Starting phenix.real_space_refine (version: dev) on Mon Dec 19 08:53:54 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7as8_11889/12_2022/7as8_11889_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7as8_11889/12_2022/7as8_11889.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7as8_11889/12_2022/7as8_11889.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7as8_11889/12_2022/7as8_11889.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7as8_11889/12_2022/7as8_11889_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7as8_11889/12_2022/7as8_11889_neut.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "0 TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 93801 Number of models: 1 Model: "" Number of chains: 33 Chain: "0" Number of atoms: 3993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 3993 Classifications: {'peptide': 536} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'PTRANS': 26, 'TRANS': 509} Chain breaks: 5 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 362 Unresolved non-hydrogen angles: 470 Unresolved non-hydrogen dihedrals: 299 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 9, 'TYR:plan': 5, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 5, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 187 Chain: "1" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 659 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "2" Number of atoms: 1563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1563 Classifications: {'RNA': 73} Modifications used: {'p5*END': 1, 'rna2p_pur': 11, 'rna2p_pyr': 5, 'rna3p_pur': 27, 'rna3p_pyr': 30} Link IDs: {'rna2p': 15, 'rna3p': 57} Chain breaks: 2 Chain: "A" Number of atoms: 60389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2812, 60389 Inner-chain residues flagged as termini: ['pdbres=" G A1220 "'] Classifications: {'RNA': 2812} Modifications used: {'5*END': 2, 'rna2p_pur': 282, 'rna2p_pyr': 143, 'rna3p_pur': 1352, 'rna3p_pyr': 1035} Link IDs: {'rna2p': 425, 'rna3p': 2386} Chain breaks: 6 Chain: "B" Number of atoms: 2392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 2392 Classifications: {'RNA': 112} Modifications used: {'5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 6, 'rna3p_pur': 52, 'rna3p_pyr': 46} Link IDs: {'rna2p': 14, 'rna3p': 97} Chain: "E" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2083 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 17, 'TRANS': 254} Chain: "F" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1569 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 10, 'TRANS': 195} Chain: "G" Number of atoms: 1561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1561 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 7, 'TRANS': 197} Chain: "H" Number of atoms: 1284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1284 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "I" Number of atoms: 1342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1342 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 9, 'TRANS': 165} Chain: "K" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 974 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 10, 'TRANS': 121} Chain: "L" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 886 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 2, 'TRANS': 110} Chain breaks: 2 Chain: "N" Number of atoms: 1123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1123 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 8, 'TRANS': 133} Chain: "O" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 920 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "P" Number of atoms: 1081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1081 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 5, 'TRANS': 140} Chain: "Q" Number of atoms: 1076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1076 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 7, 'TRANS': 127} Chain: "R" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 953 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "S" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 912 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain: "T" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 944 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "U" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 940 Classifications: {'peptide': 117} Link IDs: {'TRANS': 116} Chain: "V" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 781 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain: "W" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 842 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "X" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 725 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "Y" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 762 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 6, 'TRANS': 94} Chain: "a" Number of atoms: 624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 624 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain: "b" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "c" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 530 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Chain: "d" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 455 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "f" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 418 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 3, 'TRANS': 49} Chain: "g" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 401 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "h" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 367 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "i" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 512 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "j" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 296 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33} Time building chain proxies: 38.22, per 1000 atoms: 0.41 Number of scatterers: 93801 At special positions: 0 Unit cell: (223.04, 245.18, 223.