Starting phenix.real_space_refine on Sat Jun 21 12:22:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6w6v_21564/06_2025/6w6v_21564.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w6v_21564/06_2025/6w6v_21564.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6w6v_21564/06_2025/6w6v_21564.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w6v_21564/06_2025/6w6v_21564.map" model { file = "/net/cci-nas-00/data/ceres_data/6w6v_21564/06_2025/6w6v_21564.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w6v_21564/06_2025/6w6v_21564.cif" } resolution = 3.0 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= 0.094 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: 5 Type Number sf(0) Gaussians P 295 5.49 5 S 90 5.16 5 C 14572 2.51 5 N 4418 2.21 5 O 5475 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 24850 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 6261 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 294, 6239 Classifications: {'RNA': 294} Modifications used: {'rna2p_pur': 24, 'rna2p_pyr': 21, 'rna3p_pur': 125, 'rna3p_pyr': 124} Link IDs: {'rna2p': 45, 'rna3p': 248} Chain breaks: 7 Conformer: "B" Number of residues, atoms: 294, 6239 Classifications: {'RNA': 294} Modifications used: {'rna2p_pur': 24, 'rna2p_pyr': 21, 'rna3p_pur': 125, 'rna3p_pyr': 124} Link IDs: {'rna2p': 45, 'rna3p': 248} Chain breaks: 7 bond proxies already assigned to first conformer: 6942 Chain: "B" Number of atoms: 6345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 780, 6345 Classifications: {'peptide': 780} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 36, 'TRANS': 743} Chain breaks: 3 Chain: "D" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1759 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 5, 'TRANS': 206} Chain: "E" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1335 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 4, 'TRANS': 164} Chain: "F" Number of atoms: 1280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1280 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 154} Chain: "G" Number of atoms: 1006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1006 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain breaks: 1 Chain: "H" Number of atoms: 1033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1033 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain: "I" Number of atoms: 1891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1891 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 9, 'TRANS': 233} 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: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 648 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "L" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1032 Classifications: {'peptide': 121} Link IDs: {'TRANS': 120} Chain breaks: 1 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" P A A A 113 " occ=0.50 ... (42 atoms not shown) pdb=" C4 B A A 113 " occ=0.50 Time building chain proxies: 17.33, per 1000 atoms: 0.70 Number of scatterers: 24850 At special positions: 0 Unit cell: (125.685, 156.94, 150.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 90 16.00 P 295 15.00 O 5475 8.00 N 4418 7.00 C 14572 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 - 3.00 Amino acid : True - 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: 5.45 Conformation dependent library (CDL) restraints added in 2.2 seconds 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4390 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 15 sheets defined 36.9% alpha, 13.9% beta 78 base pairs and 137 stacking pairs defined. Time for finding SS restraints: 9.28 Creating SS restraints... Processing helix chain 'B' and resid 72 through 81 removed outlier: 3.954A pdb=" N ALA B 76 " --> pdb=" O GLN B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 97 removed outlier: 4.173A pdb=" N ARG B 97 " --> pdb=" O ARG B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 122 removed outlier: 3.686A pdb=" N ARG B 115 " --> pdb=" O ARG B 111 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA B 116 " --> pdb=" O MET B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 163 removed outlier: 4.021A pdb=" N LYS B 149 " --> pdb=" O LYS B 145 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LYS B 155 " --> pdb=" O ARG B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 232 removed outlier: 3.567A pdb=" N LYS B 232 " --> pdb=" O VAL B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 247 Processing helix chain 'B' and resid 248 through 250 No H-bonds generated for 'chain 'B' and resid 248 through 250' Processing helix chain 'B' and resid 268 through 277 removed outlier: 3.622A pdb=" N HIS B 273 " --> pdb=" O PHE B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 318 Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 374 through 383 removed outlier: 3.866A pdb=" N VAL B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE B 381 " --> pdb=" O GLN B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 386 No H-bonds generated for 'chain 'B' and resid 384 through 386' Processing helix chain 'B' and resid 408 through 413 Processing helix chain 'B' and resid 414 through 416 No H-bonds generated for 'chain 'B' and resid 414 through 416' Processing helix chain 'B' and resid 422 through 432 Processing helix chain 'B' and resid 452 through 456 removed outlier: 3.669A pdb=" N LEU B 456 " --> pdb=" O PRO B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 467 removed outlier: 3.823A pdb=" N GLN B 466 " --> pdb=" O ASN B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 480 removed outlier: 3.503A pdb=" N HIS B 479 " --> pdb=" O LEU B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 492 removed outlier: 3.769A pdb=" N VAL B 490 " --> pdb=" O GLU B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 503 Processing helix chain 'B' and resid 509 through 519 Processing helix chain 'B' and resid 520 through 523 removed outlier: 4.090A pdb=" N ALA B 523 " --> pdb=" O LEU B 520 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 520 through 523' Processing helix chain 'B' and resid 564 through 573 removed outlier: 3.659A pdb=" N LEU B 568 " --> pdb=" O TRP B 564 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU B 571 " --> pdb=" O PRO B 567 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASN