Starting phenix.real_space_refine on Fri Aug 9 18:12:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6agb_9616/08_2024/6agb_9616_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6agb_9616/08_2024/6agb_9616.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6agb_9616/08_2024/6agb_9616.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6agb_9616/08_2024/6agb_9616.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6agb_9616/08_2024/6agb_9616_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6agb_9616/08_2024/6agb_9616_neut.cif" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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 1 6.06 5 P 369 5.49 5 S 99 5.16 5 C 15766 2.51 5 N 4818 2.21 5 O 6137 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 66": "NH1" <-> "NH2" Residue "B ARG 94": "NH1" <-> "NH2" Residue "B ARG 97": "NH1" <-> "NH2" Residue "B ARG 98": "NH1" <-> "NH2" Residue "B ARG 107": "NH1" <-> "NH2" Residue "B ARG 111": "NH1" <-> "NH2" Residue "B ARG 115": "NH1" <-> "NH2" Residue "B ARG 118": "NH1" <-> "NH2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B ARG 249": "NH1" <-> "NH2" Residue "B ARG 443": "NH1" <-> "NH2" Residue "B PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 584": "NH1" <-> "NH2" Residue "B PHE 740": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 760": "NH1" <-> "NH2" Residue "B ARG 858": "NH1" <-> "NH2" Residue "C PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 144": "NH1" <-> "NH2" Residue "C PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 175": "NH1" <-> "NH2" Residue "D ARG 3": "NH1" <-> "NH2" Residue "D ARG 90": "NH1" <-> "NH2" Residue "D ARG 245": "NH1" <-> "NH2" Residue "D ARG 256": "NH1" <-> "NH2" Residue "E ARG 37": "NH1" <-> "NH2" Residue "E ARG 87": "NH1" <-> "NH2" Residue "G TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 129": "NH1" <-> "NH2" Residue "H ARG 7": "NH1" <-> "NH2" Residue "I ARG 67": "NH1" <-> "NH2" Residue "I ARG 83": "NH1" <-> "NH2" Residue "I TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 178": "NH1" <-> "NH2" Residue "I ARG 182": "NH1" <-> "NH2" Residue "I ARG 237": "NH1" <-> "NH2" Residue "J ARG 67": "NH1" <-> "NH2" Residue "J ARG 83": "NH1" <-> "NH2" Residue "J TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 182": "NH1" <-> "NH2" Residue "K ARG 51": "NH1" <-> "NH2" Residue "K ARG 64": "NH1" <-> "NH2" Residue "K ARG 122": "NH1" <-> "NH2" Residue "K ARG 137": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 27190 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 7861 Classifications: {'RNA': 369} Modifications used: {'rna2p_pur': 29, 'rna2p_pyr': 22, 'rna3p_pur': 159, 'rna3p_pyr': 159} Link IDs: {'rna2p': 51, 'rna3p': 317} Chain: "B" Number of atoms: 6389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 784, 6389 Classifications: {'peptide': 784} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 35, 'TRANS': 748} Chain breaks: 4 Chain: "C" Number of atoms: 1435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1435 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 14, 'TRANS': 160} Chain: "D" Number of atoms: 1886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1886 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 7, 'TRANS': 219} Chain breaks: 1 Chain: "E" Number of atoms: 1141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1141 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 4, 'TRANS': 141} Chain: "F" Number of atoms: 1272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1272 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 153} Chain: "G" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 961 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain breaks: 1 Chain: "H" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1079 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 1, 'TRANS': 129} Chain: "I" Number of atoms: 1881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1881 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 9, 'TRANS': 232} Chain: "J" Number of atoms: 2260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2260 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 10, 'TRANS': 282} Chain: "K" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1024 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "K" 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 26766 SG CYS K 90 69.956 73.033 54.491 1.00 75.51 S ATOM 26963 SG CYS K 115 68.220 69.065 50.918 1.00 93.76 S ATOM 26973 SG CYS K 117 66.648 69.615 54.531 1.00 94.53 S Time building chain proxies: 15.00, per 1000 atoms: 0.55 Number of scatterers: 27190 At special positions: 0 Unit cell: (153.12, 121.44, 208.56, 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 1 29.99 S 99 16.00 P 369 15.00 O 6137 8.00 N 4818 7.00 C 15766 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: 12.18 Conformation dependent library (CDL) restraints added in 3.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 201 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 115 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 90 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 117 " 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4584 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 16 sheets defined 42.6% alpha, 16.8% beta 84 base pairs and 204 stacking pairs defined. Time for finding SS restraints: 9.60 Creating SS restraints... Processing helix chain 'B' and resid 58 through 85 removed outlier: 3.652A pdb=" N SER B 85 " --> pdb=" O LYS B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 92 removed outlier: 3.890A pdb=" N LEU B 92 " --> pdb=" O PHE B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 103 removed outlier: 3.800A pdb=" N SER B 102 " --> pdb=" O ARG B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 124 Processing helix chain 'B' and resid 145 through 166 removed outlier: 3.875A pdb=" N SER B 153 " --> pdb=" O LYS B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 177 removed outlier: 3.529A pdb=" N THR B 175 " --> pdb=" O PRO B 171 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER B 177 " --> pdb=" O GLU B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 198 removed outlier: 3.802A pdb=" N ILE B 192 " --> pdb=" O LEU B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 235 Processing helix chain 'B' and resid 242 through 249 removed outlier: 3.507A pdb=" N ARG B 249 " --> pdb=" O TRP B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 276 Processing helix chain 'B' and resid 307 through 318 removed outlier: 4.473A pdb=" N LYS B 311 " --> pdb=" O GLY B 307 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER B 312 " --> pdb=" O ASP B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 330 Processing helix chain 'B' and resid 371 through 385 Processing helix chain 'B' and resid 407 through 416 Processing helix chain 'B' and resid 422 through 432 removed outlier: 3.663A pdb=" N GLU B 426 " --> pdb=" O SER B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 456 Processing helix chain 'B' and resid 465 through 469 removed outlier: 3.986A pdb=" N LYS B 468 " --> pdb=" O SER B 465 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR B 469 " --> pdb=" O GLN B 466 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 465 through 469' Processing helix chain 'B' and resid 472 through 481 removed outlier: 3.663A pdb=" N HIS B 479 " --> pdb=" O ILE B 475 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU B 480 " --> pdb=" O LEU B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 496 removed outlier: 3.567A pdb=" N ILE B 487 " --> pdb=" O PRO B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 503 removed outlier: 3.803A pdb=" N ARG B 500 " --> pdb=" O ASP B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 506 No H-bonds generated for 'chain 'B' and resid 504 through 506' Processing helix chain 'B' and resid 509 through 524 Processing helix chain 'B' and resid 564 through 571 removed outlier: 3.658A pdb=" N LEU B 568 " --> pdb=" O TRP B 564 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU B 571 " --> pdb=" O PRO B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 593 Processing helix chain 'B' and resid 597 through 602 removed outlier: 3.793A pdb=" N TYR B 602 " --> pdb=" O PHE B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 627 Processing helix chain 'B' and resid 660 through 678 removed outlier: 3.847A pdb=" N LEU B 664 " --> pdb=" O ASP B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 718 removed outlier: 4.014A pdb=" N VAL B 706 " --> pdb=" O CYS B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 798 Processing helix chain 'B' and resid 816 through 818 No H-bonds generated for 'chain 'B' and resid 816 through 818' Processing helix chain 'B' and resid 844 through 850 removed outlier: 3.722A pdb=" N GLN B 850 " --> pdb=" O ALA B 846 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 32 Processing helix chain 'C' and resid 40 through 57 removed outlier: 4.155A pdb=" N GLN C 45 " --> pdb=" O PRO C 41 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LEU C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N HIS C 57 " --> pdb=" O ASN C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 79 Processing helix chain 'C' and resid 101 through 106 removed outlier: 3.646A pdb=" N LEU C 105 " --> pdb=" O PRO C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 112 removed outlier: 3.529A pdb=" N CYS C 112 " --> pdb=" O ILE C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 136 Processing