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 102 16.00 P 2994 15.00 O 26127 8.00 N 17428 7.00 C 47150 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS f 30 " - pdb=" SG CYS f 43 " distance=2.03 Simple disulfide: pdb=" SG CYS f 33 " - pdb=" SG CYS f 46 " distance=2.02 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: 39.51 Conformation dependent library (CDL) restraints added in 3.6 seconds 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6988 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 53 sheets defined 31.9% alpha, 19.4% beta 1019 base pairs and 1614 stacking pairs defined. Time for finding SS restraints: 29.76 Creating SS restraints... Processing helix chain '0' and resid 4 through 17 Processing helix chain '0' and resid 73 through 84 removed outlier: 3.556A pdb=" N GLU 0 84 " --> pdb=" O ARG 0 80 " (cutoff:3.500A) Processing helix chain '0' and resid 147 through 151 removed outlier: 3.672A pdb=" N MET 0 150 " --> pdb=" O SER 0 147 " (cutoff:3.500A) Processing helix chain '0' and resid 180 through 185 Processing helix chain '0' and resid 186 through 190 removed outlier: 3.700A pdb=" N GLY 0 190 " --> pdb=" O PHE 0 187 " (cutoff:3.500A) Processing helix chain '0' and resid 191 through 196 removed outlier: 3.999A pdb=" N GLN 0 195 " --> pdb=" O ARG 0 191 " (cutoff:3.500A) Processing helix chain '0' and resid 204 through 213 Processing helix chain '0' and resid 223 through 236 removed outlier: 3.977A pdb=" N LEU 0 227 " --> pdb=" O LEU 0 223 " (cutoff:3.500A) Processing helix chain '0' and resid 269 through 317 removed outlier: 4.689A pdb=" N GLY 0 280 " --> pdb=" O ARG 0 276 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N GLU 0 283 " --> pdb=" O PHE 0 279 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASP 0 285 " --> pdb=" O LYS 0 281 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ARG 0 286 " --> pdb=" O ALA 0 282 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE 0 297 " --> pdb=" O ASP 0 293 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU 0 317 " --> pdb=" O GLU 0 313 " (cutoff:3.500A) Processing helix chain '0' and resid 321 through 335 removed outlier: 3.691A pdb=" N PHE 0 325 " --> pdb=" O ASN 0 321 " (cutoff:3.500A) Processing helix chain '0' and resid 368 through 413 Processing helix chain '0' and resid 415 through 429 removed outlier: 3.984A pdb=" N GLU 0 421 " --> pdb=" O ARG 0 417 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU 0 424 " --> pdb=" O SER 0 420 " (cutoff:3.500A) Processing helix chain '0' and resid 456 through 458 No H-bonds generated for 'chain '0' and resid 456 through 458' Processing helix chain '0' and resid 466 through 477 Processing helix chain '0' and resid 503 through 517 removed outlier: 3.594A pdb=" N ALA 0 511 " --> pdb=" O ILE 0 507 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR 0 512 " --> pdb=" O MET 0 508 " (cutoff:3.500A) Processing helix chain '0' and resid 534 through 536 No H-bonds generated for 'chain '0' and resid 534 through 536' Processing helix chain '0' and resid 561 through 565 Processing helix chain '1' and resid 2 through 10 Processing helix chain '1' and resid 15 through 26 Processing helix chain '1' and resid 68 through 73 removed outlier: 4.216A pdb=" N ALA 1 73 " --> pdb=" O LYS 1 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 214 removed outlier: 4.126A pdb=" N SER E 211 " --> pdb=" O LYS E 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 71 Processing helix chain 'F' and resid 98 through 102 removed outlier: 3.676A pdb=" N ILE F 101 " --> pdb=" O LYS F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 127 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 102 through 121 Processing helix chain 'G' and resid 135 through 146 removed outlier: 3.988A pdb=" N MET G 139 " --> pdb=" O LYS G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 166 Processing helix chain 'G' and resid 179 through 181 No H-bonds generated for 'chain 'G' and resid 179 through 181' Processing helix chain 'G' and resid 183 through 189 Processing helix chain 'G' and resid 195 through 206 Processing helix chain 'H' and resid 3 through 21 Proline residue: H 14 - end of helix Processing helix chain 'H' and resid 24 through 28 Processing helix chain 'H' and resid 46 through 49 Processing helix chain 'H' and resid 50 through 61 removed outlier: 6.297A pdb=" N GLU H 56 " --> pdb=" O SER H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 78 Processing helix chain 'H' and resid 94 through 106 Processing helix chain 'H' and resid 163 through 174 Processing helix chain 'I' and resid 59 through 82 removed outlier: 3.747A pdb=" N ALA I 64 " --> pdb=" O LYS I 60 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG I 70 " --> pdb=" O HIS I 66 " (cutoff:3.500A) Processing helix chain 'I' and resid 138 through 151 Processing helix chain 'K' and resid 20 through 30 removed outlier: 4.215A pdb=" N VAL K 24 " --> pdb=" O PRO K 20 " (cutoff:3.500A) Proline residue: K 26 - end of helix removed outlier: 3.878A pdb=" N GLN K 30 " --> pdb=" O PRO K 26 " (cutoff:3.500A) Processing helix chain 'K' and resid 34 through 46 Processing helix chain 'K' and resid 74 through 84 Processing helix chain 'K' and resid 102 through 113 Processing helix chain 'K' and resid 120 through 136 Processing helix chain 'L' and resid 6 through 22 Processing helix chain 'L' and resid 34 through 49 Processing helix chain 'L' and resid 56 through 65 Processing helix chain 'L' and resid 73 through 77 removed outlier: 3.780A pdb=" N THR L 77 " --> pdb=" O ASP L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 93 through 104 Processing helix chain 'L' and resid 119 through 128 Processing helix chain 'N' and resid 25 through 39 removed outlier: 4.125A pdb=" N GLU N 32 " --> pdb=" O ARG N 28 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA N 35 " --> pdb=" O SER N 31 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 63 Processing helix chain 'N' and resid 68 through 73 Processing helix chain 'N' and resid 90 through 97 Processing helix chain 'N' and resid 97 through 110 removed outlier: 4.114A pdb=" N MET N 101 " --> pdb=" O TYR N 97 " (cutoff:3.500A) Processing helix chain 'N' and resid 113 through 121 Processing helix chain 'O' and resid 103 through 107 removed outlier: 3.900A pdb=" N LEU O 106 " --> pdb=" O ALA O 103 " (cutoff:3.500A) Processing helix chain 'O' and resid 111 through 118 Processing helix chain 'P' and resid 56 through 61 Processing helix chain 'P' and resid 80 through 85 removed outlier: 3.654A pdb=" N GLY P 84 " --> pdb=" O LYS P 81 " (cutoff:3.500A) Processing helix chain 'P' and resid 92 through 100 Processing helix chain 'P' and resid 129 through 140 Processing helix chain 'Q' and resid 44 through 59 Processing helix chain 'Q' and resid 110 through 125 Processing helix chain 'R' and resid 9 through 28 Processing helix chain 'R' and resid 34 through 54 removed outlier: 4.240A pdb=" N SER R 42 " --> pdb=" O LYS R 38 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N VAL R 43 " --> pdb=" O GLU R 39 " (cutoff:3.500A) Processing helix chain 'R' and resid 55 through 66 Processing helix chain 'R' and resid 79 through 91 Processing helix chain 'S' and resid 6 through 20 Processing helix chain 'S' and resid 70 through 88 Processing helix chain 'S' and resid 104 through 117 Processing helix chain 'T' and resid 2 through 10 Processing helix chain 'T' and resid 53 through 56 Processing helix chain 'U' and resid 7 through 21 removed outlier: 4.067A pdb=" N ARG U 11 " --> pdb=" O GLY U 7 " (cutoff:3.500A) Processing helix chain 'U' and resid 26 through 31 Processing helix chain 'U' and resid 31 through 73 removed outlier: 3.570A pdb=" N