Starting phenix.real_space_refine on Sat Nov 18 07:34:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k0a_30036/11_2023/6k0a_30036.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k0a_30036/11_2023/6k0a_30036.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k0a_30036/11_2023/6k0a_30036.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k0a_30036/11_2023/6k0a_30036.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k0a_30036/11_2023/6k0a_30036.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k0a_30036/11_2023/6k0a_30036.pdb" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 516 5.49 5 S 38 5.16 5 C 12184 2.51 5 N 4012 2.21 5 O 5524 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 76": "OD1" <-> "OD2" Residue "A ARG 105": "NH1" <-> "NH2" Residue "A GLU 126": "OE1" <-> "OE2" Residue "C ASP 13": "OD1" <-> "OD2" Residue "C ASP 37": "OD1" <-> "OD2" Residue "C GLU 40": "OE1" <-> "OE2" Residue "C GLU 47": "OE1" <-> "OE2" Residue "C GLU 84": "OE1" <-> "OE2" Residue "C ASP 101": "OD1" <-> "OD2" Residue "C ARG 110": "NH1" <-> "NH2" Residue "C ASP 112": "OD1" <-> "OD2" Residue "C ASP 171": "OD1" <-> "OD2" Residue "C ASP 183": "OD1" <-> "OD2" Residue "E ASP 48": "OD1" <-> "OD2" Residue "E ASP 57": "OD1" <-> "OD2" Residue "E PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 26": "OE1" <-> "OE2" Residue "G ARG 84": "NH1" <-> "NH2" Residue "G TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 105": "NH1" <-> "NH2" Residue "G GLU 109": "OE1" <-> "OE2" Residue "I TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 67": "OE1" <-> "OE2" Residue "I ASP 80": "OD1" <-> "OD2" Residue "B TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 76": "OD1" <-> "OD2" Residue "B ARG 105": "NH1" <-> "NH2" Residue "B GLU 126": "OE1" <-> "OE2" Residue "D ASP 13": "OD1" <-> "OD2" Residue "D ASP 37": "OD1" <-> "OD2" Residue "D GLU 40": "OE1" <-> "OE2" Residue "D GLU 47": "OE1" <-> "OE2" Residue "D GLU 84": "OE1" <-> "OE2" Residue "D ASP 101": "OD1" <-> "OD2" Residue "D ARG 110": "NH1" <-> "NH2" Residue "D ASP 112": "OD1" <-> "OD2" Residue "D ASP 171": "OD1" <-> "OD2" Residue "D ASP 183": "OD1" <-> "OD2" Residue "F ASP 48": "OD1" <-> "OD2" Residue "F ASP 57": "OD1" <-> "OD2" Residue "F PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 26": "OE1" <-> "OE2" Residue "H ARG 84": "NH1" <-> "NH2" Residue "H TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 105": "NH1" <-> "NH2" Residue "H GLU 109": "OE1" <-> "OE2" Residue "J TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 67": "OE1" <-> "OE2" Residue "J ASP 80": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 22276 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1059 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "C" Number of atoms: 1875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1875 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 4, 'TRANS': 221} Chain: "E" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 764 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 4, 'TRANS': 90} Chain: "G" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1021 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "I" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 883 Classifications: {'peptide': 116} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 111} Chain: "X" Number of atoms: 5535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 5535 Classifications: {'RNA': 258} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 14, 'rna3p_pur': 131, 'rna3p_pyr': 99} Link IDs: {'rna2p': 28, 'rna3p': 229} Chain: "B" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1059 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "D" Number of atoms: 1875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1875 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 4, 'TRANS': 221} Chain: "F" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 764 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 4, 'TRANS': 90} Chain: "H" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1021 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "J" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 883 Classifications: {'peptide': 116} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 111} Chain: "Y" Number of atoms: 5535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 5535 Classifications: {'RNA': 258} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 14, 'rna3p_pur': 131, 'rna3p_pyr': 99} Link IDs: {'rna2p': 28, 'rna3p': 229} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4232 SG CYS G 63 182.893 49.953 84.315 1.00123.20 S ATOM 4256 SG CYS G 66 180.141 52.933 85.267 1.00109.97 S ATOM 4470 SG CYS G 92 183.213 53.629 87.634 1.00128.27 S ATOM 4493 SG CYS G 95 181.038 50.386 87.761 1.00145.27 S ATOM 15369 SG CYS H 63 61.161 109.147 84.323 1.00124.80 S ATOM 15393 SG CYS H 66 63.897 106.167 85.323 1.00107.16 S ATOM 15607 SG CYS H 92 60.790 105.479 87.646 1.00135.20 S ATOM 15630 SG CYS H 95 62.965 108.721 87.797 1.00143.38 S Time building chain proxies: 11.77, per 1000 atoms: 0.53 Number of scatterers: 22276 At special positions: 0 Unit cell: (245.25, 161.32, 109, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 38 16.00 P 516 15.00 O 5524 8.00 N 4012 7.00 C 12184 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.88 Conformation dependent library (CDL) restraints added in 2.