' and resid 253 through 263 Processing helix chain 'C' and resid 276 through 291 removed outlier: 3.697A pdb=" N GLU C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE C 291 " --> pdb=" O ILE C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 335 Processing helix chain 'C' and resid 343 through 346 No H-bonds generated for 'chain 'C' and resid 343 through 346' Processing helix chain 'C' and resid 350 through 361 Processing helix chain 'C' and resid 374 through 382 removed outlier: 3.708A pdb=" N LYS C 381 " --> pdb=" O GLU C 377 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG C 382 " --> pdb=" O LEU C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 408 No H-bonds generated for 'chain 'C' and resid 406 through 408' Processing helix chain 'C' and resid 503 through 505 No H-bonds generated for 'chain 'C' and resid 503 through 505' Processing helix chain 'C' and resid 519 through 522 No H-bonds generated for 'chain 'C' and resid 519 through 522' Processing helix chain 'C' and resid 527 through 529 No H-bonds generated for 'chain 'C' and resid 527 through 529' Processing helix chain 'C' and resid 532 through 544 removed outlier: 3.539A pdb=" N GLN C 544 " --> pdb=" O ASN C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 568 Processing helix chain 'C' and resid 677 through 680 No H-bonds generated for 'chain 'C' and resid 677 through 680' Processing helix chain 'C' and resid 753 through 761 Processing helix chain 'C' and resid 792 through 794 No H-bonds generated for 'chain 'C' and resid 792 through 794' Processing helix chain 'C' and resid 856 through 862 removed outlier: 3.518A pdb=" N VAL C 859 " --> pdb=" O PRO C 856 " (cutoff:3.500A) Proline residue: C 860 - end of helix No H-bonds generated for 'chain 'C' and resid 856 through 862' Processing helix chain 'C' and resid 866 through 880 Processing helix chain 'C' and resid 890 through 893 removed outlier: 3.644A pdb=" N TYR C 893 " --> pdb=" O ASP C 890 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 890 through 893' Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 956 through 958 No H-bonds generated for 'chain 'C' and resid 956 through 958' Processing helix chain 'C' and resid 989 through 997 Processing helix chain 'C' and resid 1001 through 1008 Processing helix chain 'C' and resid 1015 through 1026 Processing helix chain 'C' and resid 1038 through 1049 Processing helix chain 'D' and resid 19 through 26 Processing helix chain 'D' and resid 60 through 63 No H-bonds generated for 'chain 'D' and resid 60 through 63' Processing helix chain 'D' and resid 96 through 100 removed outlier: 4.041A pdb=" N ARG D 99 " --> pdb=" O SER D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 118 No H-bonds generated for 'chain 'D' and resid 115 through 118' Processing helix chain 'D' and resid 124 through 128 Processing helix chain 'D' and resid 133 through 140 Processing helix chain 'D' and resid 164 through 170 Processing helix chain 'D' and resid 189 through 198 Processing helix chain 'D' and resid 202 through 213 Processing helix chain 'D' and resid 219 through 236 removed outlier: 3.862A pdb=" N LYS D 223 " --> pdb=" O GLN D 219 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN D 233 " --> pdb=" O ARG D 229 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE D 234 " --> pdb=" O VAL D 230 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE D 235 " --> pdb=" O ILE D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 244 removed outlier: 3.543A pdb=" N MET D 244 " --> pdb=" O ALA D 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 241 through 244' Processing helix chain 'D' and resid 272 through 291 Processing helix chain 'D' and resid 296 through 314 Processing helix chain 'D' and resid 344 through 348 Processing helix chain 'D' and resid 377 through 383 removed outlier: 3.972A pdb=" N GLU D 382 " --> pdb=" O GLU D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 394 Processing helix chain 'D' and resid 401 through 410 Processing helix chain 'D' and resid 413 through 422 removed outlier: 3.746A pdb=" N SER D 417 " --> pdb=" O PRO D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 440 No H-bonds generated for 'chain 'D' and resid 438 through 440' Processing helix chain 'D' and resid 461 through 464 No H-bonds generated for 'chain 'D' and resid 461 through 464' Processing helix chain 'D' and resid 481 through 489 Processing helix chain 'D' and resid 493 through 495 No H-bonds generated for 'chain 'D' and resid 493 through 495' Processing helix chain 'D' and resid 513 through 520 Processing helix chain 'D' and resid 538 through 547 Processing helix chain 'D' and resid 611 through 624 Processing helix chain 'E' and resid 11 through 21 Processing helix chain 'E' and resid 28 through 43 Processing helix chain 'E' and resid 55 through 67 Processing helix chain 'F' and resid 72 through 81 Processing helix chain 'F' and resid 88 through 115 Processing helix chain 'F' and resid 174 through 205 removed outlier: 4.060A pdb=" N ASN F 197 " --> pdb=" O MET F 193 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU F 198 " --> pdb=" O VAL F 194 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ARG F 199 " --> pdb=" O GLN F 195 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LEU F 200 " --> pdb=" O SER F 196 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL F 201 " --> pdb=" O ASN F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 231 Processing helix chain 'F' and resid 235 through 237 No H-bonds generated for 'chain 'F' and resid 235 through 237' Processing helix chain 'F' and resid 241 through 259 Processing helix chain 'F' and resid 268 through 287 Processing helix chain 'F' and resid 294 through 301 Processing helix chain 'F' and resid 305 through 314 Processing helix chain 'F' and resid 333 through 336 Processing helix chain 'F' and resid 344 through 363 removed outlier: 4.316A pdb=" N THR F 363 " --> pdb=" O ASN F 359 " (cutoff:3.500A) Processing helix chain 'F' and resid 366 through 376 Processing helix chain 'F' and resid 386 through 392 Processing helix chain 'F' and resid 397 through 411 Processing helix chain 'F' and resid 420 through 423 Processing helix chain 'Z' and resid 10 through 23 removed outlier: 3.970A pdb=" N ARG Z 22 " --> pdb=" O ALA Z 18 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ARG Z 23 " --> pdb=" O LEU Z 19 " (cutoff:3.500A) Processing helix chain 'Z' and resid 27 through 47 Processing helix chain 'Z' and resid 62 through 82 Processing helix chain 'Z' and resid 87 through 115 Processing helix chain 'Z' and resid 121 through 127 Processing helix chain 'Z' and resid 134 through 140 Processing helix chain 'Z' and resid 169 through 188 removed outlier: 3.738A pdb=" N GLY Z 178 " --> pdb=" O ILE Z 174 " (cutoff:3.500A) Processing helix chain 'Z' and resid 190 through 204 removed outlier: 3.609A pdb=" N SER Z 204 " --> pdb=" O LEU Z 200 " (cutoff:3.500A) Processing helix chain 'Z' and resid 235 through 238 No H-bonds generated for 'chain 'Z' and resid 235 through 238' Processing helix chain 'Z' and resid 265 through 272 Processing helix chain 'Z' and resid 294 through 297 No H-bonds generated for 'chain 'Z' and resid 294 through 297' Processing helix chain 'Z' and resid 313 through 330 Proline residue: Z 324 - end of helix Processing helix chain 'Z' and resid 332 through 335 removed outlier: 3.584A pdb=" N THR Z 335 " --> pdb=" O THR Z 332 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 332 through 335' Processing helix chain 'Z' and resid 426 through 429 No H-bonds generated for 'chain 'Z' and resid 426 through 429' Processing helix chain 'Z' and resid 629 through 631 No H-bonds generated for 'chain 'Z' and resid 629 through 631' Processing helix chain 'Z' and resid 979 through 990 Proline residue: Z 984 - end of helix Processing helix chain 'Z' and resid 1061 through 1072 Processing helix chain 'Z' and resid 1078 through 1104 removed outlier: 3.881A pdb=" N GLN Z1104 " --> pdb=" O VAL Z1100 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1110 through 1120 removed outlier: 3.994A pdb=" N ILE Z1116 " --> pdb=" O HIS Z1112 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1142 through 1153 Processing helix chain 'Z' and resid 1171 through 1174 No H-bonds generated for 'chain 'Z' and resid 1171 through 1174' Processing helix chain 'Z' and resid 1179 through 1185 Processing helix chain 'Z' and resid 1188 through 1198 Processing helix chain 'Z' and resid 1207 through 1213 Processing helix chain 'Z' and resid 1220 through 1222 No H-bonds generated for 'chain 'Z' and resid 1220 through 1222' Processing sheet with id= A, first strand: chain 'A' and resid 5 through 10 removed outlier: 3.648A pdb=" N GLU A 26 " --> pdb=" O GLN A 5 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LYS A 22 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LYS A 195 " --> pdb=" O ILE A 187 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS A 179 " --> pdb=" O TRP A 203 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 87 through 89 Processing sheet with id= C, first strand: chain 'A' and resid 95 through 102 removed outlier: 3.939A pdb=" N ALA A 55 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLU A 143 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N VAL A 53 " --> pdb=" O GLU A 143 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N GLY A 145 " --> pdb=" O ALA A 51 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ALA A 51 " --> pdb=" O GLY A 145 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 105 through 108 Processing sheet with id= E, first strand: chain 'B' and resid 5 through 14 removed outlier: 6.679A pdb=" N LYS B 22 " --> pdb=" O VAL B 9 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N SER B 11 " --> pdb=" O TYR B 20 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N TYR B 20 " --> pdb=" O SER B 11 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N THR B 13 " --> pdb=" O GLN B 18 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N GLN B 18 " --> pdb=" O THR B 13 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLN B 19 " --> pdb=" O THR B 200 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 87 through 89 Processing sheet with id= G, first strand: chain 'B' and resid 95 through 102 removed outlier: 3.959A pdb=" N ALA B 55 " --> pdb=" O ARG B 141 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N GLU B 143 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N VAL B 53 " --> pdb=" O GLU B 143 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N GLY B 145 " --> pdb=" O ALA B 51 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ALA B 51 " --> pdb=" O GLY B 145 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 105 through 107 