GLN U 38 " --> pdb=" O VAL U 34 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS U 41 " --> pdb=" O GLN U 37 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG U 51 " --> pdb=" O PHE U 47 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N LYS U 54 " --> pdb=" O ARG U 50 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG U 55 " --> pdb=" O ARG U 51 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG U 58 " --> pdb=" O LYS U 54 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS U 59 " --> pdb=" O ARG U 55 " (cutoff:3.500A) Processing helix chain 'U' and resid 75 through 87 Processing helix chain 'U' and resid 91 through 101 Processing helix chain 'U' and resid 102 through 117 removed outlier: 3.541A pdb=" N PHE U 106 " --> pdb=" O ASP U 102 " (cutoff:3.500A) Processing helix chain 'W' and resid 13 through 25 removed outlier: 3.767A pdb=" N ALA W 17 " --> pdb=" O ALA W 13 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ILE W 24 " --> pdb=" O VAL W 20 " (cutoff:3.500A) Processing helix chain 'W' and resid 28 through 39 Processing helix chain 'W' and resid 43 through 62 Processing helix chain 'W' and resid 65 through 67 No H-bonds generated for 'chain 'W' and resid 65 through 67' Processing helix chain 'X' and resid 3 through 7 Processing helix chain 'X' and resid 14 through 23 removed outlier: 3.565A pdb=" N GLU X 23 " --> pdb=" O ASP X 19 " (cutoff:3.500A) Processing helix chain 'X' and resid 35 through 48 Processing helix chain 'b' and resid 20 through 22 No H-bonds generated for 'chain 'b' and resid 20 through 22' Processing helix chain 'b' and resid 51 through 55 Processing helix chain 'c' and resid 2 through 8 Processing helix chain 'c' and resid 12 through 35 Processing helix chain 'c' and resid 40 through 65 removed outlier: 4.159A pdb=" N ARG c 44 " --> pdb=" O THR c 40 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE c 57 " --> pdb=" O MET c 53 " (cutoff:3.500A) Processing helix chain 'd' and resid 16 through 27 Processing helix chain 'd' and resid 40 through 51 Processing helix chain 'f' and resid 9 through 17 Processing helix chain 'h' and resid 8 through 16 Processing helix chain 'h' and resid 17 through 24 removed outlier: 3.626A pdb=" N SER h 24 " --> pdb=" O SER h 20 " (cutoff:3.500A) Processing helix chain 'h' and resid 24 through 37 Processing helix chain 'i' and resid 7 through 14 Processing helix chain 'i' and resid 37 through 45 Processing helix chain 'i' and resid 51 through 59 Processing helix chain 'i' and resid 60 through 63 removed outlier: 3.867A pdb=" N ALA i 63 " --> pdb=" O GLN i 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 60 through 63' Processing helix chain 'j' and resid 29 through 32 Processing sheet with id=AA1, first strand: chain '0' and resid 23 through 31 removed outlier: 6.586A pdb=" N HIS 0 38 " --> pdb=" O THR 0 25 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ILE 0 27 " --> pdb=" O ILE 0 36 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE 0 36 " --> pdb=" O ILE 0 27 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N GLN 0 29 " --> pdb=" O ASP 0 34 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ASP 0 34 " --> pdb=" O GLN 0 29 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '0' and resid 87 through 92 removed outlier: 5.393A pdb=" N ILE 0 88 " --> pdb=" O LYS 0 105 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LYS 0 105 " --> pdb=" O ILE 0 88 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ILE 0 129 " --> pdb=" O GLY 0 142 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLY 0 142 " --> pdb=" O ILE 0 129 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU 0 131 " --> pdb=" O ILE 0 140 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '0' and resid 250 through 253 removed outlier: 3.651A pdb=" N TYR 0 253 " --> pdb=" O ASN 0 242 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASN 0 242 " --> pdb=" O TYR 0 253 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '0' and resid 345 through 349 Processing sheet with id=AA5, first strand: chain '0' and resid 451 through 454 removed outlier: 3.530A pdb=" N TYR 0 453 " --> pdb=" O ILE 0 461 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE 0 461 " --> pdb=" O TYR 0 453 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY 0 464 " --> pdb=" O HIS 0 494 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N HIS 0 494 " --> pdb=" O GLY 0 464 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ILE 0 497 " --> pdb=" O ILE 0 483 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ILE 0 483 " --> pdb=" O ILE 0 497 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '1' and resid 33 through 34 removed outlier: 6.796A pdb=" N LEU 1 55 " --> pdb=" O GLU 1 81 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLU 1 81 " --> pdb=" O LEU 1 55 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N THR 1 57 " --> pdb=" O LEU 1 79 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 3 through 5 Processing sheet with id=AA8, first strand: chain 'E' and resid 34 through 35 Processing sheet with id=AA9, first strand: chain 'E' and resid 101 through 105 removed outlier: 6.612A pdb=" N ILE E 91 " --> pdb=" O VAL E 81 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N VAL E 81 " --> pdb=" O ILE E 91 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU E 93 " --> pdb=" O ALA E 79 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 129 through 131 removed outlier: 6.702A pdb=" N LEU E 173 " --> pdb=" O LEU E 165 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N LYS E 167 " --> pdb=" O TYR E 171 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N TYR E 171 " --> pdb=" O LYS E 167 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 4 through 14 removed outlier: 5.390A pdb=" N LYS F 9 " --> pdb=" O GLU F 29 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N GLU F 29 " --> pdb=" O LYS F 9 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY F 11 " --> pdb=" O VAL F 27 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LEU F 185 " --> pdb=" O VAL F 179 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL F 179 " --> pdb=" O LEU F 185 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU F 187 " --> pdb=" O VAL F 177 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLU F 175 " --> pdb=" O LYS F 189 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N VAL F 108 " --> pdb=" O ASN F 173 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N VAL F 113 " --> pdb=" O LEU F 199 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LEU F 199 " --> pdb=" O VAL F 113 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 79 through 84 removed outlier: 3.678A pdb=" N PHE F 79 " --> pdb=" O PHE F 53 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA F 48 " --> pdb=" O LYS F 39 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLN F 37 " --> pdb=" O GLN F 50 