B 573 " --> pdb=" O TRP B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 593 Processing helix chain 'B' and resid 605 through 614 removed outlier: 3.806A pdb=" N ILE B 610 " --> pdb=" O GLN B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 625 removed outlier: 3.933A pdb=" N LYS B 623 " --> pdb=" O ALA B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 674 removed outlier: 3.898A pdb=" N LEU B 664 " --> pdb=" O ASP B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 714 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 848 removed outlier: 3.562A pdb=" N ILE B 848 " --> pdb=" O HIS B 844 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 844 through 848' Processing helix chain 'D' and resid 77 through 105 removed outlier: 3.667A pdb=" N LYS D 86 " --> pdb=" O ASN D 82 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE D 87 " --> pdb=" O LYS D 83 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ARG D 90 " --> pdb=" O LYS D 86 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU D 91 " --> pdb=" O ILE D 87 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS D 105 " --> pdb=" O LYS D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 126 removed outlier: 3.574A pdb=" N HIS D 120 " --> pdb=" O GLU D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 130 Processing helix chain 'D' and resid 135 through 140 Processing helix chain 'D' and resid 147 through 155 removed outlier: 4.037A pdb=" N ILE D 151 " --> pdb=" O TRP D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 174 removed outlier: 3.569A pdb=" N SER D 174 " --> pdb=" O LEU D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 278 Processing helix chain 'E' and resid 27 through 36 removed outlier: 3.672A pdb=" N LEU E 32 " --> pdb=" O LYS E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 removed outlier: 3.695A pdb=" N ILE E 48 " --> pdb=" O SER E 44 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU E 49 " --> pdb=" O ILE E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 60 removed outlier: 3.692A pdb=" N ASN E 59 " --> pdb=" O SER E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 66 Processing helix chain 'E' and resid 93 through 102 Processing helix chain 'E' and resid 123 through 142 removed outlier: 3.652A pdb=" N GLU E 127 " --> pdb=" O ILE E 123 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN E 128 " --> pdb=" O LYS E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 151 Processing helix chain 'E' and resid 155 through 162 removed outlier: 3.597A pdb=" N PHE E 159 " --> pdb=" O ILE E 155 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LYS E 160 " --> pdb=" O ILE E 156 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS E 161 " --> pdb=" O ASN E 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 30 removed outlier: 3.735A pdb=" N VAL F 30 " --> pdb=" O LEU F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 35 Processing helix chain 'F' and resid 54 through 66 Processing helix chain 'F' and resid 87 through 102 removed outlier: 3.747A pdb=" N SER F 93 " --> pdb=" O GLN F 89 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE F 94 " --> pdb=" O LYS F 90 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE F 97 " --> pdb=" O SER F 93 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS F 99 " --> pdb=" O LEU F 95 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY F 101 " --> pdb=" O ILE F 97 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR F 102 " --> pdb=" O PHE F 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 52 Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'G' and resid 70 through 84 removed outlier: 3.929A pdb=" N LYS G 74 " --> pdb=" O LYS G 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 46 Processing helix chain 'H' and resid 47 through 51 Processing helix chain 'H' and resid 73 through 82 removed outlier: 3.513A pdb=" N SER H 79 " --> pdb=" O ASP H 75 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER H 82 " --> pdb=" O SER H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 118 Processing helix chain 'I' and resid 19 through 37 removed outlier: 4.196A pdb=" N VAL I 23 " --> pdb=" O THR I 19 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY I 37 " --> pdb=" O LEU I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 113 through 121 Processing helix chain 'I' and resid 142 through 152 removed outlier: 3.776A pdb=" N ILE I 146 " --> pdb=" O LYS I 142 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N SER I 148 " --> pdb=" O LYS I 144 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N CYS I 149 " --> pdb=" O SER I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 161 through 166 removed outlier: 3.851A pdb=" N ARG I 165 " --> pdb=" O GLY I 161 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ASP I 166 " --> pdb=" O TYR I 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 161 through 166' Processing helix chain 'I' and resid 166 through 184 removed outlier: 3.608A pdb=" N GLN I 172 " --> pdb=" O GLN I 168 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG I 178 " --> pdb=" O VAL I 174 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER I 179 " --> pdb=" O SER I 175 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER I 184 " --> pdb=" O VAL I 180 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 213 Processing helix chain 'I' and resid 217 through 222 removed outlier: 4.001A pdb=" N SER I 222 " --> pdb=" O SER I 218 " (cutoff:3.500A) Processing helix chain 'I' and resid 226 through 239 removed outlier: 3.587A pdb=" N LEU I 233 " --> pdb=" O ALA I 229 " (cutoff:3.500A) Processing helix chain 'I' and resid 240 through 243 removed outlier: 3.700A pdb=" N HIS I 243 " --> pdb=" O ASN I 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 240 through 243' Processing helix chain 'J' and resid 19 through 37 removed outlier: 3.540A pdb=" N VAL J 23 " --> pdb=" O THR J 19 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 60 removed outlier: 3.607A pdb=" N LEU J 60 " --> pdb=" O VAL J 57 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 69 removed outlier: 3.517A pdb=" N PHE J 69 " --> pdb=" O ILE J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 69 through 77 Processing helix chain 'J' and resid 99 through 104 removed outlier: 3.589A pdb=" N ALA J 103 " --> pdb=" O LYS J 99 