helix chain 'C' and resid 150 through 158 removed outlier: 4.917A pdb=" N GLN C 156 " --> pdb=" O LYS C 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 10 removed outlier: 3.914A pdb=" N ASP D 10 " --> pdb=" O THR D 6 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 82 removed outlier: 3.632A pdb=" N ASN D 82 " --> pdb=" O TYR D 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 78 through 82' Processing helix chain 'D' and resid 84 through 111 Processing helix chain 'D' and resid 114 through 126 removed outlier: 3.665A pdb=" N HIS D 120 " --> pdb=" O GLU D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 131 removed outlier: 3.642A pdb=" N GLU D 131 " --> pdb=" O PRO D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 155 Proline residue: D 141 - end of helix removed outlier: 4.012A pdb=" N GLU D 145 " --> pdb=" O PRO D 141 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N LEU D 146 " --> pdb=" O MET D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 176 Processing helix chain 'D' and resid 256 through 261 Processing helix chain 'D' and resid 270 through 273 removed outlier: 3.958A pdb=" N MET D 273 " --> pdb=" O CYS D 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 270 through 273' Processing helix chain 'D' and resid 274 through 279 Processing helix chain 'E' and resid 27 through 36 Processing helix chain 'E' and resid 44 through 60 Processing helix chain 'E' and resid 62 through 69 Processing helix chain 'E' and resid 92 through 102 Processing helix chain 'E' and resid 122 through 147 removed outlier: 3.915A pdb=" N ILE E 126 " --> pdb=" O THR E 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 29 removed outlier: 3.911A pdb=" N CYS F 22 " --> pdb=" O SER F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 66 removed outlier: 3.648A pdb=" N LYS F 64 " --> pdb=" O ASN F 60 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE F 66 " --> pdb=" O LEU F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 101 removed outlier: 3.851A pdb=" N PHE F 98 " --> pdb=" O ILE F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 106 removed outlier: 3.541A pdb=" N ASN F 105 " --> pdb=" O TYR F 102 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN F 106 " --> pdb=" O ILE F 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 102 through 106' Processing helix chain 'G' and resid 40 through 59 removed outlier: 4.543A pdb=" N HIS G 56 " --> pdb=" O LEU G 52 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N LYS G 57 " --> pdb=" O ASP G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 83 removed outlier: 3.866A pdb=" N GLN G 83 " --> pdb=" O GLY G 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 27 removed outlier: 3.651A pdb=" N ASP H 24 " --> pdb=" O ASP H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 45 removed outlier: 3.550A pdb=" N TRP H 34 " --> pdb=" O ASP H 30 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG H 35 " --> pdb=" O GLN H 31 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER H 45 " --> pdb=" O ALA H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 52 Processing helix chain 'H' and resid 73 through 82 removed outlier: 4.161A pdb=" N SER H 80 " --> pdb=" O THR H 76 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N SER H 82 " --> pdb=" O SER H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 133 removed outlier: 3.807A pdb=" N ASP H 129 " --> pdb=" O GLU H 125 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 37 removed outlier: 3.702A pdb=" N VAL I 23 " --> pdb=" O THR I 19 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY I 37 " --> pdb=" O LEU I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 68 through 76 removed outlier: 4.461A pdb=" N LEU I 72 " --> pdb=" O ARG I 68 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP I 74 " --> pdb=" O GLY I 70 " (cutoff:3.500A) Processing helix chain 'I' and resid 99 through 104 removed outlier: 3.694A pdb=" N ALA I 103 " --> pdb=" O LYS I 99 " (cutoff:3.500A) Processing helix chain 'I' and resid 113 through 123 removed outlier: 3.643A pdb=" N THR I 118 " --> pdb=" O GLU I 114 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 151 removed outlier: 3.742A pdb=" N ILE I 146 " --> pdb=" O LYS I 142 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER I 148 " --> pdb=" O LYS I 144 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N CYS I 149 " --> pdb=" O SER I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 161 through 165 removed outlier: 3.746A pdb=" N LEU I 164 " --> pdb=" O GLY I 161 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG I 165 " --> pdb=" O TYR I 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 161 through 165' Processing helix chain 'I' and resid 167 through 185 removed outlier: 4.335A pdb=" N ARG I 171 " --> pdb=" O VAL I 167 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLN I 172 " --> pdb=" O GLN I 168 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG I 185 " --> pdb=" O ILE I 181 " (cutoff:3.500A) Processing helix chain 'I' and resid 197 through 201 removed outlier: 4.177A pdb=" N CYS I 201 " --> pdb=" O PRO I 198 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 215 Processing helix chain 'I' and resid 217 through 242 removed outlier: 4.540A pdb=" N ALA I 229 " --> pdb=" O MET I 225 " (cutoff:3.500A) Processing helix chain 'J' and resid 19 through 36 removed outlier: 3.588A pdb=" N VAL J 23 " --> pdb=" O THR J 19 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU J 36 " --> pdb=" O THR J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 68 through 77 removed outlier: 3.982A pdb=" N ASP J 74 " --> pdb=" O GLY J 70 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ARG J 75 " --> pdb=" O GLU J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 104 removed outlier: 4.032A pdb=" N GLN J 102 " --> pdb=" O SER J 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 123 removed outlier: 3.746A pdb=" N LEU J 117 " --> pdb=" O SER J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 153 removed outlier: 3.703A pdb=" N ILE J 146 " --> pdb=" O LYS J 142 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 165 removed outlier: 3.537A pdb=" N ARG J 165 " --> pdb=" O TYR J 162 " (cutoff:3.500A) Processing helix chain 'J' and resid 168 through 184 removed outlier: 4.079A pdb=" N GLN J 172 " --> pdb=" O GLN J 168 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER J 179 " --> pdb=" O SER J 175 " (cutoff:3.500A) Processing helix chain 'J' and resid 197 through 201 removed outlier: 3.660A pdb=" N GLU J 200 " --> pdb=" O SER J 197 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N CYS J 201 " --> pdb=" O PRO J 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 197 through 201' Processing helix chain 'J' and resid 203 through 215 Processing helix chain 'J' and resid 217 through 227 Processing helix chain 'J' and resid 227 through 241 removed outlier: 3.702A pdb=" N VAL J 232 " --> pdb=" O LEU J 228 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY J 236 " --> pdb=" O VAL J 232 " (cutoff:3.500A) Processing helix chain 'K' and resid 27 through 55 removed outlier: 3.985A pdb=" N ALA K 54 " --> pdb=" O ALA K 50 " (cutoff:3.500A) Processing helix chain 'K' and resid 59 through 77 removed outlier: 3.849A pdb=" N ALA K 63 " --> pdb=" O HIS K 59 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ARG K 64 " --> pdb=" O THR K 60 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASN K 65 " --> pdb=" O PRO K 61 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR K 66 " --> pdb=" O LEU K 62 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 89 removed outlier: 3.549A pdb=" N LYS K 86 " --> pdb=" O LEU K 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 216 through 217 removed outlier: 4.038A pdb=" N GLY B 216 " --> pdb=" O ASP B 393 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP B 393 " --> pdb=" O GLY B 216 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N THR B 295 " --> pdb=" O CYS B 394 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N SER B 340 " --> pdb=" O PRO B 352 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 250 through 253 removed outlier: 6.847A pdb=" N HIS B 251 " --> pdb=" O TRP B 262 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 445 through 450 removed outlier: 3.672A pdb=" N VAL B 546 " --> pdb=" O VAL B 559 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N SER B 400 " --> pdb=" O SER B 290 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 762 through 769 removed outlier: 4.835A pdb=" N GLY B 836 " --> pdb=" O LEU B 769 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET B 837 " --> pdb=" O THR B 828 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR B 828 " --> pdb=" O MET B 837 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE B 839 " --> pdb=" O SER B 826 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N SER B 826 " --> pdb=" O ILE B 839 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N PHE B 841 " --> pdb=" O ILE B 824 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE B 824 " --> pdb=" O PHE B 841 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N ASP B 843 " --> pdb=" O GLY B 822 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N GLY B 822 " --> pdb=" O ASP B 843 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE B 781 " --> pdb=" O ILE B 821 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N PHE B 823 " --> pdb=" O ALA B 779 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ALA B 779 " --> pdb=" O