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N GLY F 52 " --> pdb=" O VAL F 35 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N VAL F 35 " --> pdb=" O GLY F 52 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 116 through 120 Processing sheet with id=AB5, first strand: chain 'G' and resid 13 through 18 removed outlier: 5.661A pdb=" N GLY G 15 " --> pdb=" O LEU G 6 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU G 6 " --> pdb=" O GLY G 15 " (cutoff:3.500A) removed outlier: 11.509A pdb=" N ILE G 123 " --> pdb=" O LYS G 3 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA G 5 " --> pdb=" O ILE G 123 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N VAL G 125 " --> pdb=" O ALA G 5 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU G 153 " --> pdb=" O LEU G 193 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ALA G 152 " --> pdb=" O THR G 174 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N VAL G 176 " --> pdb=" O ALA G 152 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ILE G 154 " --> pdb=" O VAL G 176 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 66 through 67 removed outlier: 6.840A pdb=" N VAL H 157 " --> pdb=" O GLU H 32 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ILE H 34 " --> pdb=" O VAL H 155 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL H 155 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ILE H 36 " --> pdb=" O ASP H 153 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ASP H 153 " --> pdb=" O ILE H 36 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 9 through 10 Processing sheet with id=AB8, first strand: chain 'I' and resid 16 through 19 Processing sheet with id=AB9, first strand: chain 'I' and resid 123 through 125 Processing sheet with id=AC1, first strand: chain 'I' and resid 96 through 98 Processing sheet with id=AC2, first strand: chain 'K' and resid 10 through 14 removed outlier: 3.612A pdb=" N SER K 65 " --> pdb=" O TYR K 61 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 98 through 101 Processing sheet with id=AC4, first strand: chain 'L' and resid 51 through 54 Processing sheet with id=AC5, first strand: chain 'N' and resid 123 through 125 removed outlier: 6.415A pdb=" N TRP N 16 " --> pdb=" O GLU N 139 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'N' and resid 74 through 78 Processing sheet with id=AC7, first strand: chain 'O' and resid 7 through 10 removed outlier: 6.286A pdb=" N ARG O 17 " --> pdb=" O VAL O 10 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ALA O 16 " --> pdb=" O ALA O 46 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ALA O 46 " --> pdb=" O ALA O 16 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N GLU O 18 " --> pdb=" O LYS O 44 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL O 40 " --> pdb=" O ILE O 22 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N VAL O 24 " --> pdb=" O VAL O 38 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N VAL O 38 " --> pdb=" O VAL O 24 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ALA O 83 " --> pdb=" O VAL O 63 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N CYS O 84 " --> pdb=" O ARG O 7 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LYS O 9 " --> pdb=" O CYS O 84 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N ILE O 86 " --> pdb=" O LYS O 9 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'O' and resid 76 through 79 removed outlier: 6.720A pdb=" N THR T 58 " --> pdb=" O ARG T 50 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ARG T 50 " --> pdb=" O THR T 58 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N THR T 60 " --> pdb=" O ILE T 48 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ILE T 64 " --> pdb=" O GLU T 44 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N GLU T 44 " --> pdb=" O ILE T 64 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ASP T 24 " --> pdb=" O VAL T 47 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N THR T 25 " --> pdb=" O VAL T 87 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS T 83 " --> pdb=" O HIS T 29 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LYS T 31 " --> pdb=" O ILE T 81 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE T 81 " --> pdb=" O LYS T 31 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'P' and resid 75 through 77 removed outlier: 6.052A pdb=" N ALA P 75 " --> pdb=" O LYS P 110 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N VAL P 109 " --> pdb=" O LYS P 127 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'P' and resid 90 through 91 removed outlier: 6.304A pdb=" N VAL P 123 " --> pdb=" O GLU P 144 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'Q' and resid 102 through 104 removed outlier: 6.665A pdb=" N VAL Q 102 " --> pdb=" O ALA Q 36 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ALA Q 36 " --> pdb=" O VAL Q 102 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE Q 104 " --> pdb=" O ILE Q 34 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'Q' and resid 40 through 43 removed outlier: 5.392A pdb=" N ALA Q 76 " --> pdb=" O PRO Q 90 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY Q 92 " --> pdb=" O TYR Q 74 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR Q 74 " --> pdb=" O GLY Q 92 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'R' and resid 29 through 33 removed outlier: 4.273A pdb=" N MET R 114 " --> pdb=" O LEU R 104 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'R' and resid 70 through 72 removed outlier: 3.702A pdb=" N ASN R 72 " --> pdb=" O GLN R 77 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'S' and resid 51 through 57 removed outlier: 6.747A pdb=" N ILE S 44 " --> pdb=" O LEU S 53 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N SER S 55 " --> pdb=" O ALA S 42 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ALA S 42 " --> pdb=" O SER S 55 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL S 33 " --> pdb=" O ASP S 96 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'V' and resid 11 through 14 Processing sheet with id=AD8, first strand: chain 'V' and resid 19 through 22 removed outlier: 3.572A pdb=" N LYS V 64 " --> pdb=" O LYS V 94 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N THR V 96 " --> pdb=" O VAL V 62 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N VAL V 62 " --> pdb=" O THR V 96 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLU V 98 " --> pdb=" O ALA V 60 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ALA V 60 " --> pdb=" O GLU V 98 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE V 100 " --> pdb=" O VAL V 58 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL V 58 " --> pdb=" O ILE V 100 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'V' and resid 71 through 75 Processing sheet with id=AE1, first strand: chain 'W' and resid 3 through 10 removed outlier: 6.337A pdb=" N SER