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE J 104 " --> pdb=" O ILE J 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 99 through 104' Processing helix chain 'J' and resid 113 through 120 Processing helix chain 'J' and resid 146 through 151 removed outlier: 4.140A pdb=" N ASN J 151 " --> pdb=" O CYS J 147 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 165 removed outlier: 3.827A pdb=" N LEU J 164 " --> pdb=" O GLY J 161 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ARG J 165 " --> pdb=" O TYR J 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 161 through 165' Processing helix chain 'J' and resid 167 through 184 removed outlier: 4.361A pdb=" N ARG J 171 " --> pdb=" O VAL J 167 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLN J 172 " --> pdb=" O GLN J 168 " (cutoff:3.500A) Processing helix chain 'J' and resid 197 through 201 Processing helix chain 'J' and resid 203 through 206 Processing helix chain 'J' and resid 207 through 213 removed outlier: 3.770A pdb=" N ASN J 213 " --> pdb=" O SER J 209 " (cutoff:3.500A) Processing helix chain 'J' and resid 217 through 225 removed outlier: 4.172A pdb=" N MET J 225 " --> pdb=" O CYS J 221 " (cutoff:3.500A) Processing helix chain 'J' and resid 226 through 238 Processing helix chain 'K' and resid 8 through 23 removed outlier: 4.173A pdb=" N ARG K 12 " --> pdb=" O LYS K 8 " (cutoff:3.500A) Processing helix chain 'K' and resid 33 through 46 Processing helix chain 'L' and resid 7 through 25 removed outlier: 4.378A pdb=" N GLN L 13 " --> pdb=" O ARG L 9 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ARG L 16 " --> pdb=" O GLU L 12 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASN L 25 " --> pdb=" O LEU L 21 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 30 removed outlier: 3.862A pdb=" N ARG L 30 " --> pdb=" O ASN L 27 " (cutoff:3.500A) Processing helix chain 'L' and resid 34 through 50 removed outlier: 4.921A pdb=" N GLU L 40 " --> pdb=" O GLY L 36 " (cutoff:3.500A) Processing helix chain 'L' and resid 69 through 76 removed outlier: 3.824A pdb=" N ARG L 72 " --> pdb=" O LYS L 69 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG L 76 " --> pdb=" O LEU L 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 89 Processing helix chain 'L' and resid 90 through 96 removed outlier: 3.661A pdb=" N GLY L 96 " --> pdb=" O VAL L 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 99 through 122 removed outlier: 4.048A pdb=" N ILE L 122 " --> pdb=" O ARG L 118 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 251 through 252 removed outlier: 6.964A pdb=" N HIS B 251 " --> pdb=" O TRP B 262 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 446 through 450 removed outlier: 6.334A pdb=" N ALA B 285 " --> pdb=" O TYR B 579 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 334 through 338 removed outlier: 3.519A pdb=" N PHE B 334 " --> pdb=" O VAL B 358 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL B 358 " --> pdb=" O PHE B 334 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY B 336 " --> pdb=" O CYS B 356 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N CYS B 356 " --> pdb=" O GLY B 336 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY B 354 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE B 297 " --> pdb=" O GLN B 392 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 762 through 769 removed outlier: 5.478A pdb=" N GLY B 836 " --> pdb=" O LEU B 769 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N PHE B 841 " --> pdb=" O ILE B 824 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ILE B 824 " --> pdb=" O PHE B 841 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ASP B 843 " --> pdb=" O GLY B 822 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N GLY B 822 " --> pdb=" O ASP B 843 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU B 820 " --> pdb=" O GLN B 783 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLN B 783 " --> pdb=" O LEU B 820 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 219 through 223 removed outlier: 7.295A pdb=" N ILE D 209 " --> pdb=" O ILE D 201 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N LEU D 183 " --> pdb=" O GLU D 233 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N GLU D 233 " --> pdb=" O LEU D 183 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N VAL D 185 " --> pdb=" O GLN D 231 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLN D 231 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS D 187 " --> pdb=" O VAL D 229 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 219 through 223 removed outlier: 7.295A pdb=" N ILE D 209 " --> pdb=" O ILE D 201 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N LEU D 183 " --> pdb=" O GLU D 233 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N GLU D 233 " --> pdb=" O LEU D 183 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N VAL D 185 " --> pdb=" O GLN D 231 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLN D 231 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS D 187 " --> pdb=" O VAL D 229 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 73 through 77 removed outlier: 6.034A pdb=" N LEU E 74 " --> pdb=" O ARG E 87 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ARG E 87 " --> pdb=" O LEU E 74 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TYR E 76 " --> pdb=" O ILE E 85 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS E 118 " --> pdb=" O LEU E 10 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLU E 12 " --> pdb=" O PRO E 116 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE E 14 " --> pdb=" O VAL E 114 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N VAL E 114 " --> pdb=" O ILE E 14 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 6 through 7 Processing sheet with id=AA9, first strand: chain 'F' and resid 47 through 48 removed outlier: 6.947A pdb=" N HIS F 47 " --> pdb=" O PHE F 82 " (cutoff:3.500A) removed outlier: 9.204A pdb=" N TYR F 84 " --> pdb=" O HIS F 47 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 16 through 17 removed outlier: 3.967A pdb=" N THR G 16 " --> pdb=" O GLU G 102 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU G 102 " --> pdb=" O THR G 16 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 55 through 57 removed outlier: 3.922A pdb=" N ILE H 67 " --> pdb=" O PHE H 