PHE B 823 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU B 856 " --> pdb=" O TYR B 782 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'K' and resid 18 through 19 removed outlier: 4.001A pdb=" N THR K 19 " --> pdb=" O ARG C 15 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLN C 17 " --> pdb=" O THR K 19 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 68 through 69 Processing sheet with id=AA7, first strand: chain 'D' and resid 197 through 199 removed outlier: 7.950A pdb=" N LEU D 183 " --> pdb=" O GLU D 233 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N GLU D 233 " --> pdb=" O LEU D 183 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N VAL D 185 " --> pdb=" O GLN D 231 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLN D 231 " --> pdb=" O VAL D 185 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 207 through 211 Processing sheet with id=AA9, first strand: chain 'E' and resid 73 through 78 removed outlier: 3.559A pdb=" N GLN E 73 " --> pdb=" O ARG E 87 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE E 85 " --> pdb=" O LYS E 75 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N PHE E 77 " --> pdb=" O THR E 83 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N THR E 83 " --> pdb=" O PHE E 77 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS E 118 " --> pdb=" O LEU E 10 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N GLU E 12 " --> pdb=" O PRO E 116 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE E 14 " --> pdb=" O VAL E 114 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N VAL E 114 " --> pdb=" O ILE E 14 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 10 through 12 removed outlier: 4.332A pdb=" N VAL F 5 " --> pdb=" O ARG F 12 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY F 4 " --> pdb=" O LYS F 121 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 10 through 12 removed outlier: 4.332A pdb=" N VAL F 5 " --> pdb=" O ARG F 12 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY F 4 " --> pdb=" O LYS F 121 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 15 through 17 removed outlier: 6.540A pdb=" N ILE G 33 " --> pdb=" O LEU G 66 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N MET G 68 " --> pdb=" O ILE G 33 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 55 through 61 removed outlier: 8.809A pdb=" N TYR H 55 " --> pdb=" O ASN H 70 " (cutoff:3.500A) removed outlier: 8.851A pdb=" N ASN H 70 " --> pdb=" O TYR H 55 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N PHE H 57 " --> pdb=" O ARG H 68 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ARG H 68 " --> pdb=" O PHE H 57 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N HIS H 59 " --> pdb=" O TYR H 66 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N TYR H 66 " --> pdb=" O HIS H 59 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N TYR H 11 " --> pdb=" O GLU H 102 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N GLU H 102 " --> pdb=" O TYR H 11 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N LYS H 13 " --> pdb=" O LEU H 100 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 3 through 8 removed outlier: 4.605A pdb=" N VAL I 3 " --> pdb=" O HIS I 40 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N ALA I 42 " --> pdb=" O VAL I 3 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU I 5 " --> pdb=" O ALA I 42 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ASN I 44 " --> pdb=" O LEU I 5 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N VAL I 7 " --> pdb=" O ASN I 44 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N THR I 46 " --> pdb=" O VAL I 7 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE I 41 " --> pdb=" O TYR I 81 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N ARG I 83 " --> pdb=" O ILE I 41 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE I 43 " --> pdb=" O ARG I 83 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N THR I 85 " --> pdb=" O ILE I 43 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N PHE I 45 " --> pdb=" O THR I 85 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N ILE I 87 " --> pdb=" O PHE I 45 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N VAL I 47 " --> pdb=" O ILE I 87 " (cutoff:3.500A) removed outlier: 9.763A pdb=" N ILE I 106 " --> pdb=" O LEU I 80 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N SER I 82 " --> pdb=" O ILE I 106 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N ALA I 108 " --> pdb=" O SER I 82 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ILE I 84 " --> pdb=" O ALA I 108 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N LEU I 110 " --> pdb=" O ILE I 84 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU I 86 " --> pdb=" O LEU I 110 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL I 107 " --> pdb=" O LEU I 128 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N THR I 130 " --> pdb=" O VAL I 107 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ALA I 109 " --> pdb=" O THR I 130 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LEU I 156 " --> pdb=" O VAL I 190 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N GLY I 192 " --> pdb=" O LEU I 156 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ILE I 158 " --> pdb=" O GLY I 192 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 3 through 8 removed outlier: 4.313A pdb=" N VAL J 3 " --> pdb=" O HIS J 40 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ALA J 42 " --> pdb=" O VAL J 3 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LEU J 5 " --> pdb=" O ALA J 42 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ASN J 44 " --> pdb=" O LEU J 5 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N VAL J 7 " --> pdb=" O ASN J 44 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N THR J 46 " --> pdb=" O VAL J 7 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ILE J 41 " --> pdb=" O TYR J 81 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N ARG J 83 " --> pdb=" O ILE J 41 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE J 43 " --> pdb=" O ARG J 83 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N THR J 85 " --> pdb=" O ILE J 43 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N PHE J 45 " --> pdb=" O THR J 85 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ILE J 87 " --> pdb=" O PHE J 45 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N VAL J 47 " --> pdb=" O ILE J 87 " (cutoff:3.500A) removed outlier: 9.379A pdb=" N ILE J 106 " --> pdb=" O LEU J 80 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N SER J 82 " --> pdb=" O ILE J 106 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N ALA J 108 " --> pdb=" O SER J 82 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ILE J 84 " --> pdb=" O ALA J 108 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL J 107 " --> pdb=" O LEU J 128 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N THR J 130 " --> pdb=" O VAL J 107 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N ALA J 109 " --> pdb=" O THR J 130 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU J 156 " --> pdb=" O VAL J 190 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N GLY J 192 " --> pdb=" O LEU J 156 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ILE J 158 " --> pdb=" O GLY J 192 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 102 through 105 removed outlier: 3.528A pdb=" N LYS K 102 " --> pdb=" O MET K 114 " (cutoff:3.500A) 793 hydrogen bonds defined for protein. 2304 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 219 hydrogen bonds 422 hydrogen bond angles 0 basepair planarities 84 basepair parallelities 204 stacking parallelities Total time for adding SS restraints: 11.57 Time building geometry restraints manager: 13.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5628 1.33 - 1.45: 8247 1.45 - 1.58: 13706 1.58 - 1.70: 737 1.70 - 1.82: 150 Bond restraints: 28468 Sorted by residual: bond pdb=" C ILE C 108 " pdb=" N PRO C 109 " ideal model delta sigma weight residual 1.337 1.388 -0.051 1.11e-02 8.12e+03 2.13e+01 bond pdb=" C PHE B 598 " pdb=" N PRO B 599 " ideal model delta sigma weight residual 1.336 1.380 -0.044 1.25e-02 6.40e+03 1.22e+01 bond pdb=" C PRO K 24 " pdb=" N PRO K 25 " ideal model delta sigma weight residual 1.334 1.406 -0.072 2.34e-02 1.83e+03 9.45e+00 bond pdb=" N GLN B 331 " pdb=" CA GLN B 331 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.29e-02 6.01e+03 4.34e+00 bond pdb=" C ASP C 87 " pdb=" N PRO C 88 " ideal model delta sigma weight residual 1.334 1.382 -0.048 2.34e-02 1.83e+03 4.24e+00 ... (remaining 28463 not shown) Histogram of bond angle deviations from ideal: 99.10 - 106.46: 2609 106.46 - 113.81: 16732 113.81 - 121.16: 13368 121.16 - 128.52: 7017 128.52 - 135.87: 502 Bond angle restraints: 40228 Sorted by residual: angle pdb=" N ILE I 112 " pdb=" CA ILE I 112 " pdb=" C ILE I 112 " ideal model delta sigma weight residual 113.10 105.97 7.13 9.70e-01 1.06e+00 5.40e+01 angle pdb=" C VAL B 361 " pdb=" N GLN B 362 " pdb=" CA GLN B 362 " ideal model delta sigma weight residual 121.54 131.50 -9.96 1.91e+00 2.74e-01 2.72e+01 angle pdb=" N ASN D 215 " pdb=" CA ASN D 215 " pdb=" C ASN D 215 " ideal model delta sigma weight residual 111.14 106.00 5.14 1.08e+00 8.57e-01 2.26e+01 angle pdb=" N VAL H 111 " pdb=" CA VAL H 111 " pdb=" C VAL H 111 " ideal model delta sigma weight residual 108.82 103.02 5.80 1.22e+00 6.72e-01 2.26e+01 angle pdb=" C3' U A 266 " pdb=" O3' U A 266 " pdb=" P U A 267 " ideal model delta