W 101 " --> pdb=" O THR W 9 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N SER W 108 " --> pdb=" O ILE W 71 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ILE W 71 " --> pdb=" O SER W 108 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'W' and resid 82 through 87 Processing sheet with id=AE3, first strand: chain 'X' and resid 8 through 10 removed outlier: 4.012A pdb=" N ARG X 77 " --> pdb=" O VAL X 30 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Y' and resid 20 through 21 Processing sheet with id=AE5, first strand: chain 'Y' and resid 23 through 27 removed outlier: 4.220A pdb=" N ALA Y 25 " --> pdb=" O LEU Y 34 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Y' and resid 40 through 44 Processing sheet with id=AE7, first strand: chain 'Y' and resid 81 through 85 removed outlier: 3.949A pdb=" N GLN Y 99 " --> pdb=" O ALA Y 94 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'a' and resid 30 through 31 removed outlier: 6.850A pdb=" N LEU a 67 " --> pdb=" O LEU a 45 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'a' and resid 38 through 39 Processing sheet with id=AF1, first strand: chain 'b' and resid 13 through 18 Processing sheet with id=AF2, first strand: chain 'b' and resid 33 through 36 Processing sheet with id=AF3, first strand: chain 'd' and resid 35 through 38 Processing sheet with id=AF4, first strand: chain 'f' and resid 27 through 29 Processing sheet with id=AF5, first strand: chain 'f' and resid 48 through 49 Processing sheet with id=AF6, first strand: chain 'g' and resid 18 through 22 Processing sheet with id=AF7, first strand: chain 'i' and resid 15 through 16 Processing sheet with id=AF8, first strand: chain 'j' and resid 2 through 3 removed outlier: 6.123A pdb=" N LYS j 2 " --> pdb=" O LYS j 35 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN j 34 " --> pdb=" O VAL j 25 " (cutoff:3.500A) 1209 hydrogen bonds defined for protein. 3378 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2599 hydrogen bonds 4236 hydrogen bond angles 0 basepair planarities 1019 basepair parallelities 1614 stacking parallelities Total time for adding SS restraints: 146.93 Time building geometry restraints manager: 42.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 18896 1.33 - 1.45: 41229 1.45 - 1.58: 35783 1.58 - 1.71: 5800 1.71 - 1.83: 188 Bond restraints: 101896 Sorted by residual: bond pdb=" CA LEU R 119 " pdb=" CB LEU R 119 " ideal model delta sigma weight residual 1.526 1.436 0.090 1.76e-02 3.23e+03 2.60e+01 bond pdb=" C1' U A 405 " pdb=" N1 U A 405 " ideal model delta sigma weight residual 1.480 1.545 -0.065 1.50e-02 4.44e+03 1.85e+01 bond pdb=" CA VAL 0 496 " pdb=" CB VAL 0 496 " ideal model delta sigma weight residual 1.553 1.529 0.024 7.40e-03 1.83e+04 1.02e+01 bond pdb=" CB THR O 6 " pdb=" CG2 THR O 6 " ideal model delta sigma weight residual 1.521 1.425 0.096 3.30e-02 9.18e+02 8.39e+00 bond pdb=" CA THR a 51 " pdb=" CB THR a 51 " ideal model delta sigma weight residual 1.531 1.442 0.089 3.28e-02 9.30e+02 7.38e+00 ... (remaining 101891 not shown) Histogram of bond angle deviations from ideal: 96.86 - 104.64: 13551 104.64 - 112.43: 58306 112.43 - 120.21: 44104 120.21 - 127.99: 30732 127.99 - 135.77: 5690 Bond angle restraints: 152383 Sorted by residual: angle pdb=" N PRO 0 544 " pdb=" CA PRO 0 544 " pdb=" CB PRO 0 544 " ideal model delta sigma weight residual 103.35 110.43 -7.08 8.70e-01 1.32e+00 6.63e+01 angle pdb=" N PRO 0 448 " pdb=" CA PRO 0 448 " pdb=" CB PRO 0 448 " ideal model delta sigma weight residual 103.17 110.28 -7.11 8.90e-01 1.26e+00 6.38e+01 angle pdb=" N PRO 0 491 " pdb=" CA PRO 0 491 " pdb=" CB PRO 0 491 " ideal model delta sigma weight residual 103.25 111.00 -7.75 1.05e+00 9.07e-01 5.45e+01 angle pdb=" N PRO 0 527 " pdb=" CA PRO 0 527 " pdb=" CB PRO 0 527 " ideal model delta sigma weight residual 102.67 110.51 -7.84 1.09e+00 8.42e-01 5.18e+01 angle pdb=" N PRO 0 559 " pdb=" CA PRO 0 559 " pdb=" CB PRO 0 559 " ideal model delta sigma weight residual 103.25 110.16 -6.91 1.05e+00 9.07e-01 4.33e+01 ... (remaining 152378 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.88: 52511 35.88 - 71.77: 1800 71.77 - 107.65: 153 107.65 - 143.53: 37 143.53 - 179.42: 47 Dihedral angle restraints: 54548 sinusoidal: 43703 harmonic: 10845 Sorted by residual: dihedral pdb=" C5' U 2 7 " pdb=" C4' U 2 7 " pdb=" C3' U 2 7 " pdb=" O3' U 2 7 " ideal model delta sinusoidal sigma weight residual 147.00 72.61 74.39 1 8.00e+00 1.56e-02 1.10e+02 dihedral pdb=" CA ASN V 50 " pdb=" C ASN V 50 " pdb=" N PRO V 51 " pdb=" CA PRO V 51 " ideal model delta harmonic sigma weight residual 180.00 129.49 50.51 0 5.00e+00 4.00e-02 1.02e+02 dihedral pdb=" C4' U 2 7 " pdb=" C3' U 2 7 " pdb=" C2' U 2 7 " pdb=" C1' U 2 7 " ideal model delta sinusoidal sigma weight residual -35.00 34.35 -69.35 1 8.00e+00 1.56e-02 9.71e+01 ... (remaining 54545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 17888 0.088 - 0.176: 1471 0.176 - 0.264: 119 0.264 - 0.352: 7 0.352 - 0.440: 4 Chirality restraints: 19489 Sorted by residual: chirality pdb=" C1' G A1757 " pdb=" O4' G A1757 " pdb=" C2' G A1757 " pdb=" N9 G A1757 " both_signs ideal model delta sigma weight residual False 2.46 2.02 0.44 2.00e-01 2.50e+01 4.84e+00 chirality pdb=" C3' G A1828 " pdb=" C4' G A1828 " pdb=" O3' G A1828 " pdb=" C2' G A1828 " both_signs ideal model delta sigma weight residual False -2.74 -2.36 -0.39 2.00e-01 2.50e+01 3.78e+00 chirality pdb=" C3' U 2 7 " pdb=" C4' U 2 7 " pdb=" O3' U 2 7 " pdb=" C2' U 2 7 " both_signs ideal model delta sigma weight residual False -2.74 -2.39 -0.36 2.00e-01 2.50e+01 3.22e+00 ... (remaining 19486 not shown) Planarity restraints: 8152 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A1757 " -0.038 2.00e-02 2.50e+03 2.08e-02 1.30e+01 pdb=" N9 G A1757 " 0.060 2.00e-02 2.50e+03 pdb=" C8 G A1757 " -0.004 2.00e-02 2.50e+03 pdb=" N7 G A1757 " -0.002 2.00e-02 2.50e+03 pdb=" C5 G A1757 " -0.003 2.00e-02 2.50e+03 pdb=" C6 G A1757 " -0.010 2.00e-02 2.50e+03 pdb=" O6 G A1757 " -0.001 2.00e-02 2.50e+03 pdb=" N1 G A1757 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G A1757 " -0.000 2.00e-02 2.50e+03 pdb=" N2 G A1757 " 0.004 2.00e-02 2.50e+03 pdb=" N3 G A1757 " 0.000 2.00e-02 2.50e+03 pdb=" C4 G A1757 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN H 9 " -0.016 2.00e-02 2.50e+03 3.34e-02 1.12e+01 pdb=" C ASN H 9 " 0.058 2.00e-02 2.50e+03 pdb=" O ASN H 9 " -0.022 2.00e-02 2.50e+03 pdb=" N LYS H 10 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A1789 " -0.043 2.00e-02 2.50e+03 2.01e-02 1.11e+01 pdb=" N9 A A1789 " 0.047 2.00e-02 2.50e+03 pdb=" C8 A A1789 " 0.006 2.00e-02 2.50e+03 pdb=" N7 A A1789 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A A1789 " -0.005 2.00e-02 2.50e+03 pdb=" C6 A A1789 " -0.012 2.00e-02 2.50e+03 pdb=" N6 A A1789 " -0.006 2.00e-02 2.50e+03 pdb=" N1 A A1789 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A A1789 " 0.004 2.00e-02 2.50e+03 pdb=" N3 A A1789 " 0.007 2.00e-02 2.50e+03 pdb=" C4 A A1789 " 0.004 2.00e-02 2.50e+03 ... (remaining 8149 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 891 2.54 - 3.13: 72420 3.13 - 3.72: 189112 3.72 - 4.31: 258264 4.31 - 4.90: 355978 Nonbonded interactions: 876665 Sorted by model distance: nonbonded pdb=" O2' G A 810 " pdb=" O5' A A 811 " model vdw 1.949 2.440 nonbonded pdb=" O2' U A1790 " pdb=" O4' A A1791 " model vdw 1.984 2.440 nonbonded pdb=" OG1 THR H 68 " pdb=" O ILE H 85 " model vdw 2.001 2.440 nonbonded pdb=" OP2 G A2806 " pdb=" O2' A A2810 " model vdw 2.016 2.440 nonbonded pdb=" O2' G A2009 " pdb=" OP2 U A2011 " model vdw 2.021 2.440 ... (remaining 876660 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2994 5.49 5 S 102 5.16 5 C 47150 2.51 5 N 17428 2.21 5 O 26127 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 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: 3.