Starting phenix.real_space_refine (version: dev) on Sun Feb 26 04:26:55 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q9k_13872/02_2023/7q9k_13872.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q9k_13872/02_2023/7q9k_13872.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q9k_13872/02_2023/7q9k_13872.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q9k_13872/02_2023/7q9k_13872.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q9k_13872/02_2023/7q9k_13872.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q9k_13872/02_2023/7q9k_13872.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.026 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 Process input model Symmetric amino acids flipped Residue "H TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 27225 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 7336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 943, 7336 Classifications: {'peptide': 943} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 45, 'TRANS': 897} Chain breaks: 8 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: 7819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7819 Classifications: {'peptide': 1002} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 49, 'TRANS': 952} Chain breaks: 7 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: 7646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 979, 7646 Classifications: {'peptide': 979} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 47, 'TRANS': 931} Chain breaks: 8 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 980 Classifications: {'peptide': 125} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 120} Chain: "L" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 812 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "D" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 980 Classifications: {'peptide': 125} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 120} Chain: "E" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 812 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "F" 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 chiralities: 2 Chain: "G" 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 chiralities: 2 Chain: "I" 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 chiralities: 2 Chain: "J" 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 chiralities: 2 Chain: "K" 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 chiralities: 2 Chain: "M" 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 chiralities: 2 Chain: "N" 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 chiralities: 2 Chain: "O" 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 chiralities: 2 Chain: "P" 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 chiralities: 2 Chain: "Q" 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 chiralities: 2 Chain: "R" 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 chiralities: 2 Chain: "S" 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 chiralities: 2 Chain: "T" 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 chiralities: 2 Chain: "U" 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 chiralities: 2 Chain: "V" 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 chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 15.38, per 1000 atoms: 0.56 Number of scatterers: 27225 At special positions: 0 Unit cell: (140.22, 141.04, 205, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 119 16.00 O 5341 8.00 N 4453 7.00 C 17312 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 587 " distance=2.03 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.03 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.03 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.03 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 587 " distance=2.03 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.03 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.03 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 376 " - pdb=" SG CYS C 429 " distance=2.03 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 522 " distance=2.03 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 587 " distance=2.03 Simple disulfide: pdb=" SG CYS C 614 " - pdb=" SG CYS C 646 " distance=2.03 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.03 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.03 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.03 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.05 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.06 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.05 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.06 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 F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 279 " " NAG A1304 " - " ASN A 328 " " NAG A1305 " - " ASN A 600 " " NAG A1306 " - " ASN A 613 " " NAG A1307 " - " ASN A 654 " " NAG A1308 " - " ASN A 706 " " NAG A1309 " - " ASN A1071 " " NAG A1310 " - " ASN A 165 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 279 " " NAG B1304 " - " ASN B 328 " " NAG B1305 " - " ASN B 600 " " NAG B1306 " - " ASN B 613 " " NAG B1307 " - " ASN B 654 " " NAG B1308 " - " ASN B 706 " " NAG B1309 " - " ASN B1071 " " NAG B1310 " - " ASN B 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 279 " " NAG C1304 " - " ASN C 328 " " NAG C1305 " - " ASN C 600 " " NAG C1306 " - " ASN