sigma weight residual 120.20 127.25 -7.05 1.50e+00 4.44e-01 2.21e+01 ... (remaining 40223 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.97: 16809 34.97 - 69.93: 965 69.93 - 104.90: 114 104.90 - 139.87: 2 139.87 - 174.84: 9 Dihedral angle restraints: 17899 sinusoidal: 10844 harmonic: 7055 Sorted by residual: dihedral pdb=" C4' A A 191 " pdb=" C3' A A 191 " pdb=" C2' A A 191 " pdb=" C1' A A 191 " ideal model delta sinusoidal sigma weight residual -35.00 35.90 -70.90 1 8.00e+00 1.56e-02 1.01e+02 dihedral pdb=" O4' A A 191 " pdb=" C2' A A 191 " pdb=" C1' A A 191 " pdb=" C3' A A 191 " ideal model delta sinusoidal sigma weight residual -35.00 33.56 -68.56 1 8.00e+00 1.56e-02 9.52e+01 dihedral pdb=" O4' U A 329 " pdb=" C1' U A 329 " pdb=" N1 U A 329 " pdb=" C2 U A 329 " ideal model delta sinusoidal sigma weight residual 200.00 43.12 156.88 1 1.50e+01 4.44e-03 8.19e+01 ... (remaining 17896 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 4422 0.076 - 0.152: 383 0.152 - 0.227: 43 0.227 - 0.303: 2 0.303 - 0.379: 2 Chirality restraints: 4852 Sorted by residual: chirality pdb=" C3' A A 367 " pdb=" C4' A A 367 " pdb=" O3' A A 367 " pdb=" C2' A A 367 " both_signs ideal model delta sigma weight residual False -2.74 -2.37 -0.38 2.00e-01 2.50e+01 3.59e+00 chirality pdb=" C3' G A 179 " pdb=" C4' G A 179 " pdb=" O3' G A 179 " pdb=" C2' G A 179 " both_signs ideal model delta sigma weight residual False -2.48 -2.17 -0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" C3' U A 266 " pdb=" C4' U A 266 " pdb=" O3' U A 266 " pdb=" C2' U A 266 " both_signs ideal model delta sigma weight residual False -2.74 -2.45 -0.30 2.00e-01 2.50e+01 2.21e+00 ... (remaining 4849 not shown) Planarity restraints: 3725 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 728 " -0.051 5.00e-02 4.00e+02 7.75e-02 9.62e+00 pdb=" N PRO B 729 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO B 729 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 729 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 44 " 0.018 2.00e-02 2.50e+03 1.79e-02 7.99e+00 pdb=" CG TRP C 44 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP C 44 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP C 44 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 44 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 44 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 44 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 44 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 44 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP C 44 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 543 " -0.045 5.00e-02 4.00e+02 6.90e-02 7.63e+00 pdb=" N PRO B 544 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO B 544 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 544 " -0.038 5.00e-02 4.00e+02 ... (remaining 3722 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 93 2.48 - 3.09: 15839 3.09 - 3.69: 42272 3.69 - 4.30: 61659 4.30 - 4.90: 93355 Nonbonded interactions: 213218 Sorted by model distance: nonbonded pdb=" O2' A A 191 " pdb=" OP1 C A 192 " model vdw 1.877 3.040 nonbonded pdb=" O2' C A 151 " pdb=" OP1 U A 190 " model vdw 1.911 3.040 nonbonded pdb=" O2' G A 96 " pdb=" O2 U A 158 " model vdw 2.251 3.040 nonbonded pdb=" O LEU J 238 " pdb=" OG SER J 242 " model vdw 2.266 3.040 nonbonded pdb=" O2' U A 363 " pdb=" O CYS D 222 " model vdw 2.272 3.040 ... (remaining 213213 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 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 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: 0.830 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: 0.020 Extract box with map and model: 1.060 Check model and map are aligned: 0.200 Set scattering table: 0.260 Process input model: 82.590 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 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 0.072 28468 Z= 0.210 Angle : 0.838 12.614 40228 Z= 0.487 Chirality : 0.044 0.379 4852 Planarity : 0.006 0.078 3725 Dihedral : 18.493 174.837 13315 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.86 % Favored : 94.06 % Rotamer: Outliers : 0.18 % Allowed : 3.20 % Favored : 96.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.53 (0.14), residues: 2372 helix: -2.63 (0.12), residues: 896 sheet: -0.72 (0.24), residues: 426 loop : -2.70 (0.16), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP C 44 HIS 0.006 0.001 HIS B 273 PHE 0.030 0.002 PHE K 34 TYR 0.029 0.002 TYR B 597 ARG 0.008 0.001 ARG B 113 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 930 residues out of total 2189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 926 time to evaluate : 2.639 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: B 79 ASN cc_start: 0.7554 (t160) cc_final: 0.7334 (t0) REVERT: B 146 GLN cc_start: 0.8079 (pt0) cc_final: 0.7530 (pt0) REVERT: B 217 VAL cc_start: 0.7608 (t) cc_final: 0.7302 (m) REVERT: B 311 LYS cc_start: 0.7498 (ttpt) cc_final: 0.6899 (mmtt) REVERT: B 342 ASN cc_start: 0.7845 (t0) cc_final: 0.7634 (t0) REVERT: B 452 ASP cc_start: 0.7214 (t0) cc_final: 0.5147 (t70) REVERT: B 588 GLN cc_start: 0.8278 (tt0) cc_final: 0.7956 (tt0) REVERT: C 19 TYR cc_start: 0.8022 (m-80) cc_final: 0.7685 (m-10) REVERT: C 91 LEU cc_start: 0.8290 (tp) cc_final: 0.8059 (tp) REVERT: C 97 ASP cc_start: 0.7371 (t0) cc_final: 0.6370 (t70) REVERT: C 103 VAL cc_start: 0.7941 (t) cc_final: 0.7669 (t) REVERT: C 118 THR cc_start: 0.6400 (m) cc_final: 0.6158 (m) REVERT: D 199 ILE cc_start: 0.8045 (mp) cc_final: 0.7776 (mt) REVERT: E 57 SER cc_start: 0.7418 (m) cc_final: 0.7014 (p) REVERT: G 41 TYR cc_start: 0.8703 (t80) cc_final: 0.8368 (t80) REVERT: G 76 LEU cc_start: 0.8774 (mt) cc_final: 0.8102 (mp) REVERT: G 98 GLU cc_start: 0.7308 (mm-30) cc_final: 0.7080 (tp30) REVERT: H 39 ASN cc_start: 0.8017 (m110) cc_final: 0.7663 (m-40) REVERT: H 55 TYR cc_start: 0.7847 (p90) cc_final: 0.7645 (p90) REVERT: H 120 LYS cc_start: 0.7962 (tttt) cc_final: 0.7585 (tptp) REVERT: I 157 GLU cc_start: 0.7520 (tm-30) cc_final: 0.7132 (tm-30) REVERT: I 159 VAL cc_start: 0.9195 (t) cc_final: 0.8872 (t) REVERT: J 191 ILE cc_start: 0.9206 (pt) cc_final: 0.8986 (pt) REVERT: K 134 TYR cc_start: 0.8083 (t80) cc_final: 0.7763 (t80) outliers start: 4 outliers final: 0 residues processed: 929 average time/residue: 0.4659 time to fit residues: 636.9443 Evaluate side-chains 492 residues out of total 2189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 492 time to evaluate : 2.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 229 optimal weight: 0.8980 chunk 206 optimal weight: 4.9990 chunk 114 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 139 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 213 optimal weight: 4.9990 chunk 82 optimal weight: 7.9990 chunk 129 optimal weight: 0.0570 chunk 158 optimal weight: 0.7980 chunk 247 optimal weight: 5.9990 overall best weight: 1.3502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 ASN B 90 GLN B 146 GLN ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 HIS B 251 HIS B 259 GLN B 266 GLN ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 392 GLN B 463 ASN ** B 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 488 ASN B 505 ASN B 590 GLN B 642 HIS B 665 GLN B 675 GLN B 677 ASN B 704 ASN B 803 ASN B 808 HIS C 25 ASN C 40 GLN C 48 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 GLN ** C 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 5 GLN D 95 ASN D 197 GLN E 50 GLN E 59 ASN ** E 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 8 ASN F 37 ASN F 54 ASN F 76 GLN F 87 HIS G 28 GLN G 58 GLN H 40 ASN I 12 ASN I 34 HIS I 49 HIS I 143 HIS I 151 ASN I 172 GLN I 203 ASN J 95 GLN ** J 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 HIS K 42 GLN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.3963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 28468 Z= 0.227 Angle : 0.664 12.675 40228 Z= 0.339 Chirality : 0.039 0.294 4852 Planarity : 0.006 0.068 3725 Dihedral : 21.037 173.929 8400 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.69 % Favored : 94.22 % Rotamer: Outliers : 3.52 % Allowed : 14.07 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.94 (0.16), residues: 2372 helix: -0.74 (0.16), residues: 934 sheet: -0.58 (0.24), residues: 452 loop : -2.10 (0.18), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 256 HIS 0.010 0.002 HIS I 49 PHE 0.025 0.002 PHE J 104 TYR 0.019 0.002 TYR F 7 ARG 0.012 0.001 ARG B 780 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 2189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 542 time to evaluate : 2.427 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: B 79 ASN cc_start: 0.7973 (t0) cc_final: 0.7398 (t0) REVERT: B 146 GLN cc_start: 0.8115 (pt0) cc_final: 0.7737 (pt0) REVERT: B 201 ASN cc_start: 0.7091 (t0) cc_final: 0.6796 (t0) REVERT: B 225 LYS cc_start: 0.6665 (mtmt) cc_final: 0.6290 (mtmt) REVERT: B 282 SER cc_start: 0.8476 (m) cc_final: 0.8222 (p) REVERT: B 311 LYS cc_start: 0.7868 (ttpt) cc_final: 0.7329 (mmtt) REVERT: B 461 LYS cc_start: 0.7945 (tptp) cc_final: 0.7478 (ttmm) REVERT: B 463 ASN cc_start: 0.6595 (OUTLIER) cc_final: 0.6060 (m-40) REVERT: B 588 GLN cc_start: 0.8758 (tt0) cc_final: 0.8507 (tt0) REVERT: B 632 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7854 (ptt90) REVERT: B 650 SER cc_start: 0.6298 (p) cc_final: 0.6085 (p) REVERT: B 665 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.7709 (pp30) REVERT: B 756 THR cc_start: 0.5844 (OUTLIER) cc_final: 0.5441 (t) REVERT: B 765 VAL cc_start: 