removed outlier: 3.675A pdb=" N GLY B 105 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA B 128 " --> pdb=" O VAL B 107 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 147 through 149 removed outlier: 4.232A pdb=" N GLY B 147 " --> pdb=" O PHE B 170 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 45 through 49 removed outlier: 3.926A pdb=" N GLU C 46 " --> pdb=" O ILE C 84 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE C 84 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N HIS C 48 " --> pdb=" O ARG C 82 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG C 82 " --> pdb=" O HIS C 48 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY C 99 " --> pdb=" O MET C 77 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL C 79 " --> pdb=" O PHE C 97 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N PHE C 97 " --> pdb=" O VAL C 79 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N THR C 81 " --> pdb=" O GLU C 95 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N GLU C 95 " --> pdb=" O THR C 81 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N LEU C 83 " --> pdb=" O GLU C 93 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N GLU C 93 " --> pdb=" O LEU C 83 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 117 through 119 Processing sheet with id= L, first strand: chain 'C' and resid 122 through 125 Processing sheet with id= M, first strand: chain 'C' and resid 128 through 132 Processing sheet with id= N, first strand: chain 'C' and resid 383 through 385 Processing sheet with id= O, first strand: chain 'C' and resid 445 through 447 Processing sheet with id= P, first strand: chain 'C' and resid 490 through 494 Processing sheet with id= Q, first strand: chain 'C' and resid 605 through 608 removed outlier: 6.664A pdb=" N GLN C 591 " --> pdb=" O VAL C 580 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N VAL C 580 " --> pdb=" O GLN C 591 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 944 through 949 removed outlier: 6.712A pdb=" N ILE C 852 " --> pdb=" O ALA C 659 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 789 through 791 removed outlier: 6.649A pdb=" N ALA C 696 " --> pdb=" O ASN C 803 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N VAL C 805 " --> pdb=" O ILE C 694 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE C 694 " --> pdb=" O VAL C 805 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ARG C 807 " --> pdb=" O PHE C 692 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N PHE C 692 " --> pdb=" O ARG C 807 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N TYR C 809 " --> pdb=" O GLU C 690 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N GLU C 690 " --> pdb=" O TYR C 809 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ALA C 811 " --> pdb=" O HIS C 688 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N HIS C 688 " --> pdb=" O ALA C 811 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LYS C 813 " --> pdb=" O SER C 686 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N SER C 686 " --> pdb=" O LYS C 813 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 821 through 823 removed outlier: 7.783A pdb=" N ILE C 674 " --> pdb=" O SER C 833 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE C 835 " --> pdb=" O ILE C 674 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 1057 through 1059 Processing sheet with id= V, first strand: chain 'C' and resid 783 through 786 removed outlier: 6.566A pdb=" N TYR C 809 " --> pdb=" O VAL C 785 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 104 through 107 Processing sheet with id= X, first strand: chain 'D' and resid 357 through 361 Processing sheet with id= Y, first strand: chain 'D' and resid 362 through 364 removed outlier: 6.150A pdb=" N ILE D 454 " --> pdb=" O VAL D 363 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'D' and resid 556 through 559 removed outlier: 6.941A pdb=" N ARG D 595 " --> pdb=" O ILE D 603 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLN D 605 " --> pdb=" O LYS D 593 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LYS D 593 " --> pdb=" O GLN D 605 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL D 585 " --> pdb=" O GLU D 596 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N THR D 584 " --> pdb=" O LEU D 580 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS D 576 " --> pdb=" O TYR D 588 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'D' and resid 146 through 149 removed outlier: 6.415A pdb=" N GLU D 185 " --> pdb=" O LEU D 148 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'Z' and resid 220 through 222 Processing sheet with id= AC, first strand: chain 'Z' and resid 353 through 356 removed outlier: 4.455A pdb=" N ILE Z 384 " --> pdb=" O LYS Z 356 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN Z 395 " --> pdb=" O TRP Z 385 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'Z' and resid 363 through 367 removed outlier: 3.632A pdb=" N ALA Z 374 " --> pdb=" O VAL Z 366 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'Z' and resid 403 through 405 removed outlier: 3.510A pdb=" N GLU Z 421 " --> pdb=" O LEU Z 404 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'Z' and resid 431 through 438 removed outlier: 3.673A pdb=" N PHE Z 971 " --> pdb=" O ALA Z 434 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL Z 438 " --> pdb=" O VAL Z 967 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N VAL Z 967 " --> pdb=" O VAL Z 438 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'Z' and resid 444 through 449 removed outlier: 3.544A pdb=" N ARG Z 942 " --> pdb=" O ILE Z 475 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'Z' and resid 453 through 456 removed outlier: 4.207A pdb=" N THR Z 464 " --> pdb=" O LYS Z 456 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'Z' and resid 479 through 482 removed outlier: 3.968A pdb=" N LEU Z 882 " --> pdb=" O ARG Z 869 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG Z 869 " --> pdb=" O LEU Z 882 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR Z 867 " --> pdb=" O GLU Z 884 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'Z' and resid 621 through 624 removed outlier: 3.591A pdb=" N ARG Z 668 " --> pdb=" O VAL Z 661 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N VAL Z 661 " --> pdb=" O ARG Z 668 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ILE Z 670 " --> pdb=" O GLU Z 659 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLU Z 659 " --> pdb=" O ILE Z 670 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ILE Z 672 " --> pdb=" O ILE Z 657 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ILE Z 657 " --> pdb=" O ILE Z 672 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'Z' and resid 710 through 714 removed outlier: 3.955A pdb=" N GLU Z 713 " --> pdb=" O LEU Z 724 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU Z 724 " --> pdb=" O GLU Z 713 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'Z' and resid 889 through 894 Processing sheet with id= AM, first strand: chain 'Z' and resid 1139 through 1141 removed outlier: 3.510A pdb=" N ASP Z1127 " --> pdb=" O ARG Z1161 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG Z1161 " --> pdb=" O ASP Z1127 " (cutoff:3.500A) 886 hydrogen bonds defined for protein. 2571 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 99 hydrogen bonds 190 hydrogen bond angles 0 basepair planarities 39 basepair parallelities 79 stacking parallelities Total time for adding SS restraints: 12.34 Time building geometry restraints manager: 12.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8376 1.33 - 1.45: 5380 1.45 - 1.57: 16939 1.57 - 1.69: 208 1.69 - 1.81: 143 Bond restraints: 31046 Sorted by residual: bond pdb=" N ARG A 153 " pdb=" CA ARG A 153 " ideal model delta sigma weight residual 1.457 1.492 -0.034 1.29e-02 6.01e+03 7.00e+00 bond pdb=" N ASP C 170 " pdb=" CA ASP C 170 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.23e-02 6.61e+03 6.18e+00 bond pdb=" C3' DA 2 17 " pdb=" O3' DA 2 17 " ideal model delta sigma weight residual 1.422 1.495 -0.073 3.00e-02 1.11e+03 5.84e+00 bond pdb=" CA THR Z 528 " pdb=" CB THR Z 528 " ideal model delta sigma weight residual 1.527 1.562 -0.035 1.61e-02 3.86e+03 4.83e+00 bond pdb=" C VAL Z 900 " pdb=" N LYS Z 901 " ideal model delta sigma weight residual 1.331 1.364 -0.033 1.59e-02 3.96e+03 4.37e+00 ... (remaining 31041 not shown) Histogram of bond angle deviations from ideal: 97.42 - 104.78: 897 104.78 - 112.13: 15358 112.13 - 119.49: 10691 119.49 - 126.84: 15017 126.84 - 134.19: 591 Bond angle restraints: 42554 Sorted by residual: angle pdb=" C ILE C 169 " pdb=" N ASP C 170 " pdb=" CA ASP C 170 " ideal model delta sigma weight residual 120.82 130.37 -9.55 1.50e+00 4.44e-01 4.06e+01 angle pdb=" N VAL Z1042 " pdb=" CA VAL Z1042 " pdb=" C VAL Z1042 " ideal model delta sigma weight residual 113.53 108.10 5.43 9.80e-01 1.04e+00 3.06e+01 angle pdb=" C ILE Z 527 " pdb=" N THR Z 528 " pdb=" CA THR Z 528 " ideal model delta sigma weight residual 122.82 129.93 -7.11 1.42e+00 4.96e-01 2.51e+01 angle pdb=" C GLY D 74 " pdb=" N LYS D 75 " pdb=" CA LYS D 75 " ideal model delta sigma weight residual 121.54 130.23 -8.69 1.91e+00 2.74e-01 2.07e+01 angle pdb=" C ALA Z 289 " pdb=" N ARG Z 290 " pdb=" CA ARG Z 290 " ideal model delta sigma weight residual 121.54 129.63 -8.09 1.91e+00 2.74e-01 1.79e+01 ... (remaining 42549 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.17: 17955 35.17 - 70.35: 628 70.35 - 105.52: 28 105.52 - 140.70: 1 140.70 - 175.87: 6 Dihedral angle restraints: 18618 sinusoidal: 8026 harmonic: 10592 Sorted by residual: dihedral pdb=" CA GLY Z 870 " pdb=" C GLY Z 870 " pdb=" N ILE Z 871 " pdb=" CA ILE Z 871 " ideal model delta harmonic sigma weight residual 180.00 -142.35 -37.65 0 5.00e+00 4.00e-02 5.67e+01 dihedral pdb=" O3B CTP 23001 " pdb=" O3A CTP 23001 " pdb=" PB CTP 23001 " pdb=" PA CTP 23001 " ideal model delta sinusoidal sigma weight residual 320.71 149.07 171.64 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" CA LYS A 15 " pdb=" C LYS A 15 " pdb=" N ASN A 16 " pdb=" CA ASN A 16 " ideal model delta harmonic sigma weight residual 180.00 150.97 29.03 0 5.00e+00 4.00e-02 3.37e+01 ... (remaining 18615 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 3696 0.053 - 0.105: 924 0.105 - 0.158: 250 0.158 - 0.211: 30 0.211 - 0.263: 5 Chirality restraints: 4905 Sorted by residual: chirality pdb=" CB ILE B 68 " pdb=" CA ILE B 68 " pdb=" CG1 ILE B 68 " pdb=" CG2 ILE B 68 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CB ILE C 852 " pdb=" CA ILE C 852 " pdb=" CG1 ILE C 852 " pdb=" CG2 ILE C 852 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CB ILE Z 927 " pdb=" CA ILE Z 927 " pdb=" CG1 ILE Z 