12 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 3 through 8 removed outlier: 4.471A pdb=" N VAL I 3 " --> pdb=" O HIS I 40 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N ALA I 42 " --> pdb=" O VAL I 3 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N LEU I 5 " --> pdb=" O ALA I 42 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ASN I 44 " --> pdb=" O LEU I 5 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL I 7 " --> pdb=" O ASN I 44 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ILE I 41 " --> pdb=" O TYR I 81 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ARG I 83 " --> pdb=" O ILE I 41 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N ILE I 43 " --> pdb=" O ARG I 83 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N THR I 85 " --> pdb=" O ILE I 43 " (cutoff:3.500A) removed outlier: 10.157A pdb=" N ILE I 106 " --> pdb=" O LEU I 80 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N SER I 82 " --> pdb=" O ILE I 106 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N ALA I 108 " --> pdb=" O SER I 82 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE I 84 " --> pdb=" O ALA I 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'I' and resid 156 through 158 removed outlier: 6.267A pdb=" N LEU I 156 " --> pdb=" O VAL I 190 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'J' and resid 3 through 4 removed outlier: 7.193A pdb=" N ASP J 4 " --> pdb=" O ALA J 42 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 46 through 48 removed outlier: 3.864A pdb=" N LEU J 128 " --> pdb=" O VAL J 107 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU J 157 " --> pdb=" O LEU J 129 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU J 156 " --> pdb=" O VAL J 190 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N GLY J 192 " --> pdb=" O LEU J 156 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE J 158 " --> pdb=" O GLY J 192 " (cutoff:3.500A) 613 hydrogen bonds defined for protein. 1701 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 197 hydrogen bonds 366 hydrogen bond angles 0 basepair planarities 78 basepair parallelities 137 stacking parallelities Total time for adding SS restraints: 11.08 Time building geometry restraints manager: 6.67 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: 5800 1.33 - 1.45: 6533 1.45 - 1.57: 12859 1.57 - 1.69: 584 1.69 - 1.81: 139 Bond restraints: 25915 Sorted by residual: bond pdb=" C PRO B 171 " pdb=" N PRO B 172 " ideal model delta sigma weight residual 1.334 1.375 -0.041 2.34e-02 1.83e+03 3.07e+00 bond pdb=" CB PRO I 54 " pdb=" CG PRO I 54 " ideal model delta sigma weight residual 1.492 1.576 -0.084 5.00e-02 4.00e+02 2.84e+00 bond pdb=" CG1 ILE J 181 " pdb=" CD1 ILE J 181 " ideal model delta sigma weight residual 1.513 1.454 0.059 3.90e-02 6.57e+02 2.33e+00 bond pdb=" CG PRO I 54 " pdb=" CD PRO I 54 " ideal model delta sigma weight residual 1.503 1.540 -0.037 3.40e-02 8.65e+02 1.22e+00 bond pdb=" CG LEU G 66 " pdb=" CD2 LEU G 66 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.21e+00 ... (remaining 25910 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 36081 2.68 - 5.36: 252 5.36 - 8.04: 21 8.04 - 10.72: 6 10.72 - 13.40: 1 Bond angle restraints: 36361 Sorted by residual: angle pdb=" C TYR K 68 " pdb=" N VAL K 69 " pdb=" CA VAL K 69 " ideal model delta sigma weight residual 123.25 117.24 6.01 1.10e+00 8.26e-01 2.99e+01 angle pdb=" CA ARG B 626 " pdb=" CB ARG B 626 " pdb=" CG ARG B 626 " ideal model delta sigma weight residual 114.10 124.73 -10.63 2.00e+00 2.50e-01 2.82e+01 angle pdb=" CA LEU G 66 " pdb=" CB LEU G 66 " pdb=" CG LEU G 66 " ideal model delta sigma weight residual 116.30 129.70 -13.40 3.50e+00 8.16e-02 1.47e+01 angle pdb=" CA PRO I 54 " pdb=" N PRO I 54 " pdb=" CD PRO I 54 " ideal model delta sigma weight residual 112.00 106.75 5.25 1.40e+00 5.10e-01 1.41e+01 angle pdb=" CA GLY I 192 " pdb=" C GLY I 192 " pdb=" N SER I 193 " ideal model delta sigma weight residual 114.65 117.93 -3.28 9.20e-01 1.18e+00 1.27e+01 ... (remaining 36356 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.37: 14349 22.37 - 44.75: 1191 44.75 - 67.12: 467 67.12 - 89.49: 76 89.49 - 111.87: 5 Dihedral angle restraints: 16088 sinusoidal: 9327 harmonic: 6761 Sorted by residual: dihedral pdb=" CA VAL D 140 " pdb=" C VAL D 140 " pdb=" N PRO D 141 " pdb=" CA PRO D 141 " ideal model delta harmonic sigma weight residual -180.00 -151.02 -28.98 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA PHE D 207 " pdb=" C PHE D 207 " pdb=" N PHE D 208 " pdb=" CA PHE D 208 " ideal model delta harmonic sigma weight residual 180.00 155.93 24.07 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA ARG D 260 " pdb=" C ARG D 260 " pdb=" N ALA D 261 " pdb=" CA ALA D 261 " ideal model delta harmonic sigma weight residual -180.00 -159.00 -21.00 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 16085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 3358 0.044 - 0.088: 764 0.088 - 0.132: 192 0.132 - 0.176: 26 0.176 - 0.220: 5 Chirality restraints: 4345 Sorted by residual: chirality pdb=" CG LEU G 66 " pdb=" CB LEU G 66 " pdb=" CD1 LEU G 66 " pdb=" CD2 LEU G 66 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CB ILE B 700 " pdb=" CA ILE B 700 " pdb=" CG1 ILE B 700 " pdb=" CG2 ILE B 700 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" C1' A A 86 " pdb=" O4' A A 86 " pdb=" C2' A A 86 " pdb=" N9 A A 86 " both_signs ideal model delta sigma weight residual False 2.46 2.25 0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 4342 not shown) Planarity restraints: 3525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE I 53 " -0.066 5.00e-02 4.00e+02 9.74e-02 1.52e+01 pdb=" N PRO I 54 " 0.168 5.00e-02 4.00e+02 pdb=" CA PRO I 54 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO I 54 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 140 " 0.043 5.00e-02 4.00e+02 6.44e-02 6.64e+00 pdb=" N PRO D 141 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO D 141 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 141 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 560 " -0.037 5.00e-02 4.00e+02 5.57e-02 4.97e+00 pdb=" N PRO B 561 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 561 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 561 " -0.031 5.00e-02 4.00e+02 ... (remaining 3522 