C 613 " " NAG C1307 " - " ASN C 654 " " NAG C1308 " - " ASN C 706 " " NAG C1309 " - " ASN C1071 " " NAG C1310 " - " ASN C 165 " " NAG F 1 " - " ASN A 234 " " NAG G 1 " - " ASN A 714 " " NAG I 1 " - " ASN A 798 " " NAG J 1 " - " ASN A1095 " " NAG K 1 " - " ASN A1131 " " NAG M 1 " - " ASN B 234 " " NAG N 1 " - " ASN B 714 " " NAG O 1 " - " ASN B 798 " " NAG P 1 " - " ASN B1095 " " NAG Q 1 " - " ASN B1131 " " NAG R 1 " - " ASN C 234 " " NAG S 1 " - " ASN C 714 " " NAG T 1 " - " ASN C 798 " " NAG U 1 " - " ASN C1095 " " NAG V 1 " - " ASN C1131 " Time building additional restraints: 10.40 Conformation dependent library (CDL) restraints added in 4.0 seconds 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6312 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 49 sheets defined 24.2% alpha, 31.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.38 Creating SS restraints... Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 362 through 368 removed outlier: 3.563A pdb=" N TYR A 366 " --> pdb=" O TYR A 362 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER A 368 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 385 removed outlier: 4.247A pdb=" N ASN A 385 " --> pdb=" O THR A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 405 removed outlier: 4.363A pdb=" N ARG A 405 " --> pdb=" O GLY A 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 401 through 405' Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 734 through 740 Processing helix chain 'A' and resid 743 through 751 Processing helix chain 'A' and resid 752 through 756 removed outlier: 7.054A pdb=" N SER A 755 " --> pdb=" O GLN A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 780 removed outlier: 3.594A pdb=" N ASN A 761 " --> pdb=" O CYS A 757 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP A 772 " --> pdb=" O ALA A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 821 Processing helix chain 'A' and resid 863 through 882 Processing helix chain 'A' and resid 883 through 888 removed outlier: 3.771A pdb=" N ALA A 887 " --> pdb=" O TRP A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 905 Processing helix chain 'A' and resid 909 through 916 removed outlier: 4.071A pdb=" N LEU A 913 " --> pdb=" O THR A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 938 Processing helix chain 'A' and resid 939 through 941 No H-bonds generated for 'chain 'A' and resid 939 through 941' Processing helix chain 'A' and resid 942 through 962 removed outlier: 3.898A pdb=" N VAL A 948 " --> pdb=" O LYS A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 965 No H-bonds generated for 'chain 'A' and resid 963 through 965' Processing helix chain 'A' and resid 973 through 979 Processing helix chain 'A' and resid 982 through 1030 removed outlier: 4.603A pdb=" N VAL A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1144 Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 335 through 340 Processing helix chain 'B' and resid 362 through 368 removed outlier: 3.563A pdb=" N TYR B 366 " --> pdb=" O TYR B 362 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER B 368 " --> pdb=" O VAL B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 385 removed outlier: 4.247A pdb=" N ASN B 385 " --> pdb=" O THR B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 405 removed outlier: 4.362A pdb=" N ARG B 405 " --> pdb=" O GLY B 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 401 through 405' Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 499 through 502 Processing helix chain 'B' and resid 734 through 740 Processing helix chain 'B' and resid 743 through 751 Processing helix chain 'B' and resid 752 through 756 removed outlier: 7.054A pdb=" N SER B 755 " --> pdb=" O GLN B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 780 removed outlier: 3.595A pdb=" N ASN B 761 " --> pdb=" O CYS B 757 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP B 772 " --> pdb=" O ALA B 768 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 821 Processing helix chain 'B' and resid 863 through 882 Processing helix chain 'B' and resid 883 through 888 removed outlier: 3.772A pdb=" N ALA B 887 " --> pdb=" O TRP B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 905 Processing helix chain 'B' and resid 909 through 916 removed outlier: 4.068A pdb=" N LEU B 913 " --> pdb=" O THR B 909 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 938 Processing helix chain 'B' and resid 939 through 941 No H-bonds generated for 'chain 'B' and resid 939 through 941' Processing helix chain 'B' and resid 942 through 962 removed outlier: 3.896A pdb=" N VAL B 948 " --> pdb=" O LYS B 944 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 965 No H-bonds generated for 'chain 'B' and resid 963 through 965' Processing helix chain 'B' and resid 973 through 979 Processing helix chain 'B' and resid 982 through 1030 removed outlier: 4.603A pdb=" N VAL B 988 " --> pdb=" O PRO B 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 1138 through 1144 Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 335 through 340 Processing helix chain 'C' and resid 362 through 368 removed outlier: 3.563A pdb=" N TYR C 366 " --> pdb=" O TYR C 362 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER C 368 " --> pdb=" O VAL C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 385 removed outlier: 4.247A pdb=" N ASN C 385 " --> pdb=" O THR