927 " pdb=" CG2 ILE Z 927 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 4902 not shown) Planarity restraints: 5204 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 252 " 0.049 5.00e-02 4.00e+02 7.46e-02 8.92e+00 pdb=" N PRO D 253 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO D 253 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 253 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP Z 149 " -0.044 5.00e-02 4.00e+02 6.67e-02 7.13e+00 pdb=" N PRO Z 150 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO Z 150 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO Z 150 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 373 " -0.042 5.00e-02 4.00e+02 6.30e-02 6.35e+00 pdb=" N PRO C 374 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO C 374 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 374 " -0.035 5.00e-02 4.00e+02 ... (remaining 5201 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.46: 71 2.46 - 3.07: 16851 3.07 - 3.68: 45048 3.68 - 4.29: 67110 4.29 - 4.90: 109738 Nonbonded interactions: 238818 Sorted by model distance: nonbonded pdb="MG MG D2003 " pdb=" O1B CTP 23001 " model vdw 1.845 2.170 nonbonded pdb="MG MG D2001 " pdb=" O2A CTP 23001 " model vdw 2.057 2.170 nonbonded pdb=" OD1 ASP D 469 " pdb="MG MG D2001 " model vdw 2.154 2.170 nonbonded pdb=" OD1 ASP D 467 " pdb="MG MG D2001 " model vdw 2.160 2.170 nonbonded pdb="MG MG D2003 " pdb=" O2A CTP 23001 " model vdw 2.224 2.170 ... (remaining 238813 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 154 or resid 166 through 187 or (resid 188 throu \ gh 189 and (name N or name CA or name C or name O or name CB )) or resid 190 thr \ ough 191 or (resid 192 and (name N or name CA or name C or name O or name CB )) \ or resid 193 through 230)) selection = (chain 'B' and (resid 4 through 50 or (resid 51 and (name N or name CA or name C \ or name O )) or resid 52 through 92 or (resid 93 and (name N or name CA or name \ C or name O or name CB )) or resid 94 through 131 or (resid 132 and (name N or \ name CA or name C or name O or name CB )) or (resid 133 through 135 and (name N \ or name CA or name C or name O or name CB )) or resid 136 through 151 or (resid \ 152 through 153 and (name N or name CA or name C or name O or name CB )) or resi \ d 154 through 225 or (resid 226 and (name N or name CA or name C or name O or na \ me CB )))) } 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=0.30 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: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.260 Construct map_model_manager: 0.020 Extract box with map and model: 6.360 Check model and map are aligned: 0.430 Set scattering table: 0.270 Process input model: 91.540 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 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 : 0.004 0.073 31046 Z= 0.279 Angle : 0.769 12.282 42554 Z= 0.433 Chirality : 0.051 0.263 4905 Planarity : 0.006 0.075 5204 Dihedral : 16.759 175.871 11808 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.14 % Allowed : 5.10 % Favored : 94.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.25 (0.11), residues: 3665 helix: -2.26 (0.11), residues: 1193 sheet: -0.99 (0.21), residues: 501 loop : -2.44 (0.11), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 875 HIS 0.006 0.001 HIS D 547 PHE 0.019 0.002 PHE Z1179 TYR 0.026 0.002 TYR C 680 ARG 0.004 0.000 ARG Z 242 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7330 Ramachandran restraints generated. 3665 Oldfield, 0 Emsley, 3665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7330 Ramachandran restraints generated. 3665 Oldfield, 0 Emsley, 3665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 484 time to evaluate : 3.569 Fit side-chains REVERT: A 95 GLN cc_start: 0.7575 (mm-40) cc_final: 0.7346 (mm110) REVERT: C 132 LYS cc_start: 0.7788 (ptmt) cc_final: 0.7579 (ttmt) REVERT: C 358 GLU cc_start: 0.7370 (tm-30) cc_final: 0.7136 (tp30) REVERT: C 610 GLN cc_start: 0.8251 (pt0) cc_final: 0.8044 (pt0) REVERT: C 698 GLN cc_start: 0.7271 (mt0) cc_final: 0.7035 (mm-40) REVERT: C 800 PRO cc_start: 0.7476 (Cg_endo) cc_final: 0.7217 (Cg_exo) REVERT: C 804 MET cc_start: 0.8027 (ptp) cc_final: 0.7720 (ptp) REVERT: C 887 THR cc_start: 0.8949 (t) cc_final: 0.8745 (m) REVERT: C 1016 GLN cc_start: 0.7318 (mp10) cc_final: 0.6869 (mm-40) REVERT: D 311 ASP cc_start: 0.8050 (m-30) cc_final: 0.7759 (m-30) REVERT: D 406 LYS cc_start: 0.8088 (tttt) cc_final: 0.7804 (ttmp) REVERT: E 17 GLU cc_start: 0.7597 (tp30) cc_final: 0.7266 (tm-30) REVERT: F 104 LEU cc_start: 0.7678 (tp) cc_final: 0.7443 (tp) REVERT: F 347 GLU cc_start: 0.7182 (mm-30) cc_final: 0.6762 (mm-30) REVERT: F 374 LEU cc_start: 0.7902 (mp) cc_final: 0.7567 (mm) REVERT: Z 365 LYS cc_start: 0.6670 (pttp) cc_final: 0.5185 (mtpm) REVERT: Z 437 ASP cc_start: 0.5653 (m-30) cc_final: 0.5355 (m-30) outliers start: 4 outliers final: 1 residues processed: 488 average time/residue: 1.6792 time to fit residues: 941.7573 Evaluate side-chains 301 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 300 time to evaluate : 3.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 916 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 316 optimal weight: 0.0970 chunk 284 optimal weight: 0.9990 chunk 157 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 191 optimal weight: 0.9980 chunk 151 optimal weight: 3.9990 chunk 293 optimal weight: 10.0000 chunk 113 optimal weight: 7.9990 chunk 178 optimal weight: 1.9990 chunk 218 optimal weight: 20.0000 chunk 340 optimal weight: 8.