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 20.090 Check model and map are aligned: 1.040 Convert atoms to be neutral: 0.610 Process input model: 315.720 Find NCS groups from input model: 1.540 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:12.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 354.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9032 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 : 0.011 0.103 101896 Z= 0.672 Angle : 0.936 13.973 152383 Z= 0.483 Chirality : 0.054 0.440 19489 Planarity : 0.006 0.072 8152 Dihedral : 15.511 179.419 47554 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.68 % Favored : 91.16 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.36 % Twisted General : 0.06 % 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: -3.78 (0.12), residues: 3734 helix: -1.75 (0.12), residues: 1135 sheet: -2.93 (0.16), residues: 711 loop : -2.82 (0.13), residues: 1888 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1193 residues out of total 3199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1192 time to evaluate : 4.183 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: 1 outliers final: 4 residues processed: 1193 average time/residue: 1.7830 time to fit residues: 2848.5199 Evaluate side-chains 804 residues out of total 3199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 800 time to evaluate : 4.128 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 3 average time/residue: 1.4558 time to fit residues: 10.6040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 667 random chunks: chunk 563 optimal weight: 20.0000 chunk 505 optimal weight: 6.9990 chunk 280 optimal weight: 10.0000 chunk 172 optimal weight: 0.8980 chunk 341 optimal weight: 7.9990 chunk 270 optimal weight: 0.8980 chunk 522 optimal weight: 8.9990 chunk 202 optimal weight: 5.9990 chunk 317 optimal weight: 0.8980 chunk 389 optimal weight: 9.9990 chunk 605 optimal weight: 2.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 33 HIS ** 0 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 326 GLN 0 335 ASN ** 1 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 GLN E 86 ASN E 199 GLN ** F 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 GLN F 50 GLN F 173 ASN F 191 ASN G 67 GLN G 182 ASN H 9 ASN ** I 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 73 ASN N 96 ASN P 27 ASN P 114 ASN ** Q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 12 GLN ** R 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 77 GLN S 49 ASN T 29 HIS U 44 ASN U 52 GLN U 72 ASN U 108 GLN V 81 ASN W 95 GLN Y 2 HIS b 16 ASN ** d 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 33 GLN g 4 ASN h 6 GLN h 8 ASN h 9 ASN i 60 GLN i 64 ASN j 34 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9036 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.074 101896 Z= 0.196 Angle : 0.662 12.990 152383 Z= 0.337 Chirality : 0.037 0.562 19489 Planarity : 0.005 0.074 8152 Dihedral : 15.929 179.952 40083 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.32 % Favored : 93.60 % Rotamer Outliers : 3.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.13), residues: 3734 helix: -0.20 (0.15), residues: 1141 sheet: -1.77 (0.18), residues: 686 loop : -2.07 (0.13), residues: 1907 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1116 residues out of total 3199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 997 time to evaluate : 4.206 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 outliers start: 119 outliers final: 38 residues processed: 1040 average time/residue: 1.6456 time to fit residues: 2364.8764 Evaluate side-chains 876 residues out of total 3199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 838 time to evaluate : 4.194 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 20 residues processed: 23 average time/residue: 0.6910 time to fit residues: 34.3972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 667 random chunks: chunk 336 optimal weight: 10.0000 chunk 187 optimal weight: 10.0000 chunk 504 optimal weight: 7.9990 chunk 412 optimal weight: 4.9990 chunk 167 optimal weight: 10.0000 chunk 606 optimal weight: 0.9990 chunk 655 optimal weight: 10.0000 chunk 540 optimal weight: 3.9990 chunk 601 optimal weight: 1.9990 chunk 206 optimal weight: 10.0000 chunk 486 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 145 HIS 1 61 ASN E 111 GLN E 199 GLN F 50 GLN F 173 ASN ** F 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 46 GLN I 20 ASN ** I 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 73 ASN ** Q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 61 GLN R 77 GLN S 43 GLN ** S 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 103 HIS T 2 GLN U 38 GLN U 44 ASN U 52 GLN ** U 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 108 GLN U 116 GLN X 55 ASN Y 44 HIS ** Y 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 33 GLN g 25 ASN h 9 ASN i 60 GLN i 64 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9081 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.094 101896 Z= 0.226 Angle : 0.629 12.589 152383 Z= 0.324 Chirality : 0.036 0.526 19489 Planarity : 0.005 0.069 8152 Dihedral : 15.803 179.233 40083 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.21 % Favored : 93.73 % Rotamer Outliers : 5.