C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 405 removed outlier: 4.363A pdb=" N ARG C 405 " --> pdb=" O GLY C 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 401 through 405' Processing helix chain 'C' and resid 413 through 419 Processing helix chain 'C' and resid 499 through 502 Processing helix chain 'C' and resid 734 through 740 Processing helix chain 'C' and resid 743 through 751 Processing helix chain 'C' and resid 752 through 756 removed outlier: 7.054A pdb=" N SER C 755 " --> pdb=" O GLN C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 780 removed outlier: 3.597A pdb=" N ASN C 761 " --> pdb=" O CYS C 757 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP C 772 " --> pdb=" O ALA C 768 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 821 Processing helix chain 'C' and resid 863 through 882 Processing helix chain 'C' and resid 883 through 888 removed outlier: 3.772A pdb=" N ALA C 887 " --> pdb=" O TRP C 883 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 905 Processing helix chain 'C' and resid 909 through 916 removed outlier: 4.069A pdb=" N LEU C 913 " --> pdb=" O THR C 909 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 938 Processing helix chain 'C' and resid 939 through 941 No H-bonds generated for 'chain 'C' and resid 939 through 941' Processing helix chain 'C' and resid 942 through 962 removed outlier: 3.898A pdb=" N VAL C 948 " --> pdb=" O LYS C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 963 through 965 No H-bonds generated for 'chain 'C' and resid 963 through 965' Processing helix chain 'C' and resid 973 through 979 Processing helix chain 'C' and resid 982 through 1030 removed outlier: 4.602A pdb=" N VAL C 988 " --> pdb=" O PRO C 984 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1144 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.744A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 107 through 111 removed outlier: 3.846A pdb=" N TRP H 111 " --> pdb=" O SER H 108 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.742A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'D' and resid 107 through 111 removed outlier: 3.846A pdb=" N TRP D 111 " --> pdb=" O SER D 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.504A pdb=" N THR A 29 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL A 62 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N ASN A 61 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N TYR A 266 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.747A pdb=" N ALA C 572 " --> pdb=" O GLY C 563 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ASP C 571 " --> pdb=" O ILE C 584 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLU C 321 " --> pdb=" O CYS C 535 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 52 removed outlier: 3.590A pdb=" N VAL A 47 " --> pdb=" O TYR A 276 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.331A pdb=" N LEU A 141 " --> pdb=" O SER A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.902A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ILE A 101 " --> pdb=" O ILE A 243 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 308 through 313 removed outlier: 6.892A pdb=" N VAL A 592 " --> pdb=" O THR A 312 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 321 through 325 removed outlier: 4.387A pdb=" N GLU A 321 " --> pdb=" O CYS A 535 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ASP A 571 " --> pdb=" O ILE A 584 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA A 572 " --> pdb=" O GLY A 563 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N PHE A 562 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 351 through 355 removed outlier: 3.646A pdb=" N ASN A 391 " --> pdb=" O GLU A 513 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 651 through 652 removed outlier: 5.954A pdb=" N GLU A 651 " --> pdb=" O ALA A 691 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N THR A 693 " --> pdb=" O GLU A 651 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE A 667 " --> pdb=" O ILE A 663 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 708 through 725 removed outlier: 6.381A pdb=" N SER A 708 " --> pdb=" O THR A1073 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR A1073 " --> pdb=" O SER A 708 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ALA A 710 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ASN A1071 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLU A1069 " --> pdb=" O PRO A 712 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ASN A 714 " --> pdb=" O ALA A1067 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N TYR A1064 " --> pdb=" O HIS A1045 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N HIS A1045 " --> pdb=" O TYR A1064 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 708 through 725 removed outlier: 6.381A pdb=" N SER A 708 " --> pdb=" O THR A1073 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR A1073 " --> pdb=" O SER A 708 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ALA A 710 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ASN A1071 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLU A1069 " --> pdb=" O PRO A 712 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ASN A 714 " --> pdb=" O ALA A1067 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA A1075 " --> pdb=" O PHE A1092 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N PHE A1092 " --> pdb=" O ALA A1075 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 730 through 733 removed outlier: 4.560A pdb=" N LYS A 730 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1117 through 1122 removed outlier: 4.491A pdb=" N ALA A1084 " --> pdb=" O SER A1120 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.504A pdb=" N THR B 29 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N ASN B 61 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N TYR B 266 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.589A pdb=" N VAL B 47 " --> pdb=" O TYR B 276 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.329A pdb=" N LEU B 141 " --> pdb=" O SER B 244 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.902A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ILE B 101 " --> pdb=" O ILE B 243 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 308 through 313 removed outlier: 6.892A pdb=" N VAL B 592 " --> pdb=" O THR B 312 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 321 through 325 removed outlier: 4.385A pdb=" N GLU B 321 " --> pdb=" O CYS B 535 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ASP B 571 " --> pdb=" O ILE B 584 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA B 572 " --> pdb=" O GLY B 563 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N PHE B 562 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 351 through 355 removed outlier: 3.646A pdb=" N ASN B 391 " --> pdb=" O GLU B 513 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AC4, first strand: chain 'B' and resid 470 through 471 Processing sheet with id=AC5, first strand: chain 'B' and resid 651 through 652 removed outlier: 5.954A pdb=" N GLU B 651 " --> pdb=" O ALA B 691 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N THR B 693 " --> pdb=" O GLU B 651 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE B 667 " --> pdb=" O ILE B 663 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 708 through 725 removed outlier: 6.380A pdb=" N SER B 708 " --> pdb=" O THR B1073 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR B1073 " --> pdb=" O SER B 708 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ALA B 710 " --> pdb=" O ASN B1071 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ASN B1071 " --> pdb=" O ALA B 710 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N GLU B1069 " --> pdb=" O PRO B 712 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ASN B 714 " --> pdb=" O ALA B1067 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N TYR B1064 " --> pdb=" O HIS B1045 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N HIS B1045 " --> pdb=" O TYR B1064 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 708 through 725 removed outlier: 6.380A pdb=" N SER B 708 " --> pdb=" O THR B1073 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR B1073 " --> pdb=" O SER B 708 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ALA B 710 " --> pdb=" O ASN B1071 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ASN B1071 " --> pdb=" O ALA B 710 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N GLU B1069 " --> pdb=" O PRO B 712 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ASN B 714 " --> pdb=" O ALA B1067 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA B1075 " --> pdb=" O PHE B1092 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE B1092 " --> pdb=" O ALA B1075 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 730 through 733 removed outlier: 4.559A pdb=" N LYS B 730 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1117 through 1122 removed outlier: 4.491A pdb=" N ALA B1084 " --> pdb=" O SER B1120 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.504A pdb=" N THR C 29 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N ASN C 61 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N TYR C 266 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 47 through 52 removed outlier: 3.589A pdb=" N VAL C 47 " --> pdb=" O TYR C 276 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.331A pdb=" N LEU C 141 " --> pdb=" O SER C 244 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.902A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ILE C 101 " --> pdb=" O ILE C 243 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 308 through 313 removed outlier: 6.893A pdb=" N VAL C 592 " --> pdb=" O THR C 312 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY C 591 " --> pdb=" O GLN C 610 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 351 through 355 removed outlier: 3.645A pdb=" N ASN C 391 " --> pdb=" O GLU C 513 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 449 through 450 Processing sheet with id=AD8, first strand: chain 'C' and resid 651 through 652 removed outlier: 5.955A pdb=" N GLU C 651 " --> pdb=" O ALA C 691 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N THR C 693 " --> pdb=" O GLU C 651 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE C 667 " --> pdb=" O ILE C 663 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 708 through 725 removed outlier: 6.380A pdb=" N SER C 708 " --> pdb=" O THR C1073 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N THR C1073 " --> pdb=" O SER C 708 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ALA C 710 " --> pdb=" O ASN C1071 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ASN C1071 " --> pdb=" O ALA C 710 