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 169 GLN B 205 GLN C 76 GLN ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 496 GLN C 778 ASN C 903 HIS C 923 HIS D 114 HIS D 157 GLN D 240 GLN D 283 ASN D 472 GLN D 553 HIS D 560 HIS F 97 GLN F 402 GLN Z 108 GLN Z 305 HIS Z 395 GLN Z 462 ASN Z 468 GLN Z1059 ASN Z1102 GLN Z1210 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 31046 Z= 0.204 Angle : 0.538 9.575 42554 Z= 0.289 Chirality : 0.043 0.188 4905 Planarity : 0.005 0.073 5204 Dihedral : 16.375 177.471 5191 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.50 % Allowed : 12.11 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.86 (0.12), residues: 3665 helix: -0.37 (0.14), residues: 1195 sheet: -0.63 (0.21), residues: 537 loop : -2.01 (0.12), residues: 1933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 875 HIS 0.004 0.001 HIS C 197 PHE 0.019 0.001 PHE A 174 TYR 0.018 0.001 TYR C 680 ARG 0.006 0.000 ARG D 48 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7330 Ramachandran restraints generated. 3665 Oldfield, 0 Emsley, 3665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7330 Ramachandran restraints generated. 3665 Oldfield, 0 Emsley, 3665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 328 time to evaluate : 3.373 Fit side-chains REVERT: A 95 GLN cc_start: 0.7469 (mm-40) cc_final: 0.7258 (mm110) REVERT: B 74 ASP cc_start: 0.7224 (OUTLIER) cc_final: 0.6613 (p0) REVERT: B 136 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7439 (tp) REVERT: C 358 GLU cc_start: 0.7385 (tm-30) cc_final: 0.7142 (tp30) REVERT: C 497 GLU cc_start: 0.6803 (OUTLIER) cc_final: 0.5974 (tp30) REVERT: C 698 GLN cc_start: 0.7219 (mt0) cc_final: 0.6930 (tm-30) REVERT: C 794 LYS cc_start: 0.6932 (OUTLIER) cc_final: 0.6093 (mtmt) REVERT: C 804 MET cc_start: 0.7925 (ptp) cc_final: 0.7659 (ptp) REVERT: C 949 MET cc_start: 0.9047 (mmt) cc_final: 0.8484 (mmm) REVERT: C 1016 GLN cc_start: 0.7334 (mp10) cc_final: 0.6888 (mm-40) REVERT: D 406 LYS cc_start: 0.8030 (tttt) cc_final: 0.7766 (ttmp) REVERT: D 506 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8366 (pt) REVERT: E 17 GLU cc_start: 0.7589 (tp30) cc_final: 0.7242 (tm-30) REVERT: F 419 ILE cc_start: 0.7028 (OUTLIER) cc_final: 0.6746 (tp) REVERT: Z 34 ASP cc_start: 0.7801 (t0) cc_final: 0.7454 (t0) REVERT: Z 189 ARG cc_start: 0.7451 (mmt180) cc_final: 0.7239 (mmm160) REVERT: Z 365 LYS cc_start: 0.6557 (pttp) cc_final: 0.5101 (mtpm) REVERT: Z 713 GLU cc_start: 0.3962 (pm20) cc_final: 0.3761 (pm20) REVERT: Z 958 ASP cc_start: 0.4742 (OUTLIER) cc_final: 0.4509 (OUTLIER) outliers start: 73 outliers final: 26 residues processed: 367 average time/residue: 1.4918 time to fit residues: 638.5437 Evaluate side-chains 317 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 285 time to evaluate : 3.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 497 GLU Chi-restraints excluded: chain C residue 576 THR Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 794 LYS Chi-restraints excluded: chain D residue 480 SER Chi-restraints excluded: chain D residue 506 ILE Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain F residue 281 THR Chi-restraints excluded: chain F residue 396 THR Chi-restraints excluded: chain F residue 419 ILE Chi-restraints excluded: chain Z residue 23 ARG Chi-restraints excluded: chain Z residue 223 THR Chi-restraints excluded: chain Z residue 247 ASP Chi-restraints excluded: chain Z residue 330 MET Chi-restraints excluded: chain Z residue 499 VAL Chi-restraints excluded: chain Z residue 538 VAL Chi-restraints excluded: chain Z residue 641 GLU Chi-restraints excluded: chain Z residue 669 GLU Chi-restraints excluded: chain Z residue 710 SER Chi-restraints excluded: chain Z residue 890 LEU Chi-restraints excluded: chain Z residue 958 ASP Chi-restraints excluded: chain Z residue 966 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 189 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 283 optimal weight: 5.9990 chunk 231 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 chunk 341 optimal weight: 4.9990 chunk 368 optimal weight: 7.9990 chunk 303 optimal weight: 8.9990 chunk 338 optimal weight: 0.0970 chunk 116 optimal weight: 8.9990 chunk 273 optimal weight: 4.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 654 GLN C 778 ASN D 143 ASN D 328 ASN D 608 GLN F 195 GLN Z 664 ASN Z1059 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 31046 Z= 0.450 Angle : 0.693 10.263 42554 Z= 0.366 Chirality : 0.050 0.220 4905 Planarity : 0.006 0.066 5204 Dihedral : 16.665 178.660 5189 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.56 % Allowed : 14.41 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.53 (0.13), residues: 3665 helix: 0.08 (0.15), residues: 1174 sheet: -0.59 (0.21), residues: 558 loop : -1.88 (0.12), residues: 1933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 732 HIS 0.008 0.002 HIS C 409 PHE 0.029 0.003 PHE A 174 TYR 0.032 0.003 TYR Z 6 ARG 0.007 0.001 ARG Z 210 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7330 Ramachandran restraints generated. 3665 Oldfield, 0 Emsley, 3665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7330 Ramachandran restraints generated. 