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.36 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.13), residues: 3734 helix: 0.28 (0.15), residues: 1123 sheet: -1.19 (0.19), residues: 709 loop : -1.71 (0.13), residues: 1902 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1140 residues out of total 3199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 974 time to evaluate : 4.299 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: 166 outliers final: 69 residues processed: 1036 average time/residue: 1.5616 time to fit residues: 2264.4473 Evaluate side-chains 931 residues out of total 3199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 862 time to evaluate : 4.210 Switching outliers to nearest non-outliers outliers start: 69 outliers final: 31 residues processed: 42 average time/residue: 0.9132 time to fit residues: 68.6985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 667 random chunks: chunk 599 optimal weight: 9.9990 chunk 456 optimal weight: 20.0000 chunk 314 optimal weight: 10.0000 chunk 67 optimal weight: 20.0000 chunk 289 optimal weight: 10.0000 chunk 407 optimal weight: 10.0000 chunk 608 optimal weight: 6.9990 chunk 644 optimal weight: 3.9990 chunk 318 optimal weight: 10.0000 chunk 577 optimal weight: 1.9990 chunk 173 optimal weight: 10.0000 overall best weight: 6.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 50 GLN ** F 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 9 GLN G 53 ASN ** H 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 129 GLN I 148 ASN ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 114 ASN Q 13 HIS R 12 GLN R 27 ASN R 77 GLN U 38 GLN U 52 GLN ** U 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 108 GLN V 81 ASN X 55 ASN Y 39 ASN ** Y 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 9 ASN i 60 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9141 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.117 101896 Z= 0.372 Angle : 0.677 12.820 152383 Z= 0.351 Chirality : 0.040 0.536 19489 Planarity : 0.005 0.096 8152 Dihedral : 15.908 179.413 40083 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.70 % Favored : 93.25 % Rotamer Outliers : 5.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.36 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.13), residues: 3734 helix: 0.31 (0.15), residues: 1121 sheet: -1.04 (0.19), residues: 735 loop : -1.57 (0.14), residues: 1878 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1102 residues out of total 3199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 927 time to evaluate : 4.179 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 outliers start: 175 outliers final: 90 residues processed: 993 average time/residue: 1.5259 time to fit residues: 2127.9824 Evaluate side-chains 991 residues out of total 3199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 901 time to evaluate : 4.137 Switching outliers to nearest non-outliers outliers start: 90 outliers final: 40 residues processed: 53 average time/residue: 0.8590 time to fit residues: 82.4221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 667 random chunks: chunk 536 optimal weight: 6.9990 chunk 365 optimal weight: 8.9990 chunk 9 optimal weight: 40.0000 chunk 480 optimal weight: 40.0000 chunk 266 optimal weight: 10.0000 chunk 550 optimal weight: 4.9990 chunk 445 optimal weight: 8.9990 chunk 0 optimal weight: 50.0000 chunk 329 optimal weight: 10.0000 chunk 578 optimal weight: 2.9990 chunk 162 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 307 ASN ** 1 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 172 GLN ** I 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 148 ASN P 114 ASN R 27 ASN ** R 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 43 GLN U 44 ASN U 52 GLN ** U 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 108 GLN V 81 ASN Y 39 ASN a 58 ASN ** d 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 9 ASN i 60 GLN i 64 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9157 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.096 101896 Z= 0.368 Angle : 0.675 12.127 152383 Z= 0.351 Chirality : 0.040 0.524 19489 Planarity : 0.005 0.067 8152 Dihedral : 16.001 179.352 40083 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.75 % Favored : 93.20 % Rotamer Outliers : 6.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.13), residues: 3734 helix: 0.33 (0.15), residues: 1125 sheet: -0.92 (0.19), residues: 729 loop : -1.51 (0.14), residues: 1880 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1158 residues out of total 3199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 966 time to evaluate : 4.156 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 outliers start: 192 outliers final: 103 residues processed: 1041 average time/residue: 1.5024 time to fit residues: 2210.0961 Evaluate side-chains 987 residues out of total 3199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 884 time to evaluate : 4.256 Switching outliers to nearest non-outliers outliers start: 103 outliers final: 53 residues processed: 55 average time/residue: 0.8319 time to fit residues: 84.2789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 667 random chunks: chunk 216 optimal weight: 10.0000 chunk 580 optimal weight: 5.9990 chunk 127 optimal weight: 10.0000 chunk 378 optimal weight: 8.9990 chunk 159 optimal weight: 10.0000 chunk 645 optimal weight: 3.9990 chunk 535 optimal weight: 5.9990 chunk 298 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 213 optimal weight: 20.0000 chunk 338 optimal weight: 10.0000 overall best weight: 6.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 289 GLN ** 1 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 120 GLN ** F 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 148 ASN R 27 ASN ** R 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 43 GLN T 41 GLN ** U 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 81 ASN X 55 ASN Y 39 ASN ** a 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 58 ASN ** d 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 4 ASN h 9 ASN i 60 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9164 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.071 101896 Z= 0.389 Angle : 0.692 12.215 152383 Z= 0.359 Chirality : 0.041 0.519 19489 Planarity : 0.005 0.094 8152 Dihedral : 16.025 179.358 40083 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.88 % Favored : 93.06 % Rotamer Outliers : 5.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.13), residues: 3734 helix: 0.37 (0.15), residues: 1123 sheet: -0.84 (0.19), residues: 741 loop : -1.47 (0.14), residues: 1870 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1098 residues out of total 3199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 913 time to evaluate : 4.202 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: 185 outliers final: 109 residues processed: 993 average time/residue: 1.4888 time to fit residues: 2098.0787 Evaluate side-chains 996 residues out of total 3199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 887 time to evaluate : 4.952 Switching outliers to nearest non-outliers outliers start: 109 outliers final: 56 residues processed: 58 average time/residue: 0.7603 time to fit residues: 84.6191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 667 random chunks: chunk 622 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 367 optimal weight: 9.9990 chunk 471 optimal weight: 6.9990 chunk 365 optimal weight: 6.9990 chunk 543 optimal weight: 7.9990 chunk 360 optimal weight: 6.9990 chunk 642 optimal weight: 0.9980 chunk 402 optimal weight: 4.9990 chunk 391 optimal weight: 7.9990 chunk 296 optimal weight: 10.0000 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 199 GLN F 120 GLN ** F 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 66 HIS I 148 ASN R 27 ASN R 61 GLN ** R 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 43 GLN T 41 GLN ** U 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 55 ASN Y 39 ASN a 37 GLN ** d 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 9 ASN i 64 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9151 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.086 101896 Z= 0.315 Angle : 0.669 13.331 152383 Z= 0.346 Chirality : 0.039 0.508 19489 Planarity : 0.005 0.066 8152 Dihedral : 16.002 179.338 40083 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.83 % Favored : 93.12 % Rotamer Outliers : 5.