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N GLU C1069 " --> pdb=" O PRO C 712 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ASN C 714 " --> pdb=" O ALA C1067 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N TYR C1064 " --> pdb=" O HIS C1045 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N HIS C1045 " --> pdb=" O TYR C1064 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 708 through 725 removed outlier: 6.380A pdb=" N SER C 708 " --> pdb=" O THR C1073 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N THR C1073 " --> pdb=" O SER C 708 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ALA C 710 " --> pdb=" O ASN C1071 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ASN C1071 " --> pdb=" O ALA C 710 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N GLU C1069 " --> pdb=" O PRO C 712 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ASN C 714 " --> pdb=" O ALA C1067 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA C1075 " --> pdb=" O PHE C1092 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N PHE C1092 " --> pdb=" O ALA C1075 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 730 through 733 removed outlier: 4.558A pdb=" N LYS C 730 " --> pdb=" O LEU C 858 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 1117 through 1122 removed outlier: 4.492A pdb=" N ALA C1084 " --> pdb=" O SER C1120 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AE5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.749A pdb=" N MET H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N TRP H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 4 through 7 removed outlier: 4.228A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 10 through 14 removed outlier: 6.345A pdb=" N VAL L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N LYS L 107 " --> pdb=" O VAL L 11 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ALA L 13 " --> pdb=" O LYS L 107 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L' and resid 10 through 14 removed outlier: 6.345A pdb=" N VAL L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N LYS L 107 " --> pdb=" O VAL L 11 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ALA L 13 " --> pdb=" O LYS L 107 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AF1, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.749A pdb=" N MET D 34 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N TRP D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N TRP D 36 " --> pdb=" O MET D 48 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 4 through 7 removed outlier: 4.228A pdb=" N ASP E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER E 67 " --> pdb=" O ASP E 70 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 10 through 14 removed outlier: 6.346A pdb=" N VAL E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N LYS E 107 " --> pdb=" O VAL E 11 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ALA E 13 " --> pdb=" O LYS E 107 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA E 84 " --> pdb=" O VAL E 104 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 10 through 14 removed outlier: 6.346A pdb=" N VAL E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N LYS E 107 " --> pdb=" O VAL E 11 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ALA E 13 " --> pdb=" O LYS E 107 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA E 84 " --> pdb=" O VAL E 104 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR E 97 " --> pdb=" O GLN E 90 " (cutoff:3.500A) 1164 hydrogen bonds defined for protein. 3162 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: 13.08 Time building geometry restraints manager: 11.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.02 - 1.18: 1 1.18 - 1.35: 8616 1.35 - 1.51: 8406 1.51 - 1.67: 10655 1.67 - 1.83: 153 Bond restraints: 27831 Sorted by residual: bond pdb=" C ASN A 328 " pdb=" N ILE A 329 " ideal model delta sigma weight residual 1.331 1.020 0.311 1.05e-02 9.07e+03 8.78e+02 bond pdb=" C TYR D 104 " pdb=" O TYR D 104 " ideal model delta sigma weight residual 1.233 1.346 -0.113 1.21e-02 6.83e+03 8.76e+01 bond pdb=" C TYR H 104 " pdb=" O TYR H 104 " ideal model delta sigma weight residual 1.233 1.345 -0.112 1.21e-02 6.83e+03 8.56e+01 bond pdb=" N PRO B 524 " pdb=" CD PRO B 524 " ideal model delta sigma weight residual 1.473 1.524 -0.051 1.40e-02 5.10e+03 1.35e+01 bond pdb=" CA TYR H 104 " pdb=" C TYR H 104 " ideal model delta sigma weight residual 1.523 1.557 -0.033 1.30e-02 5.92e+03 6.63e+00 ... (remaining 27826 not shown) Histogram of bond angle deviations from ideal: 46.89 - 67.91: 2 67.91 - 88.93: 0 88.93 - 109.95: 4598 109.95 - 130.98: 33181 130.98 - 152.00: 80 Bond angle restraints: 37861 Sorted by residual: angle pdb=" C ASN A 328 " pdb=" N ILE A 329 " pdb=" CA ILE A 329 " ideal model delta sigma weight residual 122.48 49.07 73.41 1.25e+00 6.40e-01 3.45e+03 angle pdb=" CA ASN A 328 " pdb=" C ASN A 328 " pdb=" N ILE A 329 " ideal model delta sigma weight residual 116.84 46.89 69.95 1.71e+00 3.42e-01 1.67e+03 angle pdb=" O ASN A 328 " pdb=" C ASN A 328 " pdb=" N ILE A 329 " ideal model delta sigma weight residual 122.59 152.00 -29.41 1.33e+00 5.65e-01 4.89e+02 angle pdb=" CA LYS A 525 " pdb=" C LYS A 525 " pdb=" N LYS A 526 " ideal model delta sigma weight residual 115.78 98.22 17.56 1.35e+00 5.49e-01 1.69e+02 angle pdb=" C LYS A 525 " pdb=" N LYS A 526 " pdb=" CA LYS A 526 " ideal