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 549 2.65 - 3.22: 21917 3.22 - 3.78: 36703 3.78 - 4.34: 50494 4.34 - 4.90: 78226 Nonbonded interactions: 187889 Sorted by model distance: nonbonded pdb=" OG SER K 33 " pdb=" O VAL K 69 " model vdw 2.092 3.040 nonbonded pdb=" OG1 THR B 242 " pdb=" OD2 ASP B 289 " model vdw 2.104 3.040 nonbonded pdb=" O ASP H 75 " pdb=" OG SER H 79 " model vdw 2.145 3.040 nonbonded pdb=" O GLY I 206 " pdb=" OG SER I 209 " model vdw 2.186 3.040 nonbonded pdb=" OE1 GLU H 54 " pdb=" OG SER I 179 " model vdw 2.204 3.040 ... (remaining 187884 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 22.070 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: 1.000 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 63.980 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 25915 Z= 0.175 Angle : 0.633 13.397 36361 Z= 0.350 Chirality : 0.041 0.220 4345 Planarity : 0.004 0.097 3525 Dihedral : 18.065 111.867 11698 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.94 % Favored : 89.06 % Rotamer: Outliers : 0.05 % Allowed : 0.24 % Favored : 99.71 % 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: -2.45 (0.17), residues: 2276 helix: -0.56 (0.20), residues: 725 sheet: -0.45 (0.28), residues: 356 loop : -2.79 (0.16), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 870 HIS 0.007 0.001 HIS K 22 PHE 0.025 0.001 PHE G 51 TYR 0.032 0.002 TYR L 35 ARG 0.010 0.000 ARG B 626 Details of bonding type rmsd hydrogen bonds : bond 0.15780 ( 792) hydrogen bonds : angle 6.08986 ( 2067) covalent geometry : bond 0.00381 (25915) covalent geometry : angle 0.63313 (36361) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 383 time to evaluate : 2.635 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 626 ARG cc_start: 0.7695 (tmt170) cc_final: 0.6940 (tmt170) REVERT: B 811 LYS cc_start: 0.7745 (mmpt) cc_final: 0.7537 (ptmt) REVERT: B 849 ARG cc_start: 0.8057 (mtm110) cc_final: 0.7840 (ptt90) REVERT: E 76 TYR cc_start: 0.8412 (t80) cc_final: 0.8147 (t80) REVERT: G 104 ILE cc_start: 0.8412 (pt) cc_final: 0.8073 (pp) REVERT: I 125 ASP cc_start: 0.7921 (m-30) cc_final: 0.7209 (t0) REVERT: J 72 LEU cc_start: 0.8302 (tt) cc_final: 0.8094 (mp) REVERT: J 123 ASN cc_start: 0.7096 (t0) cc_final: 0.6872 (t0) REVERT: K 8 LYS cc_start: 0.8539 (tmmt) cc_final: 0.8325 (ttmt) outliers start: 1 outliers final: 1 residues processed: 384 average time/residue: 1.4125 time to fit residues: 624.4887 Evaluate side-chains 272 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 271 time to evaluate : 2.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 206 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 215 optimal weight: 3.9990 chunk 193 optimal weight: 6.9990 chunk 107 optimal weight: 9.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.0670 chunk 103 optimal weight: 7.9990 chunk 199 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 121 optimal weight: 6.9990 chunk 148 optimal weight: 5.9990 chunk 231 optimal weight: 5.9990 overall best weight: 1.7322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 612 ASN ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN H 36 GLN H 71 HIS J 168 GLN J 240 ASN J 264 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.135283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.101528 restraints weight = 90644.012| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 4.14 r_work: 0.3183 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3187 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3186 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 25915 Z= 0.146 Angle : 0.618 13.816 36361 Z= 0.318 Chirality : 0.040 0.172 4345 Planarity : 0.004 0.064 3525 Dihedral : 18.763 112.249 6986 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 2.29 % Allowed : 12.55 % Favored : 85.16 % 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: -2.09 (0.17), residues: 2276 helix: -0.07 (0.20), residues: 732 sheet: -0.23 (0.28), residues: 342 loop : -2.72 (0.16), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP L 87 HIS 0.006 0.001 HIS I 34 PHE 0.024 0.001 PHE K 72 TYR 0.025 0.001 TYR I 160 ARG 0.008 0.001 ARG K 30 Details of bonding type rmsd hydrogen bonds : bond 0.04651 ( 792) hydrogen bonds : angle 4.55800 ( 2067) covalent geometry : bond 0.00326 (25915) covalent geometry : angle 0.61825 (36361) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 311 time to evaluate : 2.933 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 393 ASP cc_start: 0.8019 (m-30) cc_final: 0.7347 (OUTLIER) REVERT: B 557 ILE cc_start: 0.8563 (mt) cc_final: 0.8329 (mp) REVERT: B 728 ILE cc_start: 0.8445 (mt) cc_final: 0.8239 (mm) REVERT: B 811 LYS cc_start: 0.8060 (mmpt) cc_final: 0.7397 (ptmt) REVERT: E 76 TYR cc_start: 0.8770 (t80) cc_final: 0.8352 (t80) REVERT: F 49 ILE cc_start: 0.8828 (OUTLIER) cc_final: 0.8487 (mm) REVERT: F 122 ARG cc_start: 0.8646 (mtm110) cc_final: 0.8401 (mtm110) REVERT: F 130 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.7965 (pm20) REVERT: F 132 ARG cc_start: 0.7237 (pmm-80) cc_final: 0.6517 (pmt170) REVERT: G 85 GLN cc_start: 0.7849 (tm-30) cc_final: 0.7628 (tm-30) REVERT: G 102 GLU cc_start: 0.7788 (mp0) cc_final: 0.7586 (mp0) REVERT: G 104 ILE cc_start: 0.8227 (pt) cc_final: 0.7858 (pp) REVERT: H 13 LYS cc_start: 0.7204 (tttt) cc_final: 0.6943 (ttpt) REVERT: H 118 TRP cc_start: 0.8496 (OUTLIER) cc_final: 0.7982 (m-90) REVERT: I 125 ASP cc_start: 0.8126 (m-30) cc_final: 0.7217 (t0) REVERT: J 38 TYR cc_start: 0.8004 (m-10) cc_final: 0.7717 (m-10) REVERT: J 123 ASN cc_start: 0.6911 (t0) cc_final: 0.6666 (t0) REVERT: K 8 LYS cc_start: 0.8409 (tmmt) cc_final: 0.8146 (ttmt) outliers start: 48 outliers final: 15 residues processed: 327 average time/residue: 1.3139 time to fit residues: 498.2893 Evaluate side-chains 279 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 262 time to evaluate : 2.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 799 VAL Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 108 ASP Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 80 CYS Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain H residue 118 TRP Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 136 ARG Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 260 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 75 optimal weight: 0.7980 chunk 198 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 79 optimal weight: 0.8980 chunk 125 optimal weight: 6.9990 chunk 190 optimal weight: 7.9990 chunk 11 optimal weight: 10.0000 chunk 248 optimal weight: 7.9990 chunk 40 optimal weight: 7.9990 chunk 246 optimal weight: 2.