0.8042 (m) cc_final: 0.7536 (m) REVERT: B 803 ASN cc_start: 0.8615 (t160) cc_final: 0.8388 (t0) REVERT: B 819 ASP cc_start: 0.7351 (m-30) cc_final: 0.7133 (m-30) REVERT: C 70 THR cc_start: 0.8133 (p) cc_final: 0.7448 (m) REVERT: C 123 GLN cc_start: 0.6681 (tm-30) cc_final: 0.6342 (tm-30) REVERT: C 147 ASP cc_start: 0.6291 (p0) cc_final: 0.5756 (p0) REVERT: D 109 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7375 (mm-30) REVERT: E 8 TYR cc_start: 0.7776 (m-80) cc_final: 0.7552 (m-80) REVERT: E 57 SER cc_start: 0.7908 (m) cc_final: 0.7486 (p) REVERT: F 82 PHE cc_start: 0.8210 (p90) cc_final: 0.7941 (p90) REVERT: F 122 ARG cc_start: 0.7104 (ptm160) cc_final: 0.6849 (ptm160) REVERT: G 98 GLU cc_start: 0.7299 (mm-30) cc_final: 0.7079 (tp30) REVERT: H 49 PHE cc_start: 0.7972 (m-80) cc_final: 0.7746 (m-80) REVERT: H 51 GLU cc_start: 0.7337 (tp30) cc_final: 0.7124 (tp30) REVERT: H 120 LYS cc_start: 0.7892 (tttt) cc_final: 0.7476 (tptp) REVERT: I 5 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7348 (pp) REVERT: I 79 LYS cc_start: 0.6439 (pmmt) cc_final: 0.5711 (ptpp) REVERT: I 157 GLU cc_start: 0.7893 (tm-30) cc_final: 0.7472 (tm-30) REVERT: I 238 LEU cc_start: 0.7130 (mt) cc_final: 0.6596 (pp) REVERT: J 95 GLN cc_start: 0.6067 (mt0) cc_final: 0.5751 (pt0) REVERT: J 222 SER cc_start: 0.6832 (m) cc_final: 0.6375 (p) REVERT: J 279 MET cc_start: 0.7775 (mtp) cc_final: 0.7334 (mtp) REVERT: K 42 GLN cc_start: 0.8419 (tt0) cc_final: 0.8152 (mt0) REVERT: K 134 TYR cc_start: 0.8546 (t80) cc_final: 0.8218 (t80) outliers start: 77 outliers final: 40 residues processed: 596 average time/residue: 0.4056 time to fit residues: 374.0218 Evaluate side-chains 460 residues out of total 2189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 415 time to evaluate : 4.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 463 ASN Chi-restraints excluded: chain B residue 552 LYS Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 632 ARG Chi-restraints excluded: chain B residue 665 GLN Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 774 HIS Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain D residue 105 LYS Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 264 LYS Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 50 GLN Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 88 CYS Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 21 GLN Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 132 ARG Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain H residue 9 TRP Chi-restraints excluded: chain H residue 24 ASP Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain I residue 49 HIS Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 56 ASP Chi-restraints excluded: chain J residue 82 SER Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 143 HIS Chi-restraints excluded: chain J residue 230 SER Chi-restraints excluded: chain K residue 35 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 137 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 205 optimal weight: 5.9990 chunk 168 optimal weight: 9.9990 chunk 68 optimal weight: 5.9990 chunk 247 optimal weight: 0.8980 chunk 267 optimal weight: 8.9990 chunk 220 optimal weight: 0.6980 chunk 245 optimal weight: 6.9990 chunk 84 optimal weight: 0.5980 chunk 198 optimal weight: 4.9990 overall best weight: 2.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 442 GLN B 803 ASN ** C 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 ASN ** E 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN H 27 HIS H 40 ASN I 143 HIS J 213 ASN J 261 ASN J 264 GLN K 30 ASN K 94 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.5949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 28468 Z= 0.340 Angle : 0.723 10.114 40228 Z= 0.371 Chirality : 0.042 0.230 4852 Planarity : 0.006 0.073 3725 Dihedral : 20.889 175.230 8400 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.82 % Favored : 94.14 % Rotamer: Outliers : 4.84 % Allowed : 16.45 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.27 (0.17), residues: 2372 helix: -0.01 (0.17), residues: 939 sheet: -0.45 (0.24), residues: 441 loop : -1.79 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 9 HIS 0.063 0.003 HIS I 49 PHE 0.032 0.003 PHE B 657 TYR 0.024 0.003 TYR D 150 ARG 0.010 0.001 ARG B 780 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 2189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 469 time to evaluate : 2.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 ASN cc_start: 0.8197 (t0) cc_final: 0.7568 (t0) REVERT: B 225 LYS cc_start: 0.7635 (mtmt) cc_final: 0.7395 (mtmt) REVERT: B 311 LYS cc_start: 0.8063 (ttpt) cc_final: 0.7402 (mmtt) REVERT: B 389 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8225 (pp) REVERT: B 543 ILE cc_start: 0.9091 (pt) cc_final: 0.8852 (pt) REVERT: B 632 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.8134 (ptt90) REVERT: B 650 SER cc_start: 0.7279 (p) cc_final: 0.7006 (p) REVERT: B 655 ASP cc_start: 0.7974 (t70) cc_final: 0.7566 (t0) REVERT: B 714 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7591 (tt0) REVERT: B 819 ASP cc_start: 0.8130 (m-30) cc_final: 0.7816 (m-30) REVERT: C 29 ASN cc_start: 0.7747 (p0) cc_final: 0.6923 (p0) REVERT: C 70 THR cc_start: 0.8407 (p) cc_final: 0.7960 (m) REVERT: C 73 ASN cc_start: 0.7133 (OUTLIER) cc_final: 0.5725 (m110) REVERT: C 123 GLN cc_start: 0.7283 (tm-30) cc_final: 0.6688 (tm-30) REVERT: C 131 THR cc_start: 0.8866 (OUTLIER) cc_final: 0.8646 (p) REVERT: D 277 ILE cc_start: 0.6997 (mm) cc_final: 0.6506 (mm) REVERT: E 57 SER cc_start: 0.8284 (m) cc_final: 0.7969 (p) REVERT: F 68 MET cc_start: 0.7266 (ppp) cc_final: 0.4778 (mmp) REVERT: F 122 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7599 (ptm160) REVERT: H 36 GLN cc_start: 0.8612 (tm-30) cc_final: 0.8308 (tp40) REVERT: H 39 ASN cc_start: 0.8842 (m110) cc_final: 0.8149 (m110) REVERT: I 5 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8051 (pp) REVERT: I 157 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7839 (tt0) REVERT: I 186 SER cc_start: 0.8788 (m) cc_final: 0.8541 (t) outliers start: 106 outliers final: 62 residues processed: 542 average time/residue: 0.3743 time to fit residues: 320.2603 Evaluate side-chains 435 residues out of total 2189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 367 time to evaluate : 2.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 552 LYS Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 632 ARG Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 774 HIS Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 143 TYR Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 88 CYS Chi-restraints excluded: chain E residue 103 MET Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain F residue 21 GLN Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 122 ARG Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 135 GLU Chi-restraints excluded: chain H residue 9 TRP Chi-restraints excluded: chain H residue 24 ASP Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 80 SER Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 112 ILE Chi-restraints excluded: chain I residue 149 CYS Chi-restraints excluded: chain I residue 166 ASP Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 213 ASN Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 82 SER Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 126 ILE Chi-restraints excluded: chain J residue 143 HIS Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain J residue 232 VAL Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 119 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 244 optimal weight: 3.9990 chunk 186 optimal weight: 0.2980 chunk 128 optimal weight: 2.9990 chunk 27 optimal weight: 9.9990 chunk 118 optimal weight: 8.9990 chunk 166 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 chunk 262 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 235 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 392 GLN ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 588 GLN B 665 GLN B 669 ASN ** B 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 803 ASN ** B 844 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 GLN D 126 HIS ** E 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 GLN F 153 HIS H 27 HIS I 44 ASN J 40 HIS ** J 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 255 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.6756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 28468 Z= 0.261 Angle : 0.640 11.701 40228 Z= 0.327 Chirality : 0.040 0.210 4852 Planarity : 0.005 0.063 3725 Dihedral : 20.802 174.641 8400 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 4.93 % Allowed : 19.60 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.17), residues: 2372 helix: 0.40 (0.17), residues: 954 sheet: -0.48 (0.24), residues: 436 loop : -1.75 (0.19), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 9 HIS 0.009 0.002 HIS I 49 PHE 0.035 0.002 PHE B 740 TYR 0.021 0.002 TYR K 66 ARG 0.009 0.001 ARG D 252 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 2189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 414 time to evaluate : 2.