model delta sigma weight residual 121.54 99.60 21.94 1.91e+00 2.74e-01 1.32e+02 ... (remaining 37856 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 15672 17.85 - 35.71: 503 35.71 - 53.56: 116 53.56 - 71.41: 69 71.41 - 89.27: 20 Dihedral angle restraints: 16380 sinusoidal: 6558 harmonic: 9822 Sorted by residual: dihedral pdb=" CB CYS B1029 " pdb=" SG CYS B1029 " pdb=" SG CYS B1040 " pdb=" CB CYS B1040 " ideal model delta sinusoidal sigma weight residual -86.00 -163.36 77.36 1 1.00e+01 1.00e-02 7.50e+01 dihedral pdb=" CB CYS A1029 " pdb=" SG CYS A1029 " pdb=" SG CYS A1040 " pdb=" CB CYS A1040 " ideal model delta sinusoidal sigma weight residual -86.00 -163.35 77.35 1 1.00e+01 1.00e-02 7.50e+01 dihedral pdb=" CB CYS C1029 " pdb=" SG CYS C1029 " pdb=" SG CYS C1040 " pdb=" CB CYS C1040 " ideal model delta sinusoidal sigma weight residual -86.00 -163.34 77.34 1 1.00e+01 1.00e-02 7.50e+01 ... (remaining 16377 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 4081 0.088 - 0.176: 364 0.176 - 0.264: 6 0.264 - 0.352: 7 0.352 - 0.439: 2 Chirality restraints: 4460 Sorted by residual: chirality pdb=" CA ASN A 328 " pdb=" N ASN A 328 " pdb=" C ASN A 328 " pdb=" CB ASN A 328 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.83e+00 chirality pdb=" C1 NAG C1304 " pdb=" ND2 ASN C 328 " pdb=" C2 NAG C1304 " pdb=" O5 NAG C1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.79 0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" C1 NAG B1301 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B1301 " pdb=" O5 NAG B1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.90e+00 ... (remaining 4457 not shown) Planarity restraints: 4849 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 525 " -0.075 2.00e-02 2.50e+03 1.62e-01 2.61e+02 pdb=" C LYS A 525 " 0.279 2.00e-02 2.50e+03 pdb=" O LYS A 525 " -0.119 2.00e-02 2.50e+03 pdb=" N LYS A 526 " -0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 328 " 0.125 2.00e-02 2.50e+03 1.33e-01 2.23e+02 pdb=" CG ASN C 328 " -0.048 2.00e-02 2.50e+03 pdb=" OD1 ASN C 328 " -0.043 2.00e-02 2.50e+03 pdb=" ND2 ASN C 328 " -0.202 2.00e-02 2.50e+03 pdb=" C1 NAG C1304 " 0.168 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 328 " -0.016 2.00e-02 2.50e+03 1.00e-01 1.01e+02 pdb=" C ASN A 328 " -0.157 2.00e-02 2.50e+03 pdb=" O ASN A 328 " 0.071 2.00e-02 2.50e+03 pdb=" N ILE A 329 " 0.102 2.00e-02 2.50e+03 ... (remaining 4846 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.14: 12 2.14 - 2.83: 8211 2.83 - 3.52: 34867 3.52 - 4.21: 65473 4.21 - 4.90: 112251 Nonbonded interactions: 220814 Sorted by model distance: nonbonded pdb=" CB PRO B 518 " pdb=" OH TYR C 200 " model vdw 1.447 3.440 nonbonded pdb=" CB ASN A 328 " pdb=" N ILE A 329 " model vdw 1.680 2.816 nonbonded pdb=" O ASN A 328 " pdb=" CA ILE A 329 " model vdw 1.849 2.776 nonbonded pdb=" CG PRO B 518 " pdb=" CZ TYR C 200 " model vdw 1.927 3.660 nonbonded pdb=" CG PRO B 518 " pdb=" CE1 TYR C 200 " model vdw 1.952 3.740 ... (remaining 220809 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 27 through 439 or resid 499 through 1144 or resid 1301 thr \ ough 1310)) selection = (chain 'C' and (resid 27 through 439 or resid 499 through 1144 or resid 1301 thr \ ough 1310)) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 119 5.16 5 C 17312 2.51 5 N 4453 2.21 5 O 5341 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.720 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: 0.030 Extract box with map and model: 15.870 Check model and map are aligned: 0.420 Process input model: 70.950 Find NCS groups from input model: 2.020 Set up NCS constraints: 0.370 Set refine NCS operators: 0.000 Set scattering table: 0.250 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6523 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 0.311 27831 Z= 0.269 Angle : 0.851 73.409 37861 Z= 0.539 Chirality : 0.048 0.439 4460 Planarity : 0.005 0.162 4804 Dihedral : 11.020 89.267 9945 Min Nonbonded Distance : 1.447 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.73 % Favored : 95.91 % Rotamer Outliers : 0.44 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.73 % 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: 0.13 (0.14), residues: 3328 helix: 0.67 (0.19), residues: 660 sheet: 0.45 (0.16), residues: 913 loop : -0.25 (0.14), residues: 1755 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 378 time to evaluate : 3.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 4 residues processed: 389 average time/residue: 0.4529 time to fit residues: 267.1697 Evaluate side-chains 195 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 191 time to evaluate : 3.270 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.4161 time to fit residues: 6.8812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 282 optimal weight: 6.9990 chunk 253 optimal weight: 8.9990 chunk 140 optimal weight: 7.9990 chunk 86 optimal weight: 10.0000 chunk 171 optimal weight: 7.9990 chunk 135 optimal weight: 10.0000 chunk 262 optimal weight: 0.9990 chunk 101 optimal weight: 30.0000 chunk 159 optimal weight: 10.0000 chunk 195 optimal weight: 0.9980 chunk 304 optimal weight: 30.0000 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 801 GLN A 869 GLN A 898 GLN A 999 GLN A1007 GLN ** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1116 ASN B 87 ASN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 495 GLN ** B 