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN G 201 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 66 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 63 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 95 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 92 " pdb=" ZN H 201 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 66 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 63 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 95 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 92 " Number of angles added : 12 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2600 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 10 sheets defined 46.3% alpha, 15.0% beta 120 base pairs and 324 stacking pairs defined. Time for finding SS restraints: 9.39 Creating SS restraints... Processing helix chain 'A' and resid 30 through 46 removed outlier: 3.597A pdb=" N ASN A 36 " --> pdb=" O GLY A 32 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU A 44 " --> pdb=" O LYS A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 55 removed outlier: 3.554A pdb=" N GLY A 50 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N SER A 52 " --> pdb=" O SER A 48 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS A 53 " --> pdb=" O TRP A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 80 removed outlier: 3.675A pdb=" N VAL A 78 " --> pdb=" O ASN A 74 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA A 80 " --> pdb=" O ASP A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 111 removed outlier: 3.960A pdb=" N ILE A 109 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N PHE A 111 " --> pdb=" O ALA A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 125 removed outlier: 4.061A pdb=" N VAL A 122 " --> pdb=" O LYS A 118 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG A 124 " --> pdb=" O TRP A 120 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG A 125 " --> pdb=" O PHE A 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 21 removed outlier: 3.542A pdb=" N LYS C 18 " --> pdb=" O ILE C 14 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU C 20 " --> pdb=" O LEU C 16 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS C 21 " --> pdb=" O LEU C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 47 removed outlier: 3.583A pdb=" N GLU C 41 " --> pdb=" O ASP C 37 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS C 43 " --> pdb=" O TYR C 39 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA C 44 " --> pdb=" O GLU C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 75 removed outlier: 3.642A pdb=" N ASP C 69 " --> pdb=" O LYS C 65 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS C 70 " --> pdb=" O GLN C 66 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS C 72 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LYS C 73 " --> pdb=" O ASP C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 97 removed outlier: 3.993A pdb=" N VAL C 95 " --> pdb=" O ASN C 91 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU C 96 " --> pdb=" O ARG C 92 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU C 97 " --> pdb=" O ALA C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 127 removed outlier: 3.515A pdb=" N ALA C 120 " --> pdb=" O ASP C 116 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG C 121 " --> pdb=" O HIS C 117 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER C 124 " --> pdb=" O ALA C 120 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ASN C 125 " --> pdb=" O ARG C 121 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N HIS C 126 " --> pdb=" O LEU C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 140 removed outlier: 3.515A pdb=" N ASN C 139 " --> pdb=" O THR C 136 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LYS C 140 " --> pdb=" O LEU C 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 136 through 140' Processing helix chain 'C' and resid 141 through 162 removed outlier: 3.548A pdb=" N THR C 148 " --> pdb=" O GLU C 144 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS C 157 " --> pdb=" O ARG C 153 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU C 158 " --> pdb=" O ASN C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 192 removed outlier: 3.667A pdb=" N LEU C 184 " --> pdb=" O ASN C 180 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL C 192 " --> pdb=" O LEU C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 217 removed outlier: 3.540A pdb=" N LYS C 198 " --> pdb=" O PRO C 194 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS C 199 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE C 200 " --> pdb=" O TYR C 196 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N MET C 201 " --> pdb=" O ALA C 197 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU C 202 " --> pdb=" O LYS C 198 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N CYS C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE C 210 