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 ASN cc_start: 0.8063 (t0) cc_final: 0.7702 (t0) REVERT: B 201 ASN cc_start: 0.7256 (t0) cc_final: 0.6982 (t0) REVERT: B 311 LYS cc_start: 0.8155 (ttpt) cc_final: 0.7374 (mmtt) REVERT: B 650 SER cc_start: 0.7114 (p) cc_final: 0.6850 (p) REVERT: B 655 ASP cc_start: 0.7864 (OUTLIER) cc_final: 0.7658 (t0) REVERT: B 757 PHE cc_start: 0.7500 (t80) cc_final: 0.7225 (t80) REVERT: B 819 ASP cc_start: 0.8233 (m-30) cc_final: 0.7869 (m-30) REVERT: C 70 THR cc_start: 0.8435 (p) cc_final: 0.8184 (m) REVERT: D 194 ILE cc_start: 0.8582 (pt) cc_final: 0.8350 (mt) REVERT: D 233 GLU cc_start: 0.8524 (mp0) cc_final: 0.8270 (mp0) REVERT: D 277 ILE cc_start: 0.7599 (mm) cc_final: 0.7321 (mm) REVERT: E 8 TYR cc_start: 0.8294 (m-80) cc_final: 0.7924 (m-80) REVERT: E 54 ARG cc_start: 0.8518 (ptp-110) cc_final: 0.8302 (ptp-110) REVERT: E 57 SER cc_start: 0.8546 (m) cc_final: 0.8149 (p) REVERT: F 68 MET cc_start: 0.7208 (ppp) cc_final: 0.4684 (mmp) REVERT: F 106 ASN cc_start: 0.8040 (t0) cc_final: 0.7733 (t0) REVERT: G 28 GLN cc_start: 0.8884 (tt0) cc_final: 0.8649 (mt0) REVERT: G 68 MET cc_start: 0.8603 (ptm) cc_final: 0.8207 (ptt) REVERT: H 36 GLN cc_start: 0.8615 (tm-30) cc_final: 0.8335 (tp40) REVERT: I 5 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8078 (pp) REVERT: I 157 GLU cc_start: 0.8300 (tm-30) cc_final: 0.7884 (tt0) REVERT: J 95 GLN cc_start: 0.6364 (mt0) cc_final: 0.6049 (pt0) REVERT: J 212 LYS cc_start: 0.8538 (mmmt) cc_final: 0.8285 (mtmm) REVERT: J 222 SER cc_start: 0.7529 (m) cc_final: 0.7076 (p) outliers start: 108 outliers final: 73 residues processed: 489 average time/residue: 0.3825 time to fit residues: 295.9519 Evaluate side-chains 434 residues out of total 2189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 359 time to evaluate : 2.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 339 TYR Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 600 ASP Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain B residue 655 ASP Chi-restraints excluded: chain B residue 665 GLN Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 774 HIS Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain C residue 45 GLN Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 9 TRP Chi-restraints excluded: chain H residue 24 ASP Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 81 ILE Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 44 ASN Chi-restraints excluded: chain I residue 112 ILE Chi-restraints excluded: chain I residue 149 CYS Chi-restraints excluded: chain I residue 166 ASP Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 191 ILE Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 82 SER Chi-restraints excluded: chain J residue 112 ILE Chi-restraints excluded: chain J residue 143 HIS Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain J residue 272 ILE Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 119 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 218 optimal weight: 5.9990 chunk 149 optimal weight: 0.0970 chunk 3 optimal weight: 5.9990 chunk 195 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 224 optimal weight: 3.9990 chunk 181 optimal weight: 0.0170 chunk 0 optimal weight: 8.9990 chunk 134 optimal weight: 6.9990 chunk 235 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 overall best weight: 1.6020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 502 GLN ** B 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 803 ASN ** B 808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 832 ASN ** B 844 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 845 HIS C 158 GLN ** E 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 153 HIS I 44 ASN ** J 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 255 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.7159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 28468 Z= 0.221 Angle : 0.610 9.902 40228 Z= 0.310 Chirality : 0.038 0.211 4852 Planarity : 0.005 0.063 3725 Dihedral : 20.750 175.051 8400 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 4.52 % Allowed : 21.29 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.17), residues: 2372 helix: 0.70 (0.17), residues: 947 sheet: -0.49 (0.25), residues: 436 loop : -1.62 (0.20), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 9 HIS 0.007 0.001 HIS B 180 PHE 0.030 0.002 PHE B 740 TYR 0.016 0.002 TYR K 66 ARG 0.006 0.001 ARG K 51 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 2189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 379 time to evaluate : 2.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 ASN cc_start: 0.8159 (t0) cc_final: 0.7845 (t0) REVERT: B 389 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8089 (pp) REVERT: B 632 ARG cc_start: 0.9031 (OUTLIER) cc_final: 0.8570 (ptt90) REVERT: B 650 SER cc_start: 0.7100 (p) cc_final: 0.6795 (p) REVERT: B 819 ASP cc_start: 0.8254 (m-30) cc_final: 0.7862 (m-30) REVERT: C 33 MET cc_start: 0.6915 (mmm) cc_final: 0.6685 (mmt) REVERT: C 70 THR cc_start: 0.8481 (p) cc_final: 0.8186 (m) REVERT: C 129 MET cc_start: 0.5701 (ppp) cc_final: 0.4906 (ptt) REVERT: D 194 ILE cc_start: 0.8740 (pt) cc_final: 0.8530 (mt) REVERT: D 220 ILE cc_start: 0.9086 (mm) cc_final: 0.8765 (mt) REVERT: D 233 GLU cc_start: 0.8593 (mp0) cc_final: 0.8257 (mp0) REVERT: D 277 ILE cc_start: 0.7766 (mm) cc_final: 0.7450 (mm) REVERT: E 8 TYR cc_start: 0.8233 (m-80) cc_final: 0.7896 (m-80) REVERT: E 54 ARG cc_start: 0.8473 (ptp-110) cc_final: 0.8229 (ptp-110) REVERT: E 57 SER cc_start: 0.8582 (m) cc_final: 0.8247 (p) REVERT: F 68 MET cc_start: 0.7236 (ppp) cc_final: 0.4672 (mmp) REVERT: F 82 PHE cc_start: 0.8365 (p90) cc_final: 0.8043 (p90) REVERT: F 132 ARG cc_start: 0.7519 (mtp85) cc_final: 0.7015 (mtp85) REVERT: G 28 GLN cc_start: 0.8920 (tt0) cc_final: 0.8694 (mt0) REVERT: G 41 TYR cc_start: 0.9249 (t80) cc_final: 0.9038 (t80) REVERT: G 68 MET cc_start: 0.8627 (ptm) cc_final: 0.8401 (ptt) REVERT: I 157 GLU cc_start: 0.8285 (tm-30) cc_final: 0.7834 (tt0) REVERT: I 208 THR cc_start: 0.9052 (m) cc_final: 0.8708 (p) REVERT: J 95 GLN cc_start: 0.6367 (mt0) cc_final: 0.6045 (pt0) REVERT: J 136 ARG cc_start: 0.7777 (ttm110) cc_final: 0.7577 (ttm110) REVERT: J 212 LYS cc_start: 0.8595 (mmmt) cc_final: 0.8295 (ttpp) REVERT: J 222 SER cc_start: 0.7482 (m) cc_final: 0.6978 (p) REVERT: K 42 GLN cc_start: 0.8785 (tt0) cc_final: 0.8424 (mt0) REVERT: K 94 HIS cc_start: 0.7761 (m90) cc_final: 0.7515 (m-70) outliers start: 99 outliers final: 69 residues processed: 443 average time/residue: 0.3873 time to fit residues: 275.6895 Evaluate side-chains 413 residues out of total 2189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 342 time to evaluate : 2.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 335 GLN Chi-restraints excluded: chain B residue 339 TYR Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 552 LYS Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain B residue 610 ILE Chi-restraints excluded: chain B residue 632 ARG Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 774 HIS Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 132 PHE Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain F residue 21 GLN Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 135 GLU Chi-restraints excluded: chain H residue 9 TRP Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain H residue 24 ASP Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 81 ILE Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 112 ILE Chi-restraints excluded: chain I residue 149 CYS Chi-restraints excluded: chain I residue 166 ASP Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 191 ILE Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 82 SER Chi-restraints excluded: chain J residue 112 ILE Chi-restraints excluded: chain J residue 143 HIS Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 197 SER Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 119 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 88 optimal weight: 0.8980 chunk 236 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 154 optimal weight: 0.0770 chunk 64 optimal weight: 6.9990 chunk 263 optimal weight: 5.9990 chunk 218 optimal weight: 6.9990 chunk 121 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 overall best weight: 0.9942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 HIS B 466 GLN B 665 GLN ** B 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 803 ASN ** B 808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 844 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 197 GLN ** E 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 45 GLN G 85 GLN ** J 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.7322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 28468 Z= 0.172 Angle : 0.577 11.214 40228 Z= 0.293 Chirality : 0.037 0.200 4852 Planarity : 0.004 0.062 3725 Dihedral : 20.686 175.178 8400 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 4.43 % Allowed : 21.84 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.17), residues: 2372 helix: 0.90 (0.17), residues: 962 sheet: -0.49 (0.24), residues: 442 loop : -1.67 (0.20), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 9 HIS 0.007 0.001 HIS B 437 PHE 0.033 0.002 PHE B 740 TYR 0.027 0.002 TYR K 134 ARG 0.006 0.001 ARG J 67 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 2189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 387 time to evaluate : 2.