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.13), residues: 3734 helix: 0.40 (0.16), residues: 1121 sheet: -0.78 (0.19), residues: 739 loop : -1.44 (0.14), residues: 1874 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1090 residues out of total 3199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 934 time to evaluate : 4.180 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 outliers start: 156 outliers final: 94 residues processed: 1001 average time/residue: 1.4995 time to fit residues: 2134.8440 Evaluate side-chains 1004 residues out of total 3199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 910 time to evaluate : 4.531 Switching outliers to nearest non-outliers outliers start: 94 outliers final: 55 residues processed: 44 average time/residue: 0.8961 time to fit residues: 71.8460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 667 random chunks: chunk 397 optimal weight: 3.9990 chunk 256 optimal weight: 10.0000 chunk 383 optimal weight: 6.9990 chunk 193 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 408 optimal weight: 9.9990 chunk 437 optimal weight: 1.9990 chunk 317 optimal weight: 10.0000 chunk 59 optimal weight: 0.3980 chunk 505 optimal weight: 10.0000 overall best weight: 4.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 199 GLN F 120 GLN ** F 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 148 ASN L 66 GLN R 27 ASN R 61 GLN ** R 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 43 GLN T 2 GLN T 41 GLN U 52 GLN ** U 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 81 ASN X 55 ASN a 37 GLN ** d 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 4 ASN h 9 ASN i 60 GLN i 64 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9142 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.068 101896 Z= 0.280 Angle : 0.664 13.654 152383 Z= 0.343 Chirality : 0.038 0.490 19489 Planarity : 0.005 0.064 8152 Dihedral : 15.974 179.282 40083 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.88 % Favored : 93.06 % Rotamer Outliers : 4.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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: -1.07 (0.13), residues: 3734 helix: 0.41 (0.16), residues: 1120 sheet: -0.74 (0.19), residues: 733 loop : -1.38 (0.14), residues: 1881 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1074 residues out of total 3199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 929 time to evaluate : 4.198 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 outliers start: 145 outliers final: 83 residues processed: 1000 average time/residue: 1.5055 time to fit residues: 2141.3422 Evaluate side-chains 979 residues out of total 3199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 896 time to evaluate : 4.232 Switching outliers to nearest non-outliers outliers start: 83 outliers final: 53 residues processed: 36 average time/residue: 0.8276 time to fit residues: 56.7141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/modules/cctbx_project/iotbx/cli_parser.py", line 864, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/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-4807/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-4807/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-4807/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-4807/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-4807/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-4807/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-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/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-4807/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-4807/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-4807/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: 50.7973 > 50: distance: 22 - 39: 3.724 distance: 34 - 39: 4.165 distance: 39 - 40: 6.815 distance: 40 - 41: 7.936 distance: 40 - 43: 8.734 distance: 41 - 42: 11.167 distance: 41 - 48: 15.690 distance: 43 - 44: 6.068 distance: 45 - 46: 7.767 distance: 46 - 47: 10.243 distance: 48 - 49: 8.294 distance: 49 - 50: 16.976 distance: 49 - 52: 9.903 distance: 50 - 51: 21.982 distance: 50 - 57: 26.078 distance: 52 - 53: 11.236 distance: 53 - 54: 6.801 distance: 54 - 55: 10.763 distance: 54 - 56: 7.300 distance: 57 - 58: 23.051 distance: 58 - 59: 20.760 distance: 58 - 61: 21.541 distance: 59 - 60: 22.808 distance: 59 - 66: 13.983 distance: 61 - 62: 20.633 distance: 62 - 63: 27.199 distance: 63 - 64: 11.278 distance: 63 - 65: 13.607 distance: 66 - 67: 10.916 distance: 67 - 68: 11.283 distance: 67 - 70: 14.592 distance: 68 - 69: 16.118 distance: 68 - 74: 3.737 distance: 70 - 71: 11.299 distance: 71 - 72: 10.263 distance: 71 - 73: 15.267 distance: 74 - 75: 9.722 distance: 75 - 76: 6.917 distance: 75 - 78: 5.493 distance: 76 - 77: 16.235 distance: 76 - 85: 7.335 distance: 78 - 79: 11.595 distance: 79 - 80: 6.529 distance: 80 - 81: 11.005 distance: 81 - 82: 5.164 distance: 82 - 83: 4.334 distance: 82 - 84: 5.359 distance: 85 - 86: 5.309 distance: 86 - 87: 10.550 distance: 86 - 89: 12.600 distance: 87 - 88: 29.714 distance: 87 - 92: 17.113 distance: 89 - 90: 20.416 distance: 89 - 91: 7.272 distance: 92 - 93: 12.245 distance: 93 - 94: 13.825 distance: 93 - 96: 12.488 distance: 94 - 95: 12.223 distance: 94 - 100: 14.931 distance: 96 - 97: 15.080 distance: 97 - 98: 9.812 distance: 97 - 99: 7.225 distance: 100 - 101: 14.385 distance: 101 - 102: 9.492 distance: 101 - 104: 21.835 distance: 102 - 103: 14.196 distance: 102 - 108: 10.620 distance: 104 - 105: 13.304 distance: 105 - 106: 34.230 distance: 105 - 107: 8.739 distance: 108 - 109: 8.538 distance: 108 - 114: 9.218 distance: 109 - 110: 18.557 distance: 109 - 112: 5.006 distance: 110 - 111: 22.538 distance: 110 - 115: 13.379 distance: 112 - 113: 6.312 distance: 115 - 116: 11.393 distance: 116 - 117: 15.201 distance: 116 - 119: 12.982 distance: 117 - 118: 11.979 distance: 117 - 120: 13.496