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N MET C 215 " --> pdb=" O ARG C 211 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASP C 217 " --> pdb=" O TYR C 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 87 removed outlier: 4.250A pdb=" N LYS E 86 " --> pdb=" O GLU E 82 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS E 87 " --> pdb=" O GLU E 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 82 through 87' Processing helix chain 'G' and resid 4 through 29 removed outlier: 3.777A pdb=" N GLU G 15 " --> pdb=" O LYS G 11 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP G 18 " --> pdb=" O TYR G 14 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU G 20 " --> pdb=" O ARG G 16 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N MET G 21 " --> pdb=" O ILE G 17 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU G 26 " --> pdb=" O SER G 22 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU G 27 " --> pdb=" O LEU G 23 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS G 29 " --> pdb=" O GLU G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 51 removed outlier: 3.543A pdb=" N VAL G 40 " --> pdb=" O ALA G 36 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N MET G 48 " --> pdb=" O ARG G 44 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS G 49 " --> pdb=" O ARG G 45 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N MET G 50 " --> pdb=" O ILE G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 121 removed outlier: 3.754A pdb=" N GLU G 109 " --> pdb=" O ARG G 105 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS G 110 " --> pdb=" O GLU G 106 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 25 removed outlier: 3.684A pdb=" N LYS I 15 " --> pdb=" O GLU I 11 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLU I 16 " --> pdb=" O GLU I 12 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA I 22 " --> pdb=" O LEU I 18 " (cutoff:3.500A) Processing helix chain 'I' and resid 30 through 41 removed outlier: 3.522A pdb=" N VAL I 34 " --> pdb=" O GLY I 30 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR I 35 " --> pdb=" O ALA I 31 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU I 39 " --> pdb=" O THR I 35 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG I 40 " --> pdb=" O LYS I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 54 through 58 removed outlier: 3.909A pdb=" N VAL I 57 " --> pdb=" O PRO I 54 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 69 removed outlier: 4.409A pdb=" N TYR I 63 " --> pdb=" O ALA I 59 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU I 67 " --> pdb=" O TYR I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 78 through 86 Processing helix chain 'I' and resid 99 through 101 No H-bonds generated for 'chain 'I' and resid 99 through 101' Processing helix chain 'I' and resid 102 through 110 removed outlier: 3.918A pdb=" N VAL I 107 " --> pdb=" O GLU I 103 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU I 108 " --> pdb=" O GLU I 104 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 117 removed outlier: 3.612A pdb=" N LEU I 115 " --> pdb=" O LYS I 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 46 removed outlier: 3.598A pdb=" N ASN B 36 " --> pdb=" O GLY B 32 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU B 44 " --> pdb=" O LYS B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 55 removed outlier: 3.553A pdb=" N GLY B 50 " --> pdb=" O TYR B 46 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N SER B 52 " --> pdb=" O SER B 48 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS B 53 " --> pdb=" O TRP B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 80 removed outlier: 3.676A pdb=" N VAL B 78 " --> pdb=" O ASN B 74 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA B 80 " --> pdb=" O ASP B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 111 removed outlier: 3.958A pdb=" N ILE B 109 " --> pdb=" O ARG B 105 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N PHE B 111 " --> pdb=" O ALA B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 125 removed outlier: 4.062A pdb=" N VAL B 122 " --> pdb=" O LYS B 118 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG B 124 " --> pdb=" O TRP B 120 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG B 125 " --> pdb=" O PHE B 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 21 removed outlier: 3.541A pdb=" N LYS D 18 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU D 20 " --> pdb=" O LEU D 16 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS D 21 " --> pdb=" O LEU D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 47 removed outlier: 3.584A pdb=" N GLU D 41 " --> pdb=" O ASP D 37 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS D 43 " --> pdb=" O TYR D 39 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA D 44 " --> pdb=" O GLU D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 75 removed outlier: 3.642A pdb=" N ASP D 69 " --> pdb=" O LYS D 65 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS D 70 " --> pdb=" O GLN D 66 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS D 72 " --> pdb=" O ARG D 68 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS D 73 " --> pdb=" O ASP D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 97 removed outlier: 3.993A pdb=" N VAL D 95 " --> pdb=" O ASN D 91 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU D 96 " --> pdb=" O ARG D 92 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU D 97 " --> pdb=" O ALA D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 127 removed outlier: 3.515A pdb=" N ALA D 120 " --> pdb=" O ASP D 116 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG D 121 " --> pdb=" O HIS D 117 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER D 124 " --> pdb=" O ALA D 120 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ASN D 125 " --> pdb=" O ARG D 121 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N HIS D 126 " --> pdb=" O LEU D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 140 removed outlier: 3.514A pdb=" N ASN D 139 " --> pdb=" O THR D 136 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LYS D 140 " --> pdb=" O LEU D 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 136 through 140' Processing helix chain 'D' and resid 141 through 162 removed outlier: 3.547A pdb=" N THR D 148 " --> pdb=" O GLU D 144 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS D 157 " --> pdb=" O ARG D 153 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU D 158 " --> pdb=" O ASN D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 192 removed outlier: 3.666A pdb=" N LEU D 184 " --> pdb=" O ASN D 180 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL D 192 " --> pdb=" O LEU D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 217 removed outlier: 3.540A pdb=" N LYS D 198 " --> pdb=" O PRO D 194 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS D 199 " --> pdb=" O LEU D 195 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE D 200 " --> pdb=" O TYR D 196 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N MET D 201 " --> pdb=" O ALA D 197 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU D 202 " --> pdb=" O LYS D 198 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N CYS D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE D 210 " --> pdb=" O LYS D 206 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N MET D 215 " --> pdb=" O ARG D 211 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASP D 217 " --> pdb=" O TYR D 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 87 removed outlier: 4.248A pdb=" N LYS F 86 " --> pdb=" O GLU F 82 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS F 87 " --> pdb=" O GLU F 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 82 through 87' Processing helix chain 'H' and resid 4 through 29 removed outlier: 3.777A pdb=" N GLU H 15 " --> pdb=" O LYS H 11 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP H 18 " --> pdb=" O TYR H 14 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU H 20 " --> pdb=" O ARG H 16 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N MET H 21 " --> pdb=" O ILE H 17 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU H 26 " --> pdb=" O SER H 22 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU H 27 " --> pdb=" O LEU H 23 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS H 29 " --> pdb=" O GLU H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 32 through 51 removed outlier: 3.545A pdb=" N VAL H 40 " --> pdb=" O ALA H 36 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N MET H 48 " --> pdb=" O ARG H 44 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS H 49 " --> pdb=" O ARG H 45 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N MET H 50 " --> pdb=" O ILE H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 121 removed outlier: 3.753A pdb=" N GLU H 109 " --> pdb=" O ARG H 105 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS H 110 " --> pdb=" O GLU H 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 25 removed outlier: 3.683A pdb=" N LYS J 15 " --> pdb=" O GLU J 11 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLU J 16 " --> pdb=" O GLU J 12 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA J 22 " --> pdb=" O LEU J 18 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 41 removed outlier: 3.522A pdb=" N VAL J 34 " --> pdb=" O GLY J 30 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR J 35 " --> pdb=" O ALA J 31 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU J 39 " --> pdb=" O THR J 35 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG J 40 " --> pdb=" O LYS J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 54 through 58 removed outlier: 3.907A pdb=" N VAL J 57 " --> pdb=" O PRO J 54 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 69 removed outlier: 4.409A pdb=" N TYR J 63 " --> pdb=" O ALA J 59 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU J 67 " --> pdb=" O TYR J 63 " (cutoff:3.500A) Processing helix chain 'J' and resid 78 through 86 Processing helix chain 'J' and resid 99 through 101 No H-bonds generated for 'chain 'J' and resid 99 through 101' Processing helix chain 'J' and resid 102 through 110 removed outlier: 3.919A pdb=" N VAL J 107 " --> pdb=" O GLU J 103 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU J 108 " --> pdb=" O GLU J 104 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 117 removed outlier: 3.613A pdb=" N LEU J 115 " --> pdb=" O LYS J 111 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 57 through 60 removed outlier: 3.542A pdb=" N VAL A 59 " --> pdb=" O ILE A 67 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ILE A 67 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N TYR A 18 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N VAL A 100 " --> pdb=" O TYR A 18 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA A 20 " --> pdb=" O LEU A 98 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 3 through 6 removed outlier: 6.442A pdb=" N ASP C 4 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N TYR C 28 " --> pdb=" O ASP C 4 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ASN C 6 " --> pdb=" O TYR C 28 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N PHE C 25 " --> pdb=" O TYR C 54 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N GLY C 56 " --> pdb=" O PHE C 25 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N PHE C 27 " --> pdb=" O GLY C 56 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N LYS C 58 " --> pdb=" O PHE C 27 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE C 80 " --> pdb=" O SER C 55 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU C 82 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE C 59 " --> pdb=" O LEU C 82 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLU C 84 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ILE C 81 " --> pdb=" O ILE C 102 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N SER C 104 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE C 83 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N LEU C 103 " --> pdb=" O GLU C 131 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ASN C 133 " --> pdb=" O LEU C 103 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 223 through 225 removed outlier: 3.767A pdb=" N VAL C 224 " --> pdb=" O LYS E 71 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS E 71 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N VAL E 60 " --> pdb=" O VAL E 20 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL E 20 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LYS E 16 " --> pdb=" O GLN E 64 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL E 43 " --> pdb=" O VAL E 35 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N GLU E 37 " --> pdb=" O THR E 41 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N THR E 41 " --> pdb=" O GLU E 37 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE E 44 " --> pdb=" O VAL E 52 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 79 through 81 removed outlier: 3.697A pdb=" N ARG G 79 " --> pdb=" O VAL G 89 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 27 through 29 removed outlier: 4.483A pdb=" N LEU I 45 " --> pdb=" O ILE I 96 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N VAL I 46 " --> pdb=" O ALA I 73 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N VAL I 75 " --> pdb=" O VAL I 46 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ILE I 48 " --> pdb=" O VAL I 75 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 57 through 60 removed outlier: 3.543A pdb=" N VAL B 59 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ILE B 67 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N TYR B 18 " --> pdb=" O VAL B 100 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL B 100 " --> pdb=" O TYR B 18 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA B 20 " --> pdb=" O LEU B 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 3 through 6 removed outlier: 6.443A pdb=" N ASP D 4 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N TYR D 28 " --> pdb=" O ASP D 4 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ASN D 6 " --> pdb=" O TYR D 28 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N PHE D 25 " --> pdb=" O TYR D 54 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N GLY D 56 " --> pdb=" O PHE D 25 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N PHE D 27 " --> pdb=" O GLY D 56 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N LYS D 58 " --> pdb=" O PHE D 27 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE D 80 " --> pdb=" O SER D 55 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU D 82 " --> pdb=" O VAL D 57 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE D 59 " --> pdb=" O LEU D 82 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLU D 84 " --> pdb=" O ILE D 59 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ILE D 81 " --> pdb=" O ILE D 102 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N SER D 104 " --> pdb=" O ILE D 81 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE D 83 " --> pdb=" O SER D 104 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N LEU D 103 " --> pdb=" O GLU D 131 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ASN D 133 " --> pdb=" O LEU D 103 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 223 through 225 removed outlier: 3.775A pdb=" N VAL D 224 " --> pdb=" O LYS F 71 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS F 71 " --> pdb=" O VAL D 224 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N VAL F 60 " --> pdb=" O VAL F 20 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL F 20 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LYS F 16 " --> pdb=" O GLN F 64 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL F 43 " --> pdb=" O VAL F 35 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N GLU F 37 " --> pdb=" O THR F 41 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N THR F 41 " --> pdb=" O GLU F 37 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE F 44 " --> pdb=" O VAL F 52 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 79 through 81 removed outlier: 3.697A pdb=" N ARG H 79 " --> pdb=" O VAL H 89 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 27 through 29 removed outlier: 4.484A pdb=" N LEU J 45 " --> pdb=" O ILE J 96 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N VAL J 46 " --> pdb=" O ALA J 73 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N VAL J 75 " --> pdb=" O VAL J 46 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE J 48 " --> pdb=" O VAL J 75 " (cutoff:3.500A) 362 hydrogen bonds defined for protein. 1068 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 302 hydrogen bonds 564 hydrogen bond angles 0 basepair planarities 120 basepair parallelities 324 stacking parallelities Total time for adding SS restraints: 7.07 Time building geometry restraints manager: 10.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4782 1.34 - 1.45: 7556 1.45 - 1.57: 10348 1.57 - 1.69: 1030 1.69 - 1.81: 56 Bond restraints: 23772 Sorted by residual: bond pdb=" CA THR C 61 " pdb=" CB THR C 61 " ideal model delta sigma weight residual 1.527 1.557 -0.029 1.61e-02 3.86e+03 3.36e+00 bond pdb=" CA THR D 61 " pdb=" CB THR D 61 " ideal model delta sigma weight residual 1.527 1.556 -0.029 1.61e-02 3.86e+03 3.26e+00 bond pdb=" C3' U Y 198 " pdb=" O3' U Y 198 " ideal model delta sigma weight residual 1.427 1.452 -0.025 1.50e-02 4.44e+03 2.69e+00 bond pdb=" C3' U X 198 " pdb=" O3' U X 198 " ideal model delta sigma weight residual 1.427 1.451 -0.024 1.50e-02 4.44e+03 2.59e+00 bond pdb=" C THR C 105 " pdb=" N PRO C 106 " ideal model delta sigma weight residual 1.333 1.344 -0.011 7.80e-03 1.64e+04 2.01e+00 ... (remaining 23767 not shown) Histogram of bond angle deviations from ideal: 100.28 - 107.02: 3237 107.02 - 113.76: 14218 113.76 - 120.49: 9037 120.49 - 127.23: 6925 127.23 - 133.97: 1153 Bond angle restraints: 34570 Sorted by residual: angle pdb=" C LYS C 60 " pdb=" N THR C 61 " pdb=" CA THR C 61 " ideal model delta sigma weight residual 122.82 130.31 -7.49 1.42e+00 4.96e-01 2.78e+01 angle pdb=" C LYS D 60 " pdb=" N THR D 61 " pdb=" CA THR D 61 " ideal model delta sigma weight residual 122.82 130.31 -7.49 1.42e+00 4.96e-01 2.78e+01 angle pdb=" C3' U X 198 " pdb=" O3' U X 198 " pdb=" P U X 199 " ideal model delta sigma weight residual 120.20 126.54 -6.34 1.50e+00 4.44e-01 1.78e+01 angle pdb=" C3' U Y 198 " pdb=" O3' U Y 198 " pdb=" P U Y 199 " ideal model delta sigma weight residual 120.20 126.50 -6.30 1.50e+00 4.44e-01 1.77e+01 angle pdb=" CA LYS D 50 " pdb=" C LYS D 50 " pdb=" N LEU D 51 " ideal model delta sigma weight residual 115.81 120.48 -4.67 1.15e+00 7.56e-01 1.65e+01 ... (remaining 34565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.76: 12790 35.76 - 71.51: 470 71.51 - 107.27: 42 107.27 - 143.03: 0 143.03 - 178.79: 6 Dihedral angle restraints: 13308 sinusoidal: 9290 harmonic: 4018 Sorted by residual: dihedral pdb=" O4' U X 207 " pdb=" C1' U X 207 " pdb=" N1 U X 207 " pdb=" C2 U X 207 " ideal model delta sinusoidal sigma weight residual 232.00 53.21 178.79 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U Y 207 " pdb=" C1' U Y 207 " pdb=" N1 U Y 207 " pdb=" C2 U Y 207 " ideal model delta sinusoidal sigma weight residual 232.00 53.24 178.76 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U X 228 " pdb=" C1' U X 228 " pdb=" N1 U X 228 " pdb=" C2 U X 228 " ideal model delta sinusoidal sigma weight residual -160.00 -98.94 -61.06 1 1.50e+01 4.44e-03 2.20e+01 ... (remaining 13305 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 3910 0.060 - 0.119: 302 0.119 - 0.178: 63 0.178 - 0.238: 7 0.238 - 0.297: 6 Chirality restraints: 4288 Sorted by residual: chirality pdb=" CB ILE H 80 " pdb=" CA ILE H 80 " pdb=" CG1 ILE H 80 " pdb=" CG2 ILE H 80 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CB ILE G 80 " pdb=" CA ILE G 80 " pdb=" CG1 ILE G 80 " pdb=" CG2 ILE G 80 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" P U Y 199 " pdb=" OP1 U Y 199 " pdb=" OP2 U Y 199 " pdb=" O5' U Y 199 " both_signs ideal model delta sigma weight residual True 2.41 -2.66 -0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 4285 not shown) Planarity restraints: 2404 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 63 " -0.045 5.00e-02 4.00e+02 6.85e-02 7.51e+00 pdb=" N PRO A 64 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 64 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 64 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 63 " -0.045 5.00e-02 4.00e+02 6.84e-02 7.49e+00 pdb=" N PRO B 64 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO B 64 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 64 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN D 180 " 0.040 5.00e-02 4.00e+02 6.07e-02 5.90e+00 pdb=" N PRO D 181 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO D 181 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 181 " 0.034 5.00e-02 4.00e+02 ... (remaining 2401 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 6327 2.83 - 3.35: 16876 3.35 - 3.87: 40547 3.87 - 4.38: 47212 4.38 - 4.90: 66607 Nonbonded interactions: 177569 Sorted by model distance: nonbonded pdb=" OP1 U X 16 " pdb=" OH TYR D 182 " model vdw 2.316 2.440 nonbonded pdb=" OH TYR J 4 " pdb=" O ALA J 49 " model vdw 2.328 2.440 nonbonded pdb=" OH TYR I 4 " pdb=" O ALA I 49 " model vdw 2.329 2.440 nonbonded pdb=" OP2 G Y 76 " pdb=" O2' A Y 252 " model vdw 2.359 2.440 nonbonded pdb=" OP2 G X 76 " pdb=" O2' A X 252 " model vdw 2.360 2.440 ... (remaining 177564 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' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'X' selection = chain 'Y' } Set up NCS constraints Number of NCS constrained groups: 6 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' } pdb_interpretation.ncs_group { reference = chain 'C' selection = chain 'D' } pdb_interpretation.ncs_group { reference = chain 'E' selection = chain 'F' } pdb_interpretation.ncs_group { reference = chain 'G' selection = chain 'H' } pdb_interpretation.ncs_group { reference = chain 'I' selection = chain 'J' } pdb_interpretation.ncs_group { reference = chain 'X' selection = chain 'Y' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.40 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: 2.330 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: 0.010 Extract box with map and model: 6.790 Check model and map are aligned: 0.330 Set scattering table: 0.210 Process input model: 67.060 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6014 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 : 0.003 0.037 23772 Z= 0.177 Angle : 0.703 11.557 34570 Z= 0.395 Chirality : 0.037 0.297 4288 Planarity : 0.005 0.069 2404 Dihedral : 15.450 178.786 10708 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 0.83 % Allowed : 7.79 % Favored : 91.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -4.65 (0.17), residues: 1344 helix: -4.88 (0.07), residues: 512 sheet: -0.44 (0.36), residues: 190 loop : -2.25 (0.19), residues: 642 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.125 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.1688 time to fit residues: 8.1910 Evaluate side-chains 26 residues out of total 114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.133 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1729 Evaluate side-chains 72 residues out of total 205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 68 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 70 average time/residue: 0.2221 time to fit residues: 16.9671 Evaluate side-chains 45 residues out of total 205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 43 time to evaluate : 0.222 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0222 time to fit residues: 0.3925 Evaluate side-chains 29 residues out of total 85 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 28 time to evaluate : 0.098 Fit side-chains 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: 28 average time/residue: 0.3164 time to fit residues: 9.1960 Evaluate side-chains 14 residues out of total 85 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 13 time to evaluate : 0.100 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0268 time to fit residues: 0.1666 Evaluate side-chains 46 residues out of total 106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.2721 time to fit residues: 13.1026 Evaluate side-chains 30 residues out of total 106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.162 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1788 Evaluate side-chains 20 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.110 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.1679 time to fit residues: 3.6777 Evaluate side-chains 10 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.102 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1391 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.165 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1978 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.155 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 4.9990 chunk 136 optimal weight: 0.9990 chunk 75 optimal weight: 10.0000 chunk 46 optimal weight: 0.3980 chunk 92 optimal weight: 0.4980 chunk 72 optimal weight: 9.9990 chunk 141 optimal weight: 0.0020 chunk 54 optimal weight: 5.9990 chunk 85 optimal weight: 20.0000 chunk 105 optimal weight: 10.0000 chunk 163 optimal weight: 9.9990 overall best weight: 1.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 91 ASN D 125 ASN ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 64 GLN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6228 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.120 23772 Z= 0.187 Angle : 0.622 8.912 34570 Z= 0.315 Chirality : 0.034 0.162 4288 Planarity : 0.005 0.052 2404 Dihedral : 14.498 179.164 7708 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.33 % Allowed : 4.98 % Favored : 94.