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 869 GLN ** B 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 904 ASN B 954 GLN B 999 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1007 GLN B1110 GLN ** C 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 898 GLN C 916 ASN C1002 GLN C1051 GLN ** C1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 117 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.071 27831 Z= 0.283 Angle : 0.689 11.758 37861 Z= 0.368 Chirality : 0.047 0.244 4460 Planarity : 0.005 0.079 4804 Dihedral : 5.010 18.311 3979 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.19 % Favored : 97.72 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % 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: 0.31 (0.14), residues: 3328 helix: 1.15 (0.20), residues: 656 sheet: 0.47 (0.16), residues: 915 loop : -0.23 (0.15), residues: 1757 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 243 time to evaluate : 3.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 247 average time/residue: 0.4300 time to fit residues: 165.5190 Evaluate side-chains 157 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 3.182 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.7569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 169 optimal weight: 9.9990 chunk 94 optimal weight: 20.0000 chunk 253 optimal weight: 4.9990 chunk 207 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 chunk 304 optimal weight: 0.6980 chunk 329 optimal weight: 50.0000 chunk 271 optimal weight: 0.9980 chunk 302 optimal weight: 50.0000 chunk 103 optimal weight: 20.0000 chunk 244 optimal weight: 3.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1116 ASN A1132 ASN B 87 ASN B 196 ASN ** B 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 759 GLN ** C 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** C1085 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1103 GLN H 117 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 27831 Z= 0.180 Angle : 0.539 8.888 37861 Z= 0.286 Chirality : 0.043 0.213 4460 Planarity : 0.004 0.123 4804 Dihedral : 4.707 16.817 3979 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.94 % Favored : 97.00 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % 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: 0.43 (0.14), residues: 3328 helix: 1.39 (0.20), residues: 667 sheet: 0.54 (0.16), residues: 907 loop : -0.22 (0.15), residues: 1754 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 219 time to evaluate : 3.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 221 average time/residue: 0.4361 time to fit residues: 151.3555 Evaluate side-chains 157 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 155 time to evaluate : 3.002 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2900 time to fit residues: 5.2181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 301 optimal weight: 50.0000 chunk 229 optimal weight: 0.9990 chunk 158 optimal weight: 2.9990 chunk 33 optimal weight: 50.0000 chunk 145 optimal weight: 0.0270 chunk 204 optimal weight: 1.9990 chunk 305 optimal weight: 40.0000 chunk 323 optimal weight: 50.0000 chunk 159 optimal weight: 0.9980 chunk 289 optimal weight: 0.9980 chunk 87 optimal weight: 20.0000 overall best weight: 1.0042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN ** B 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1085 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 117 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6848 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.054 27831 Z= 0.139 Angle : 0.513 12.215 37861 Z= 0.267 Chirality : 0.043 0.191 4460 Planarity : 0.004 0.061 4804 Dihedral : 4.550 16.746 3979 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.70 % Favored : 97.27 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % 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: 0.50 (0.14), residues: 3328 helix: 1.46 (0.21), residues: 668 sheet: 0.62 (0.16), residues: 906 loop : -0.21 (0.15), residues: 1754 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 210 time to evaluate : 3.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 211 average time/residue: 0.4369 time to fit residues: 147.1110 Evaluate side-chains 151 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 150 time to evaluate : 3.297 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3005 time to fit residues: 4.9451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 269 optimal weight: 8.9990 chunk 183 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 241 optimal weight: 7.9990 chunk 133 optimal weight: 4.9990 chunk 276 optimal weight: 10.0000 chunk 223 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 165 optimal weight: 0.2980 chunk 290 optimal weight: 8.9990 chunk 81 optimal weight: 8.9990 overall best weight: 3.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN B 484 ASN ** B 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 869 GLN B 898 GLN ** B1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 916 ASN ** C 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1051 GLN ** C1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN ** D 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.071 27831 Z= 0.229 Angle : 0.578 9.000 37861 Z= 0.310 Chirality : 0.043 0.225 4460 Planarity : 0.004 0.064 4804 Dihedral : 4.662 21.921 3979 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % 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 (0.14), residues: 3328 helix: 1.17 (0.21), residues: 663 sheet: 0.53 (0.17), residues: 900 loop : -0.25 (0.15), residues: 1765 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 206 time to evaluate : 3.