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN H 36 GLN J 168 GLN J 283 GLN L 75 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.132034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.098232 restraints weight = 84980.516| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 3.99 r_work: 0.3137 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3141 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3141 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 25915 Z= 0.227 Angle : 0.681 13.366 36361 Z= 0.349 Chirality : 0.043 0.178 4345 Planarity : 0.005 0.067 3525 Dihedral : 18.738 110.605 6984 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.90 % Favored : 89.10 % Rotamer: Outliers : 3.05 % Allowed : 16.23 % Favored : 80.72 % 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: -2.18 (0.17), residues: 2276 helix: -0.14 (0.20), residues: 740 sheet: -0.28 (0.28), residues: 353 loop : -2.82 (0.16), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 87 HIS 0.006 0.001 HIS B 180 PHE 0.017 0.002 PHE H 77 TYR 0.030 0.002 TYR H 84 ARG 0.011 0.001 ARG B 550 Details of bonding type rmsd hydrogen bonds : bond 0.05648 ( 792) hydrogen bonds : angle 4.48945 ( 2067) covalent geometry : bond 0.00510 (25915) covalent geometry : angle 0.68120 (36361) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 283 time to evaluate : 2.318 Fit side-chains revert: symmetry clash REVERT: B 291 SER cc_start: 0.8918 (m) cc_final: 0.8712 (m) REVERT: B 393 ASP cc_start: 0.8226 (m-30) cc_final: 0.7642 (t70) REVERT: B 486 GLU cc_start: 0.8380 (mm-30) cc_final: 0.7999 (mt-10) REVERT: B 626 ARG cc_start: 0.8742 (ttt-90) cc_final: 0.8189 (ttt-90) REVERT: B 811 LYS cc_start: 0.8086 (mmpt) cc_final: 0.7329 (ptmt) REVERT: B 843 ASP cc_start: 0.8832 (OUTLIER) cc_final: 0.8479 (t0) REVERT: B 849 ARG cc_start: 0.8477 (mtm-85) cc_final: 0.7379 (ptt90) REVERT: F 49 ILE cc_start: 0.8906 (OUTLIER) cc_final: 0.8571 (mm) REVERT: F 130 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.8265 (pm20) REVERT: F 132 ARG cc_start: 0.7425 (pmm-80) cc_final: 0.6661 (pmt170) REVERT: G 70 LYS cc_start: 0.8097 (OUTLIER) cc_final: 0.7701 (tptm) REVERT: G 85 GLN cc_start: 0.8075 (tm-30) cc_final: 0.7783 (tm-30) REVERT: G 102 GLU cc_start: 0.7846 (mp0) cc_final: 0.7638 (mp0) REVERT: G 104 ILE cc_start: 0.8284 (pt) cc_final: 0.7919 (pp) REVERT: H 118 TRP cc_start: 0.8516 (OUTLIER) cc_final: 0.7999 (m-90) REVERT: I 136 ARG cc_start: 0.8193 (tpm170) cc_final: 0.7083 (tpt90) REVERT: J 123 ASN cc_start: 0.7169 (t0) cc_final: 0.6850 (t0) REVERT: J 136 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7712 (mtm180) REVERT: J 282 GLU cc_start: 0.8259 (mp0) cc_final: 0.8021 (mp0) REVERT: K 8 LYS cc_start: 0.8366 (tmmt) cc_final: 0.8153 (ttmt) outliers start: 64 outliers final: 19 residues processed: 316 average time/residue: 1.3813 time to fit residues: 502.9053 Evaluate side-chains 267 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 242 time to evaluate : 2.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 799 VAL Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 80 CYS Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain H residue 118 TRP Chi-restraints excluded: chain I residue 205 LEU Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 46 THR Chi-restraints excluded: chain J residue 136 ARG Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 175 SER Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain J residue 260 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 121 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 223 optimal weight: 6.9990 chunk 245 optimal weight: 4.9990 chunk 56 optimal weight: 0.0980 chunk 157 optimal weight: 1.9990 chunk 188 optimal weight: 0.1980 chunk 195 optimal weight: 7.9990 chunk 221 optimal weight: 0.1980 chunk 58 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 16 optimal weight: 10.0000 chunk 226 optimal weight: 0.2980 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN F 87 HIS H 36 GLN H 70 ASN J 283 GLN L 71 HIS L 81 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.138745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.105192 restraints weight = 76940.521| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 3.90 r_work: 0.3256 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3250 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3250 r_free = 0.3250 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3250 r_free = 0.3250 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3250 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.081 25915 Z= 0.105 Angle : 0.566 10.572 36361 Z= 0.292 Chirality : 0.038 0.185 4345 Planarity : 0.004 0.058 3525 Dihedral : 18.532 114.008 6984 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 2.58 % Allowed : 18.90 % Favored : 78.52 % 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: -1.69 (0.18), residues: 2276 helix: 0.37 (0.21), residues: 730 sheet: 0.06 (0.28), residues: 351 loop : -2.59 (0.16), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 624 HIS 0.006 0.001 HIS L 71 PHE 0.022 0.001 PHE K 72 TYR 0.027 0.001 TYR K 37 ARG 0.008 0.000 ARG K 30 Details of bonding type rmsd hydrogen bonds : bond 0.03593 ( 792) hydrogen bonds : angle 4.08020 ( 2067) covalent geometry : bond 0.00228 (25915) covalent geometry : angle 0.56598 (36361) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 301 time to evaluate : 2.