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.82 (0.20), residues: 1344 helix: -2.75 (0.16), residues: 516 sheet: 0.05 (0.38), residues: 196 loop : -1.61 (0.22), residues: 632 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.147 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.1088 time to fit residues: 4.5709 Evaluate side-chains 21 residues out of total 114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.132 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2054 Evaluate side-chains 43 residues out of total 205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 42 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 42 average time/residue: 0.2140 time to fit residues: 9.9927 Evaluate side-chains 27 residues out of total 205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.249 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3261 Evaluate side-chains 18 residues out of total 85 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 17 time to evaluate : 0.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 18 average time/residue: 0.3135 time to fit residues: 5.9144 Evaluate side-chains 9 residues out of total 85 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 8 time to evaluate : 0.101 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0149 time to fit residues: 0.1590 Evaluate side-chains 35 residues out of total 106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.140 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1545 time to fit residues: 5.9206 Evaluate side-chains 31 residues out of total 106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.129 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1795 Evaluate side-chains 14 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.108 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.1372 time to fit residues: 2.1928 Evaluate side-chains 9 residues out of total 93 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 9 time to evaluate : 0.107 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1467 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.162 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2168 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.175 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 675, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 771, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 69.4383 > 50: distance: 0 - 1: 3.502 distance: 0 - 2: 10.302 distance: 3 - 4: 29.245 distance: 4 - 5: 18.687 distance: 4 - 7: 26.456 distance: 5 - 6: 18.030 distance: 5 - 12: 40.105 distance: 6 - 34: 56.691 distance: 7 - 8: 31.751 distance: 8 - 9: 69.438 distance: 9 - 10: 37.095 distance: 10 - 11: 37.214 distance: 12 - 13: 28.101 distance: 13 - 14: 13.719 distance: 13 - 16: 29.729 distance: 14 - 15: 13.934 distance: 14 - 21: 21.904 distance: 15 - 41: 21.800 distance: 16 - 17: 52.726 distance: 17 - 18: 44.543 distance: 18 - 19: 25.252 distance: 18 - 20: 29.301 distance: 21 - 22: 10.124 distance: 22 - 23: 37.514 distance: 23 - 24: 18.184 distance: 23 - 25: 23.267 distance: 25 - 26: 34.653 distance: 26 - 27: 27.445 distance: 26 - 29: 28.661 distance: 27 - 28: 42.907 distance: 27 - 34: 8.342 distance: 28 - 56: 47.904 distance: 29 - 30: 54.931 distance: 30 - 31: 20.177 distance: 31 - 32: 30.080 distance: 31 - 33: 18.849 distance: 34 - 35: 23.174 distance: 35 - 36: 28.934 distance: 35 - 38: 26.307 distance: 36 - 37: 21.522 distance: 36 - 41: 29.113 distance: 38 - 39: 15.569 distance: 38 - 40: 36.373 distance: 41 - 42: 45.073 distance: 42 - 43: 24.355 distance: 42 - 45: 31.885 distance: 43 - 44: 28.608 distance: 43 - 48: 36.062 distance: 44 - 72: 24.890 distance: 45 - 46: 15.797 distance: 45 - 47: 34.442 distance: 48 - 49: 6.028 distance: 49 - 50: 16.360 distance: 49 - 52: 6.492 distance: 50 - 51: 38.914 distance: 50 - 56: 41.449 distance: 51 - 83: 3.030 distance: 52 - 53: 29.634 distance: 53 - 54: 28.219 distance: 53 - 55: 25.357 distance: 56 - 57: 7.672 distance: 57 - 58: 5.734 distance: 57 - 60: 43.275 distance: 58 - 59: 36.788 distance: 58 - 64: 14.694 distance: 59 - 92: 40.405 distance: 60 - 61: 34.056 distance: 61 - 62: 11.387 distance: 61 - 63: 13.381 distance: 64 - 65: 16.173 distance: 65 - 66: 17.794 distance: 65 - 68: 19.390 distance: 66 - 67: 29.018 distance: 66 - 72: 26.757 distance: 68 - 69: 18.483 distance: 68 - 70: 27.115 distance: 69 - 71: 18.712 distance: 72 - 73: 18.409 distance: 73 - 74: 24.025 distance: 73 - 76: 22.659 distance: 74 - 75: 35.986 distance: 74 - 83: 11.918 distance: 76 - 77: 44.959 distance: 77 - 78: 26.897 distance: 78 - 79: 8.916 distance: 79 - 80: 16.467 distance: 80 - 81: 19.930 distance: 80 - 82: 13.628 distance: 83 - 84: 16.305 distance: 84 - 85: 18.629 distance: 84 - 87: 13.550 distance: 85 - 86: 11.106 distance: 85 - 92: 6.276 distance: 87 - 88: 18.670 distance: 88 - 89: 28.538 distance: 89 - 90: 19.592 distance: 90 - 91: 21.107 distance: 92 - 93: 8.980 distance: 93 - 94: 14.602 distance: 93 - 96: 14.823 distance: 94 - 95: 7.077