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 ASN cc_start: 0.8191 (t0) cc_final: 0.7883 (t0) REVERT: B 282 SER cc_start: 0.8445 (m) cc_final: 0.7932 (p) REVERT: B 389 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8182 (pp) REVERT: B 437 HIS cc_start: 0.6531 (OUTLIER) cc_final: 0.6092 (t-170) REVERT: B 632 ARG cc_start: 0.8980 (OUTLIER) cc_final: 0.8293 (ptt90) REVERT: B 650 SER cc_start: 0.6973 (p) cc_final: 0.6646 (p) REVERT: B 757 PHE cc_start: 0.7633 (t80) cc_final: 0.7424 (t80) REVERT: B 774 HIS cc_start: 0.8762 (OUTLIER) cc_final: 0.8409 (p-80) REVERT: C 33 MET cc_start: 0.6927 (mmm) cc_final: 0.6644 (mmt) REVERT: C 43 ILE cc_start: 0.4959 (tt) cc_final: 0.4386 (mp) REVERT: C 70 THR cc_start: 0.8578 (p) cc_final: 0.8243 (m) REVERT: C 111 LEU cc_start: 0.8852 (tp) cc_final: 0.8523 (tp) REVERT: D 126 HIS cc_start: 0.7280 (m-70) cc_final: 0.6948 (m90) REVERT: D 142 MET cc_start: 0.6932 (ttm) cc_final: 0.6658 (ttm) REVERT: D 211 ILE cc_start: 0.9033 (OUTLIER) cc_final: 0.8811 (tp) REVERT: D 220 ILE cc_start: 0.9054 (mm) cc_final: 0.8803 (mt) REVERT: D 233 GLU cc_start: 0.8595 (mp0) cc_final: 0.8365 (mp0) REVERT: E 8 TYR cc_start: 0.8246 (m-80) cc_final: 0.7905 (m-80) REVERT: E 57 SER cc_start: 0.8655 (m) cc_final: 0.8350 (p) REVERT: F 82 PHE cc_start: 0.8319 (p90) cc_final: 0.7930 (p90) REVERT: F 132 ARG cc_start: 0.7308 (mtp85) cc_final: 0.6827 (mtp85) REVERT: G 28 GLN cc_start: 0.8920 (tt0) cc_final: 0.8683 (mt0) REVERT: G 41 TYR cc_start: 0.9183 (t80) cc_final: 0.8981 (t80) REVERT: G 68 MET cc_start: 0.8623 (ptm) cc_final: 0.8295 (ptt) REVERT: I 157 GLU cc_start: 0.8276 (tm-30) cc_final: 0.7806 (tt0) REVERT: I 208 THR cc_start: 0.9006 (m) cc_final: 0.8685 (p) REVERT: J 212 LYS cc_start: 0.8493 (mmmt) cc_final: 0.8268 (ttpp) REVERT: J 222 SER cc_start: 0.7369 (m) cc_final: 0.6871 (p) REVERT: K 26 ARG cc_start: 0.6164 (mmm160) cc_final: 0.5411 (mtt180) REVERT: K 31 GLN cc_start: 0.8741 (tp40) cc_final: 0.8491 (tp40) REVERT: K 42 GLN cc_start: 0.8746 (tt0) cc_final: 0.8469 (mt0) REVERT: K 94 HIS cc_start: 0.7769 (m90) cc_final: 0.7518 (m-70) outliers start: 97 outliers final: 72 residues processed: 449 average time/residue: 0.3753 time to fit residues: 266.4704 Evaluate side-chains 428 residues out of total 2189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 351 time to evaluate : 2.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 ARG Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 335 GLN Chi-restraints excluded: chain B residue 339 TYR Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 437 HIS Chi-restraints excluded: chain B residue 552 LYS Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain B residue 610 ILE Chi-restraints excluded: chain B residue 632 ARG Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain B residue 665 GLN Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 774 HIS Chi-restraints excluded: chain B residue 803 ASN Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 105 LYS Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 63 TYR Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 135 GLU Chi-restraints excluded: chain H residue 9 TRP Chi-restraints excluded: chain H residue 24 ASP Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 112 ILE Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 127 ASP Chi-restraints excluded: chain I residue 149 CYS Chi-restraints excluded: chain I residue 166 ASP Chi-restraints excluded: chain I residue 191 ILE Chi-restraints excluded: chain I residue 204 ILE Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 82 SER Chi-restraints excluded: chain J residue 112 ILE Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain J residue 126 ILE Chi-restraints excluded: chain J residue 143 HIS Chi-restraints excluded: chain J residue 197 SER Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 120 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 253 optimal weight: 8.9990 chunk 29 optimal weight: 10.0000 chunk 149 optimal weight: 0.2980 chunk 192 optimal weight: 10.0000 chunk 148 optimal weight: 0.9980 chunk 221 optimal weight: 4.9990 chunk 146 optimal weight: 0.9980 chunk 262 optimal weight: 1.9990 chunk 164 optimal weight: 5.9990 chunk 159 optimal weight: 5.9990 chunk 121 optimal weight: 20.0000 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 HIS B 466 GLN ** B 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 794 GLN B 803 ASN ** B 808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 844 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 197 GLN ** E 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 ASN J 95 GLN J 213 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.7719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 28468 Z= 0.244 Angle : 0.619 11.247 40228 Z= 0.314 Chirality : 0.039 0.224 4852 Planarity : 0.005 0.063 3725 Dihedral : 20.658 176.558 8400 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 4.80 % Allowed : 22.38 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.17), residues: 2372 helix: 0.90 (0.17), residues: 961 sheet: -0.49 (0.25), residues: 420 loop : -1.66 (0.19), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP H 37 HIS 0.026 0.001 HIS B 437 PHE 0.056 0.002 PHE D 253 TYR 0.028 0.002 TYR K 134 ARG 0.013 0.001 ARG B 549 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 361 time to evaluate : 2.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 180 HIS cc_start: 0.6666 (m-70) cc_final: 0.6158 (m-70) REVERT: B 389 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8217 (pp) REVERT: B 466 GLN cc_start: 0.6133 (OUTLIER) cc_final: 0.5889 (pp30) REVERT: B 632 ARG cc_start: 0.9014 (OUTLIER) cc_final: 0.8291 (ptt90) REVERT: B 650 SER cc_start: 0.7075 (p) cc_final: 0.6721 (p) REVERT: B 673 TYR cc_start: 0.8149 (t80) cc_final: 0.7694 (t80) REVERT: B 757 PHE cc_start: 0.7695 (t80) cc_final: 0.7454 (t80) REVERT: C 43 ILE cc_start: 0.5362 (tt) cc_final: 0.4734 (mp) REVERT: C 70 THR cc_start: 0.8614 (p) cc_final: 0.8007 (t) REVERT: C 129 MET cc_start: 0.6705 (tmm) cc_final: 0.5411 (ptt) REVERT: D 109 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7780 (mm-30) REVERT: D 142 MET cc_start: 0.7065 (ttm) cc_final: 0.6781 (ttm) REVERT: D 211 ILE cc_start: 0.9059 (OUTLIER) cc_final: 0.8828 (tp) REVERT: D 220 ILE cc_start: 0.9108 (mm) cc_final: 0.8894 (mt) REVERT: E 57 SER cc_start: 0.8670 (m) cc_final: 0.8464 (p) REVERT: F 82 PHE cc_start: 0.8389 (p90) cc_final: 0.7975 (p90) REVERT: F 132 ARG cc_start: 0.7618 (mtp85) cc_final: 0.7074 (mtp85) REVERT: G 28 GLN cc_start: 0.8974 (tt0) cc_final: 0.8711 (mt0) REVERT: G 68 MET cc_start: 0.8612 (ptm) cc_final: 0.8257 (ptt) REVERT: I 157 GLU cc_start: 0.8287 (tm-30) cc_final: 0.7817 (tt0) REVERT: I 208 THR cc_start: 0.9042 (m) cc_final: 0.8674 (p) REVERT: J 1 MET cc_start: 0.7193 (OUTLIER) cc_final: 0.6740 (ptt) REVERT: J 95 GLN cc_start: 0.6392 (mt0) cc_final: 0.5965 (pt0) REVERT: J 222 SER cc_start: 0.7553 (m) cc_final: 0.7033 (p) REVERT: K 31 GLN cc_start: 0.8805 (tp40) cc_final: 0.8373 (tp40) REVERT: K 42 GLN cc_start: 0.8795 (tt0) cc_final: 0.8487 (mt0) outliers start: 105 outliers final: 78 residues processed: 427 average time/residue: 0.3796 time to fit residues: 256.6527 Evaluate side-chains 422 residues out of total 2189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 339 time to evaluate : 2.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 ARG Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 335 GLN Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 339 TYR Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 466 GLN Chi-restraints excluded: chain B residue 552 LYS Chi-restraints excluded: chain B residue 573 ASN Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 632 ARG Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 774 HIS Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 63 TYR Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 135 GLU Chi-restraints excluded: chain H residue 9 TRP Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain H residue 24 ASP Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 149 CYS Chi-restraints excluded: chain I residue 166 ASP Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 191 ILE Chi-restraints excluded: chain I residue 204 ILE Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 82 SER Chi-restraints excluded: chain J residue 87 ILE Chi-restraints excluded: chain J residue 112 ILE Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain J residue 143 HIS Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 96 LEU Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 120 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 162 optimal weight: 0.8980 chunk 104 optimal weight: 0.7980 chunk 156 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 166 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 chunk 129 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 chunk 206 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 ASN B 665 GLN B 735 ASN B 803 ASN B 808 HIS B 844 HIS C 32 HIS C 106 GLN ** E 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 70 ASN J 213 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.7866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 28468 Z= 0.182 Angle : 0.588 12.015 40228 Z= 0.296 Chirality : 0.037 0.215 4852 Planarity : 0.004 0.059 3725 Dihedral : 20.623 177.266 8400 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.79 % Allowed : 23.53 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.18), residues: 2372 helix: 1.03 (0.17), residues: 954 sheet: -0.35 (0.25), residues: 416 loop : -1.61 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP H 37 HIS 0.005 0.001 HIS E 36 PHE 0.046 0.002 PHE D 253 TYR 0.027 0.002 TYR K 134 ARG 0.007 0.001 ARG C 148 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 373 time to evaluate : 2.