3665 Oldfield, 0 Emsley, 3665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 297 time to evaluate : 3.272 Fit side-chains revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8234 (mp) REVERT: B 136 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7422 (tp) REVERT: C 78 TYR cc_start: 0.7684 (m-80) cc_final: 0.7416 (m-80) REVERT: C 107 ARG cc_start: 0.8217 (mtm110) cc_final: 0.7938 (mtp-110) REVERT: C 358 GLU cc_start: 0.7437 (tm-30) cc_final: 0.7188 (tp30) REVERT: C 497 GLU cc_start: 0.6929 (OUTLIER) cc_final: 0.6080 (tp30) REVERT: C 698 GLN cc_start: 0.7328 (mt0) cc_final: 0.7048 (tm-30) REVERT: C 804 MET cc_start: 0.7949 (ptp) cc_final: 0.7699 (ptp) REVERT: C 949 MET cc_start: 0.9043 (mmt) cc_final: 0.8509 (mmm) REVERT: C 1016 GLN cc_start: 0.7369 (mp10) cc_final: 0.6932 (mm-40) REVERT: D 48 ARG cc_start: 0.7975 (ttp80) cc_final: 0.7689 (ttp80) REVERT: D 100 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7849 (mtp180) REVERT: D 406 LYS cc_start: 0.8168 (tttt) cc_final: 0.7875 (ttmp) REVERT: D 407 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8268 (mp) REVERT: D 506 ILE cc_start: 0.8723 (OUTLIER) cc_final: 0.8302 (pt) REVERT: E 17 GLU cc_start: 0.7653 (tp30) cc_final: 0.7280 (tm-30) REVERT: E 24 SER cc_start: 0.7451 (p) cc_final: 0.7140 (t) REVERT: F 301 MET cc_start: 0.7479 (mmm) cc_final: 0.7182 (mmm) REVERT: Z 365 LYS cc_start: 0.6787 (pttp) cc_final: 0.5093 (mtpm) REVERT: Z 447 LEU cc_start: 0.5708 (OUTLIER) cc_final: 0.4978 (mt) REVERT: Z 452 VAL cc_start: 0.5974 (OUTLIER) cc_final: 0.5626 (p) REVERT: Z 952 LEU cc_start: 0.6834 (mp) cc_final: 0.6554 (mp) REVERT: Z 956 ASP cc_start: 0.5023 (OUTLIER) cc_final: 0.4335 (p0) outliers start: 104 outliers final: 47 residues processed: 366 average time/residue: 1.4858 time to fit residues: 635.1120 Evaluate side-chains 342 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 286 time to evaluate : 3.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 463 THR Chi-restraints excluded: chain C residue 484 ASN Chi-restraints excluded: chain C residue 497 GLU Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 576 THR Chi-restraints excluded: chain C residue 587 GLU Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 746 LYS Chi-restraints excluded: chain D residue 100 ARG Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 480 SER Chi-restraints excluded: chain D residue 486 GLU Chi-restraints excluded: chain D residue 506 ILE Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain F residue 263 THR Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 396 THR Chi-restraints excluded: chain Z residue 23 ARG Chi-restraints excluded: chain Z residue 201 VAL Chi-restraints excluded: chain Z residue 223 THR Chi-restraints excluded: chain Z residue 247 ASP Chi-restraints excluded: chain Z residue 330 MET Chi-restraints excluded: chain Z residue 340 THR Chi-restraints excluded: chain Z residue 447 LEU Chi-restraints excluded: chain Z residue 452 VAL Chi-restraints excluded: chain Z residue 499 VAL Chi-restraints excluded: chain Z residue 538 VAL Chi-restraints excluded: chain Z residue 641 GLU Chi-restraints excluded: chain Z residue 669 GLU Chi-restraints excluded: chain Z residue 710 SER Chi-restraints excluded: chain Z residue 733 VAL Chi-restraints excluded: chain Z residue 890 LEU Chi-restraints excluded: chain Z residue 956 ASP Chi-restraints excluded: chain Z residue 958 ASP Chi-restraints excluded: chain Z residue 966 LEU Chi-restraints excluded: chain Z residue 981 GLN Chi-restraints excluded: chain Z residue 1075 LYS Chi-restraints excluded: chain Z residue 1124 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 337 optimal weight: 20.0000 chunk 256 optimal weight: 0.9990 chunk 177 optimal weight: 0.0670 chunk 37 optimal weight: 0.9990 chunk 162 optimal weight: 5.9990 chunk 229 optimal weight: 3.9990 chunk 342 optimal weight: 3.9990 chunk 362 optimal weight: 2.9990 chunk 178 optimal weight: 5.9990 chunk 324 optimal weight: 10.0000 chunk 97 optimal weight: 0.9980 overall best weight: 1.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 GLN ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 610 GLN C 778 ASN D 307 GLN D 328 ASN Z 482 ASN Z 664 ASN Z1059 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 31046 Z= 0.201 Angle : 0.534 9.851 42554 Z= 0.284 Chirality : 0.043 0.164 4905 Planarity : 0.004 0.065 5204 Dihedral : 16.380 176.141 5189 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.56 % Allowed : 15.78 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.01 (0.13), residues: 3665 helix: 0.69 (0.15), residues: 1174 sheet: -0.48 (0.21), residues: 563 loop : -1.64 (0.12), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 732 HIS 0.003 0.001 HIS D 560 PHE 0.017 0.001 PHE A 174 TYR 0.015 0.001 TYR Z 6 ARG 0.010 0.000 ARG C 447 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7330 Ramachandran restraints generated. 3665 Oldfield, 0 Emsley, 3665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7330 Ramachandran restraints generated. 