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 119 GLU cc_start: 0.8356 (tp30) cc_final: 0.8116 (tp30) REVERT: B 219 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7806 (mm-30) REVERT: B 486 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7811 (mt-10) REVERT: B 626 ARG cc_start: 0.8771 (ttt-90) cc_final: 0.8297 (ttt-90) REVERT: B 811 LYS cc_start: 0.8064 (mmpt) cc_final: 0.7358 (ptmt) REVERT: B 843 ASP cc_start: 0.8720 (OUTLIER) cc_final: 0.8432 (t0) REVERT: D 91 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8273 (pp20) REVERT: D 142 MET cc_start: 0.7879 (ptt) cc_final: 0.7534 (ptp) REVERT: F 132 ARG cc_start: 0.7278 (pmm-80) cc_final: 0.6523 (pmt170) REVERT: G 70 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7694 (tptm) REVERT: G 85 GLN cc_start: 0.8088 (tm-30) cc_final: 0.7807 (tm-30) REVERT: G 98 GLU cc_start: 0.8578 (pm20) cc_final: 0.8036 (tt0) REVERT: G 102 GLU cc_start: 0.7963 (mp0) cc_final: 0.7544 (mp0) REVERT: H 118 TRP cc_start: 0.8511 (OUTLIER) cc_final: 0.7990 (m-90) REVERT: I 125 ASP cc_start: 0.7914 (m-30) cc_final: 0.6875 (t0) REVERT: J 123 ASN cc_start: 0.7098 (t0) cc_final: 0.6770 (t0) REVERT: J 282 GLU cc_start: 0.8112 (mp0) cc_final: 0.7593 (mp0) REVERT: K 8 LYS cc_start: 0.8241 (tmmt) cc_final: 0.7897 (ttpt) REVERT: L 26 LYS cc_start: 0.8277 (tppt) cc_final: 0.7998 (tppt) REVERT: L 81 GLN cc_start: 0.8155 (mt0) cc_final: 0.7925 (mt0) outliers start: 54 outliers final: 13 residues processed: 326 average time/residue: 1.3149 time to fit residues: 499.3999 Evaluate side-chains 279 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 263 time to evaluate : 2.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 118 TRP Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 175 SER Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 260 VAL Chi-restraints excluded: chain L residue 121 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 56 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 125 optimal weight: 4.9990 chunk 187 optimal weight: 0.6980 chunk 95 optimal weight: 7.9990 chunk 221 optimal weight: 3.9990 chunk 132 optimal weight: 0.9980 chunk 110 optimal weight: 0.8980 chunk 83 optimal weight: 0.4980 chunk 204 optimal weight: 0.0770 chunk 88 optimal weight: 5.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN F 129 GLN H 36 GLN J 283 GLN L 75 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.138754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.105228 restraints weight = 76051.153| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 3.87 r_work: 0.3257 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3250 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3250 r_free = 0.3250 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3250 r_free = 0.3250 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3250 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 25915 Z= 0.100 Angle : 0.552 9.420 36361 Z= 0.282 Chirality : 0.037 0.168 4345 Planarity : 0.004 0.054 3525 Dihedral : 18.409 113.750 6984 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 2.43 % Allowed : 20.62 % Favored : 76.95 % 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: -1.49 (0.18), residues: 2276 helix: 0.51 (0.21), residues: 734 sheet: 0.25 (0.28), residues: 353 loop : -2.49 (0.16), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 87 HIS 0.003 0.001 HIS I 143 PHE 0.017 0.001 PHE K 72 TYR 0.022 0.001 TYR H 84 ARG 0.010 0.000 ARG F 122 Details of bonding type rmsd hydrogen bonds : bond 0.03459 ( 792) hydrogen bonds : angle 3.95279 ( 2067) covalent geometry : bond 0.00218 (25915) covalent geometry : angle 0.55250 (36361) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 280 time to evaluate : 2.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 119 GLU cc_start: 0.8349 (tp30) cc_final: 0.8074 (tp30) REVERT: B 219 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7803 (mm-30) REVERT: B 486 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7730 (mt-10) REVERT: B 626 ARG cc_start: 0.8827 (ttt-90) cc_final: 0.8326 (ttt-90) REVERT: B 684 MET cc_start: 0.6912 (OUTLIER) cc_final: 0.6709 (mtp) REVERT: B 811 LYS cc_start: 0.8054 (mmpt) cc_final: 0.7356 (ptmt) REVERT: B 843 ASP cc_start: 0.8734 (OUTLIER) cc_final: 0.8404 (t0) REVERT: B 849 ARG cc_start: 0.8257 (mtm-85) cc_final: 0.7930 (mtm-85) REVERT: D 91 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8289 (pp20) REVERT: D 142 MET cc_start: 0.7956 (ptt) cc_final: 0.7684 (ptp) REVERT: F 9 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7943 (pm20) REVERT: F 49 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8552 (mm) REVERT: F 130 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.7981 (pm20) REVERT: F 132 ARG cc_start: 0.7321 (pmm-80) cc_final: 0.6569 (pmt170) REVERT: G 70 LYS cc_start: 0.8055 (OUTLIER) cc_final: 0.7791 (tptm) REVERT: G 85 GLN cc_start: 0.8085 (tm-30) cc_final: 0.7771 (tm-30) REVERT: G 102 GLU cc_start: 0.7966 (mp0) cc_final: 0.7630 (mp0) REVERT: H 118 TRP cc_start: 0.8463 (OUTLIER) cc_final: 0.7908 (m-90) REVERT: I 118 THR cc_start: 0.8968 (t) cc_final: 0.8620 (p) REVERT: I 124 LEU cc_start: 0.7134 (OUTLIER) cc_final: 0.6678 (mm) REVERT: I 125 ASP cc_start: 0.7915 (m-30) cc_final: 0.6896 (t0) REVERT: J 123 ASN cc_start: 0.7110 (t0) cc_final: 0.6801 (t0) REVERT: J 148 SER cc_start: 0.8633 (m) cc_final: 0.8416 (p) REVERT: J 282 GLU cc_start: 0.8115 (mp0) cc_final: 0.7898 (mp0) REVERT: K 8 LYS cc_start: 0.8219 (tmmt) cc_final: 0.7997 (ttmt) REVERT: K 37 TYR cc_start: 0.8452 (t80) cc_final: 0.8234 (t80) REVERT: L 81 GLN cc_start: 0.8201 (mt0) cc_final: 0.7977 (mt0) outliers start: 51 outliers final: 28 residues processed: 308 average time/residue: 1.3091 time to fit residues: 467.1606 Evaluate side-chains 289 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 253 time to evaluate : 2.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 684 MET Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 9 GLU Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 53 ASP Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 118 TRP Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 204 ILE Chi-restraints excluded: chain I residue 205 LEU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 175 SER Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 196 MET Chi-restraints excluded: chain J residue 260 VAL Chi-restraints excluded: chain J residue 283 GLN Chi-restraints excluded: chain L residue 35 TYR Chi-restraints excluded: chain L residue 121 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 213 optimal weight: 1.9990 chunk 108 optimal weight: 8.9990 chunk 19 optimal weight: 10.0000 chunk 162 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 chunk 219 optimal weight: 4.9990 chunk 143 optimal weight: 8.9990 chunk 225 optimal weight: 0.9990 chunk 175 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 593 ASN ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN H 36 GLN H 40 ASN I 102 GLN L 71 HIS L 75 