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 207 average time/residue: 0.4359 time to fit residues: 146.1916 Evaluate side-chains 147 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 146 time to evaluate : 3.129 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3054 time to fit residues: 4.5342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 108 optimal weight: 7.9990 chunk 291 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 chunk 190 optimal weight: 0.9990 chunk 79 optimal weight: 9.9990 chunk 324 optimal weight: 50.0000 chunk 269 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 26 optimal weight: 50.0000 chunk 107 optimal weight: 6.9990 chunk 170 optimal weight: 10.0000 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN ** B 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 ASN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.4505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.059 27831 Z= 0.157 Angle : 0.525 9.779 37861 Z= 0.278 Chirality : 0.048 1.441 4460 Planarity : 0.004 0.129 4804 Dihedral : 4.587 24.242 3979 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.06 % Favored : 96.91 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % 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: 0.40 (0.14), residues: 3328 helix: 1.39 (0.21), residues: 674 sheet: 0.45 (0.16), residues: 921 loop : -0.21 (0.15), residues: 1733 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 197 time to evaluate : 3.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 197 average time/residue: 0.4206 time to fit residues: 133.6825 Evaluate side-chains 140 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 139 time to evaluate : 3.110 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2992 time to fit residues: 4.7118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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-4877/modules/cctbx_project/iotbx/cli_parser.py", line 865, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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-4877/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-4877/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-4877/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-4877/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-4877/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-4877/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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-4877/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-4877/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-4877/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-4877/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: 55.2926 > 50: distance: 124 - 131: 17.392 distance: 131 - 132: 28.232 distance: 131 - 194: 20.468 distance: 132 - 133: 30.919 distance: 132 - 135: 9.157 distance: 133 - 134: 18.958 distance: 133 - 140: 14.261 distance: 135 - 136: 10.008 distance: 136 - 137: 17.861 distance: 137 - 138: 21.114 distance: 137 - 139: 24.429 distance: 140 - 141: 9.819 distance: 141 - 142: 21.402 distance: 141 - 144: 8.416 distance: 142 - 143: 6.363 distance: 142 - 145: 5.874 distance: 146 - 147: 12.259 distance: 146 - 149: 3.634 distance: 147 - 148: 17.235 distance: 147 - 153: 37.090 distance: 149 - 150: 6.938 distance: 150 - 151: 25.948 distance: 150 - 152: 26.479 distance: 153 - 154: 25.674 distance: 154 - 155: 16.902 distance: 154 - 157: 10.457 distance: 155 - 156: 21.608 distance: 155 - 159: 19.530 distance: 157 - 158: 6.435 distance: 159 - 160: 22.259 distance: 160 - 163: 13.626 distance: 161 - 162: 24.359 distance: 161 - 170: 5.217 distance: 163 - 164: 8.006 distance: 164 - 165: 30.277 distance: 164 - 166: 11.281 distance: 165 - 167: 21.272 distance: 166 - 168: 27.681 distance: 167 - 169: 4.730 distance: 168 - 169: 18.151 distance: 170 - 171: 26.564 distance: 170 - 176: 6.724 distance: 171 - 172: 36.430 distance: 171 - 174: 27.623 distance: 172 - 173: 45.699 distance: 174 - 175: 38.802 distance: 175 - 176: 13.508 distance: 177 - 178: 17.839 distance: 178 - 179: 29.816 distance: 178 - 181: 26.652 distance: 179 - 180: 13.248 distance: 179 - 191: 36.051 distance: 181 - 182: 16.507 distance: 182 - 183: 22.953 distance: 182 - 184: 20.486 distance: 183 - 185: 16.255 distance: 184 - 186: 33.932 distance: 184 - 187: 11.935 distance: 185 - 186: 29.031 distance: 186 - 188: 23.272 distance: 187 - 189: 7.638 distance: 188 - 190: 15.606 distance: 189 - 190: 12.117 distance: 191 - 192: 12.446 distance: 192 - 193: 17.283 distance: 192 - 195: 9.672 distance: 193 - 194: 30.830 distance: 193 - 198: 12.452 distance: 195 - 196: 41.516 distance: 195 - 197: 23.173 distance: 198 - 199: 6.758 distance: 199 - 200: 23.664 distance: 199 - 202: 23.040 distance: 200 - 201: 6.834 distance: 200 - 209: 32.816 distance: 202 - 203: 16.157 distance: 203 - 204: 12.789 distance: 203 - 205: 22.311 distance: 204 - 206: 33.325 distance: 205 - 207: 22.264 distance: 206 - 208: 28.402 distance: 207 - 208: 26.046 distance: 209 - 210: 22.033 distance: 210 - 211: 12.512 distance: 211 - 212: 15.920 distance: 211 - 213: 11.192