3665 Oldfield, 0 Emsley, 3665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 307 time to evaluate : 2.973 Fit side-chains REVERT: A 48 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8234 (mp) REVERT: A 138 MET cc_start: 0.8923 (OUTLIER) cc_final: 0.8702 (ttp) REVERT: B 136 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7457 (tp) REVERT: B 224 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7561 (mp) REVERT: C 78 TYR cc_start: 0.7634 (m-80) cc_final: 0.7402 (m-80) REVERT: C 107 ARG cc_start: 0.8196 (mtm110) cc_final: 0.7949 (mtp-110) REVERT: C 358 GLU cc_start: 0.7416 (tm-30) cc_final: 0.7172 (tp30) REVERT: C 467 GLU cc_start: 0.6613 (mm-30) cc_final: 0.5439 (mp0) REVERT: C 496 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.7743 (mt0) REVERT: C 497 GLU cc_start: 0.6837 (OUTLIER) cc_final: 0.6046 (tp30) REVERT: C 646 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7954 (pp20) REVERT: C 698 GLN cc_start: 0.7444 (mt0) cc_final: 0.7114 (tm-30) REVERT: C 804 MET cc_start: 0.7942 (ptp) cc_final: 0.7686 (ptp) REVERT: C 949 MET cc_start: 0.9008 (mmt) cc_final: 0.8363 (mmm) REVERT: D 41 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8279 (mtpp) REVERT: D 48 ARG cc_start: 0.7968 (ttp80) cc_final: 0.7724 (ttp80) REVERT: D 406 LYS cc_start: 0.8075 (tttt) cc_final: 0.7634 (tttm) REVERT: D 473 MET cc_start: 0.8518 (mtm) cc_final: 0.8308 (mtp) REVERT: D 506 ILE cc_start: 0.8697 (OUTLIER) cc_final: 0.8292 (pt) REVERT: E 24 SER cc_start: 0.7444 (p) cc_final: 0.7155 (t) REVERT: F 391 GLN cc_start: 0.6712 (OUTLIER) cc_final: 0.6184 (mp10) REVERT: Z 34 ASP cc_start: 0.7905 (t70) cc_final: 0.7548 (t0) REVERT: Z 365 LYS cc_start: 0.6760 (pttp) cc_final: 0.5239 (mtpm) REVERT: Z 447 LEU cc_start: 0.5577 (OUTLIER) cc_final: 0.4894 (mt) REVERT: Z 452 VAL cc_start: 0.6252 (OUTLIER) cc_final: 0.5870 (p) REVERT: Z 454 GLU cc_start: 0.5860 (OUTLIER) cc_final: 0.5237 (tm-30) REVERT: Z 958 ASP cc_start: 0.5310 (OUTLIER) cc_final: 0.5109 (OUTLIER) outliers start: 104 outliers final: 42 residues processed: 371 average time/residue: 1.4202 time to fit residues: 621.7900 Evaluate side-chains 352 residues out of total 3153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 297 time to evaluate : 3.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 463 THR Chi-restraints excluded: chain C residue 484 ASN Chi-restraints excluded: chain C residue 496 GLN Chi-restraints excluded: chain C residue 497 GLU Chi-restraints excluded: chain C residue 576 THR Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 646 GLU Chi-restraints excluded: chain C residue 754 GLU Chi-restraints excluded: chain C residue 908 GLU Chi-restraints excluded: chain C residue 944 VAL Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 480 SER Chi-restraints excluded: chain D residue 506 ILE Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain F residue 391 GLN Chi-restraints excluded: chain F residue 396 THR Chi-restraints excluded: chain Z residue 23 ARG Chi-restraints excluded: chain Z residue 49 VAL Chi-restraints excluded: chain Z residue 247 ASP Chi-restraints excluded: chain Z residue 330 MET Chi-restraints excluded: chain Z residue 447 LEU Chi-restraints excluded: chain Z residue 452 VAL Chi-restraints excluded: chain Z residue 454 GLU Chi-restraints excluded: chain Z residue 538 VAL Chi-restraints excluded: chain Z residue 641 GLU Chi-restraints excluded: chain Z residue 669 GLU Chi-restraints excluded: chain Z residue 890 LEU Chi-restraints excluded: chain Z residue 958 ASP Chi-restraints excluded: chain Z residue 959 LEU Chi-restraints excluded: chain Z residue 1049 ASP Chi-restraints excluded: chain Z residue 1075 LYS Chi-restraints excluded: chain Z residue 1078 CYS Chi-restraints excluded: chain Z residue 1124 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.3241 > 50: distance: 90 - 94: 8.283 distance: 94 - 95: 12.953 distance: 95 - 96: 21.620 distance: 95 - 98: 7.844 distance: 96 - 97: 35.746 distance: 96 - 102: 20.844 distance: 98 - 99: 11.150 distance: 98 - 100: 19.943 distance: 99 - 101: 16.572 distance: 102 - 103: 13.874 distance: 103 - 104: 11.783 distance: 103 - 106: 15.904 distance: 104 - 105: 3.747 distance: 104 - 113: 34.458 distance: 106 - 107: 11.523 distance: 107 - 108: 13.650 distance: 107 - 109: 16.994 distance: 108 - 110: 6.575 distance: 109 - 111: 11.237 distance: 110 - 112: 8.792 distance: 111 - 112: 4.915 distance: 113 - 114: 19.707 distance: 114 - 115: 4.980 distance: 114 - 117: 11.093 distance: 115 - 116: 20.961 distance: 115 - 119: 23.868 distance: 117 - 118: 34.514 distance: 119 - 120: 20.185 distance: 120 - 121: 15.611 distance: 120 - 123: 21.335 distance: 121 - 122: 13.040 distance: 121 - 128: 5.849 distance: 123 - 124: 12.850 distance: 124 - 125: 24.169 distance: 125 - 126: 22.925 distance: 125 - 127: 34.850 distance: 128 - 129: 6.768 distance: 129 - 130: 22.848 distance: 129 - 132: 18.102 distance: 130 - 131: 15.632 distance: 130 - 134: 14.199 distance: 132 - 133: 9.663 distance: 134 - 135: 5.188 distance: 135 - 136: 10.289 distance: 135 - 138: 5.084 distance: 136 - 137: 23.585 distance: 136 - 140: 13.843 distance: 138 - 139: 22.950 distance: 140 - 141: 10.516 distance: 141 - 142: 19.315 distance: 142 - 143: 15.881 distance: 142 - 144: 12.116 distance: 144 - 145: 12.722 distance: 145 - 146: 25.012 distance: 145 - 148: 8.803 distance: 146 - 147: 21.507 distance: 146 - 152: 22.045 distance: 148 - 149: 11.120 distance: 148 - 150: 12.205 distance: 149 - 151: 11.549 distance: 152 - 153: 20.530 distance: 153 - 154: 14.975 distance: 153 - 156: 13.699 distance: 154 - 155: 12.080 distance: 154 - 159: 7.657 distance: 160 - 161: 3.244 distance: 164 - 165: 3.168 distance: 165 - 167: 3.258