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.133842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.099848 restraints weight = 87680.186| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 4.06 r_work: 0.3154 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3160 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3160 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 25915 Z= 0.195 Angle : 0.636 9.055 36361 Z= 0.325 Chirality : 0.041 0.178 4345 Planarity : 0.004 0.063 3525 Dihedral : 18.437 111.424 6984 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.53 % Favored : 90.47 % Rotamer: Outliers : 3.29 % Allowed : 21.24 % Favored : 75.47 % 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: -1.69 (0.18), residues: 2276 helix: 0.31 (0.20), residues: 742 sheet: 0.04 (0.28), residues: 357 loop : -2.57 (0.17), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP L 87 HIS 0.008 0.001 HIS L 71 PHE 0.013 0.001 PHE J 140 TYR 0.025 0.002 TYR H 84 ARG 0.013 0.001 ARG F 122 Details of bonding type rmsd hydrogen bonds : bond 0.04922 ( 792) hydrogen bonds : angle 4.14483 ( 2067) covalent geometry : bond 0.00436 (25915) covalent geometry : angle 0.63633 (36361) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 270 time to evaluate : 2.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 108 ILE cc_start: 0.8239 (OUTLIER) cc_final: 0.7999 (pp) REVERT: B 119 GLU cc_start: 0.8567 (tp30) cc_final: 0.8218 (tp30) REVERT: B 204 LEU cc_start: 0.5864 (OUTLIER) cc_final: 0.5021 (mp) REVERT: B 209 MET cc_start: 0.8675 (mtt) cc_final: 0.8349 (mmt) REVERT: B 219 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7919 (mm-30) REVERT: B 486 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7813 (mt-10) REVERT: B 584 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.8411 (ttp-170) REVERT: B 626 ARG cc_start: 0.8854 (ttt-90) cc_final: 0.8323 (ttt-90) REVERT: B 811 LYS cc_start: 0.8072 (mmpt) cc_final: 0.7285 (ptmt) REVERT: B 843 ASP cc_start: 0.8839 (OUTLIER) cc_final: 0.8443 (t0) REVERT: D 91 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8328 (pp20) REVERT: D 142 MET cc_start: 0.8087 (ptt) cc_final: 0.7795 (ptp) REVERT: E 37 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.7251 (ptt-90) REVERT: E 91 GLU cc_start: 0.8964 (pm20) cc_final: 0.8548 (pp20) REVERT: F 9 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.8009 (pm20) REVERT: F 49 ILE cc_start: 0.8892 (OUTLIER) cc_final: 0.8558 (mm) REVERT: F 130 GLU cc_start: 0.8899 (OUTLIER) cc_final: 0.8098 (pm20) REVERT: G 70 LYS cc_start: 0.8053 (OUTLIER) cc_final: 0.7553 (tptm) REVERT: G 85 GLN cc_start: 0.8109 (tm-30) cc_final: 0.7809 (tm-30) REVERT: G 98 GLU cc_start: 0.8654 (pm20) cc_final: 0.8043 (tt0) REVERT: G 102 GLU cc_start: 0.7930 (mp0) cc_final: 0.7701 (mp0) REVERT: H 118 TRP cc_start: 0.8558 (OUTLIER) cc_final: 0.8018 (m-90) REVERT: J 123 ASN cc_start: 0.7222 (t0) cc_final: 0.7010 (t0) REVERT: J 136 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7563 (mtm180) REVERT: K 8 LYS cc_start: 0.8289 (tmmt) cc_final: 0.8026 (ttmt) REVERT: L 26 LYS cc_start: 0.8404 (tppt) cc_final: 0.8160 (tppt) outliers start: 69 outliers final: 31 residues processed: 307 average time/residue: 1.2497 time to fit residues: 445.3029 Evaluate side-chains 294 residues out of total 2095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 252 time to evaluate : 2.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 584 ARG Chi-restraints excluded: chain B residue 799 VAL Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 37 ARG Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 108 ASP Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 9 GLU Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 80 CYS Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 53 ASP Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain H residue 118 TRP Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain J residue 136 ARG Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 175 SER Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain J residue 260 VAL Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain K residue 63 HIS Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 35 TYR Chi-restraints excluded: chain L residue 121 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.9191 > 50: distance: 25 - 30: 9.995 distance: 30 - 31: 5.708 distance: 31 - 32: 6.173 distance: 31 - 34: 6.319 distance: 32 - 33: 7.861 distance: 32 - 42: 3.201 distance: 35 - 36: 17.210 distance: 35 - 37: 10.276 distance: 36 - 38: 9.974 distance: 37 - 39: 13.012 distance: 38 - 40: 14.550 distance: 39 - 40: 14.335 distance: 40 - 41: 8.392 distance: 42 - 43: 8.930 distance: 43 - 44: 4.845 distance: 44 - 45: 7.827 distance: 44 - 46: 3.839 distance: 46 - 47: 7.647 distance: 47 - 48: 3.706 distance: 48 - 49: 4.945 distance: 48 - 58: 11.461 distance: 51 - 52: 4.304 distance: 52 - 54: 3.307 distance: 53 - 55: 6.693 distance: 54 - 56: 4.711 distance: 58 - 59: 3.272 distance: 59 - 60: 7.053 distance: 59 - 62: 7.618 distance: 60 - 61: 12.708 distance: 60 - 63: 6.772 distance: 63 - 64: 20.900 distance: 64 - 65: 26.559 distance: 64 - 67: 19.002 distance: 65 - 66: 19.413 distance: 65 - 71: 41.624 distance: 67 - 68: 23.336 distance: 68 - 69: 9.020 distance: 68 - 70: 18.289 distance: 71 - 72: 15.678 distance: 72 - 73: 19.747 distance: 72 - 75: 10.990 distance: 73 - 74: 24.960 distance: 73 - 82: 16.199 distance: 75 - 76: 7.404 distance: 76 - 77: 8.076 distance: 77 - 78: 7.449 distance: 78 - 79: 18.152 distance: 79 - 80: 9.348 distance: 79 - 81: 8.510 distance: 82 - 83: 11.518 distance: 83 - 84: 19.955 distance: 83 - 86: 18.952 distance: 84 - 85: 13.898 distance: 84 - 90: 13.632 distance: 86 - 87: 5.526 distance: 87 - 88: 7.525 distance: 87 - 89: 6.441 distance: 90 - 91: 15.235 distance: 91 - 92: 9.693 distance: 91 - 94: 15.449 distance: 92 - 93: 9.008 distance: 92 - 97: 12.578 distance: 94 - 95: 20.837 distance: 94 - 96: 16.442 distance: 97 - 98: 12.267 distance: 98 - 99: 5.877 distance: 98 - 101: 12.519 distance: 99 - 100: 11.285 distance: 99 - 106: 14.514 distance: 101 - 102: 18.764 distance: 102 - 103: 16.697 distance: 103 - 104: 19.878 distance: 103 - 105: 13.718 distance: 106 - 107: 5.749 distance: 107 - 108: 11.195 distance: 107 - 110: 17.238 distance: 108 - 109: 9.218 distance: 108 - 111: 6.367 distance: 109 - 139: 8.147