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 389 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8147 (pp) REVERT: B 632 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.8290 (ptt90) REVERT: B 650 SER cc_start: 0.7000 (p) cc_final: 0.6662 (p) REVERT: B 757 PHE cc_start: 0.7774 (t80) cc_final: 0.7564 (t80) REVERT: B 774 HIS cc_start: 0.8821 (OUTLIER) cc_final: 0.8496 (p-80) REVERT: C 33 MET cc_start: 0.6664 (mmm) cc_final: 0.6431 (mmt) REVERT: C 43 ILE cc_start: 0.5356 (tt) cc_final: 0.4805 (mp) REVERT: C 70 THR cc_start: 0.8645 (p) cc_final: 0.8120 (t) REVERT: C 129 MET cc_start: 0.6696 (tmm) cc_final: 0.5405 (ptt) REVERT: C 130 ASP cc_start: 0.6821 (t70) cc_final: 0.6345 (t70) REVERT: D 142 MET cc_start: 0.7154 (ttm) cc_final: 0.6819 (ttm) REVERT: F 132 ARG cc_start: 0.7377 (mtp85) cc_final: 0.6930 (mtp85) REVERT: G 28 GLN cc_start: 0.8957 (tt0) cc_final: 0.8695 (mt0) REVERT: G 68 MET cc_start: 0.8624 (ptm) cc_final: 0.8296 (ptt) REVERT: I 11 GLN cc_start: 0.8590 (tt0) cc_final: 0.8383 (tt0) REVERT: I 123 ASN cc_start: 0.7771 (p0) cc_final: 0.7536 (p0) REVERT: I 157 GLU cc_start: 0.8268 (tm-30) cc_final: 0.7793 (tt0) REVERT: I 208 THR cc_start: 0.9060 (m) cc_final: 0.8697 (p) REVERT: J 222 SER cc_start: 0.7357 (m) cc_final: 0.6883 (p) REVERT: K 31 GLN cc_start: 0.8776 (tp40) cc_final: 0.8421 (tp40) REVERT: K 42 GLN cc_start: 0.8729 (tt0) cc_final: 0.8412 (mt0) REVERT: K 99 THR cc_start: 0.8935 (m) cc_final: 0.8697 (t) outliers start: 83 outliers final: 64 residues processed: 425 average time/residue: 0.3653 time to fit residues: 248.9748 Evaluate side-chains 413 residues out of total 2189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 346 time to evaluate : 2.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 ARG Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 335 GLN Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 339 TYR Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 552 LYS Chi-restraints excluded: chain B residue 573 ASN Chi-restraints excluded: chain B residue 632 ARG Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 774 HIS Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 63 TYR Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain H residue 9 TRP Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain H residue 24 ASP Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 149 CYS Chi-restraints excluded: chain I residue 166 ASP Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 191 ILE Chi-restraints excluded: chain I residue 204 ILE Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 82 SER Chi-restraints excluded: chain J residue 87 ILE Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain J residue 126 ILE Chi-restraints excluded: chain J residue 143 HIS Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 96 LEU Chi-restraints excluded: chain K residue 120 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 238 optimal weight: 0.9980 chunk 251 optimal weight: 5.9990 chunk 229 optimal weight: 4.9990 chunk 244 optimal weight: 0.0970 chunk 147 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 191 optimal weight: 9.9990 chunk 74 optimal weight: 0.8980 chunk 220 optimal weight: 0.2980 chunk 231 optimal weight: 0.0060 chunk 243 optimal weight: 6.9990 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 ASN ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 GLN C 83 HIS D 197 GLN ** E 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 70 ASN J 95 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.7899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 28468 Z= 0.150 Angle : 0.578 12.238 40228 Z= 0.291 Chirality : 0.037 0.181 4852 Planarity : 0.004 0.056 3725 Dihedral : 20.571 178.264 8400 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.11 % Allowed : 24.81 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.18), residues: 2372 helix: 1.13 (0.17), residues: 962 sheet: -0.26 (0.26), residues: 411 loop : -1.65 (0.19), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP H 37 HIS 0.008 0.001 HIS B 437 PHE 0.043 0.002 PHE D 253 TYR 0.030 0.002 TYR K 134 ARG 0.015 0.001 ARG I 67 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 371 time to evaluate : 2.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 180 HIS cc_start: 0.6154 (m-70) cc_final: 0.5584 (m-70) REVERT: B 389 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8202 (pp) REVERT: B 433 MET cc_start: 0.7719 (ptm) cc_final: 0.7470 (ptp) REVERT: B 632 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.8219 (ptt90) REVERT: B 650 SER cc_start: 0.6868 (p) cc_final: 0.6552 (p) REVERT: B 757 PHE cc_start: 0.7737 (t80) cc_final: 0.7488 (t80) REVERT: B 768 THR cc_start: 0.8930 (OUTLIER) cc_final: 0.8613 (p) REVERT: C 33 MET cc_start: 0.6855 (mmm) cc_final: 0.6392 (mmt) REVERT: C 43 ILE cc_start: 0.5507 (tt) cc_final: 0.5017 (mp) REVERT: C 70 THR cc_start: 0.8608 (p) cc_final: 0.8064 (t) REVERT: C 129 MET cc_start: 0.6631 (tmm) cc_final: 0.5231 (ptt) REVERT: C 130 ASP cc_start: 0.6748 (t70) cc_final: 0.6453 (p0) REVERT: E 8 TYR cc_start: 0.8281 (m-80) cc_final: 0.7934 (m-80) REVERT: E 46 LYS cc_start: 0.8981 (pptt) cc_final: 0.8701 (pttp) REVERT: F 122 ARG cc_start: 0.8178 (ptm160) cc_final: 0.7631 (ptm160) REVERT: F 132 ARG cc_start: 0.7220 (mtp85) cc_final: 0.6813 (mtp85) REVERT: G 41 TYR cc_start: 0.9049 (t80) cc_final: 0.8810 (t80) REVERT: H 108 LEU cc_start: 0.3917 (OUTLIER) cc_final: 0.3374 (pp) REVERT: I 157 GLU cc_start: 0.8251 (tm-30) cc_final: 0.7775 (tt0) REVERT: I 208 THR cc_start: 0.8885 (m) cc_final: 0.8616 (p) REVERT: J 1 MET cc_start: 0.7043 (OUTLIER) cc_final: 0.6841 (ptt) REVERT: J 95 GLN cc_start: 0.6380 (mt0) cc_final: 0.5977 (pt0) REVERT: J 222 SER cc_start: 0.7334 (m) cc_final: 0.6957 (p) REVERT: K 31 GLN cc_start: 0.8747 (tp40) cc_final: 0.8279 (tp40) REVERT: K 42 GLN cc_start: 0.8651 (tt0) cc_final: 0.8350 (mt0) REVERT: K 74 SER cc_start: 0.9190 (m) cc_final: 0.8964 (p) REVERT: K 76 LYS cc_start: 0.8254 (tttm) cc_final: 0.7757 (tttm) REVERT: K 99 THR cc_start: 0.8864 (m) cc_final: 0.8632 (t) outliers start: 68 outliers final: 47 residues processed: 413 average time/residue: 0.3809 time to fit residues: 250.8200 Evaluate side-chains 408 residues out of total 2189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 356 time to evaluate : 2.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 ARG Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 339 TYR Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 552 LYS Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 610 ILE Chi-restraints excluded: chain B residue 632 ARG Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 63 TYR Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain H residue 9 TRP Chi-restraints excluded: chain H residue 24 ASP Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 127 ASP Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 87 ILE Chi-restraints excluded: chain J residue 112 ILE Chi-restraints excluded: chain J residue 143 HIS Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 68 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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: 51.1421 > 50: distance: 84 - 88: 5.176 distance: 88 - 89: 4.987 distance: 89 - 90: 3.808 distance: 89 - 92: 4.449 distance: 90 - 91: 12.747 distance: 90 - 96: 4.626 distance: 92 - 93: 7.320 distance: 93 - 94: 3.686 distance: 93 - 95: 9.529 distance: 96 - 97: 13.327 distance: 97 - 98: 16.652 distance: 97 - 100: 9.904 distance: 98 - 99: 10.009 distance: 98 - 104: 3.917 distance: 100 - 101: 9.151 distance: 101 - 102: 16.618 distance: 101 - 103: 16.665 distance: 104 - 105: 6.144 distance: 105 - 108: 16.875 distance: 106 - 107: 10.097 distance: 106 - 113: 8.283 distance: 107 - 214: 12.732 distance: 108 - 109: 7.271 distance: 109 - 110: 9.359 distance: 110 - 111: 8.221 distance: 110 - 112: 4.362 distance: 113 - 114: 12.194 distance: 114 - 115: 4.210 distance: 114 - 117: 6.310 distance: 115 - 116: 7.662 distance: 115 - 121: 5.374 distance: 117 - 118: 14.915 distance: 118 - 119: 7.721 distance: 118 - 120: 12.876 distance: 121 - 122: 14.847 distance: 121 - 201: 9.583 distance: 122 - 123: 10.582 distance: 122 - 125: 12.448 distance: 123 - 124: 24.546 distance: 123 - 130: 12.999 distance: 125 - 126: 22.995 distance: 126 - 127: 26.960 distance: 127 - 128: 10.168 distance: 128 - 129: 28.402 distance: 130 - 131: 13.985 distance: 131 - 132: 16.671 distance: 131 - 134: 18.227 distance: 132 - 133: 9.071 distance: 132 - 142: 14.919 distance: 134 - 135: 8.078 distance: 135 - 136: 6.722 distance: 135 - 137: 5.472 distance: 136 - 138: 8.578 distance: 137 - 139: 9.819 distance: 138 - 140: 6.474 distance: 139 - 140: 7.630 distance: 140 - 141: 5.286 distance: 142 - 143: 30.505 distance: 143 - 144: 9.893 distance: 143 - 146: 38.883 distance: 144 - 145: 8.806 distance: 144 - 153: 6.971 distance: 146 - 147: 23.153 distance: 147 - 148: 25.542 distance: 147 - 149: 12.032 distance: 148 - 150: 10.870 distance: 149 - 151: 10.611 distance: 150 - 152: 8.911 distance: 151 - 152: 10.464 distance: 153 - 154: 4.647 distance: 154 - 157: 22.244 distance: 155 - 156: 30.026 distance: 155 - 159: 21.908 distance: 157 - 158: 5.412 distance: 159 - 160: 21.100 distance: 160 - 161: 15.364 distance: 160 - 163: 19.982 distance: 161 - 167: 12.695 distance: 163 - 164: 9.997 distance: 164 - 165: 25.070 distance: 164 - 166: 10.847 distance: 167 - 168: 13.441 distance: 168 - 169: 4.084 distance: 168 - 171: 8.974 distance: 169 - 170: 6.446 distance: 169 - 176: 19.019 distance: 171 - 172: 17.502 distance: 172 - 173: 15.645 distance: 173 - 174: 21.025 distance: 174 - 175: 19.154