Starting phenix.real_space_refine on Sun Jun 15 06:04:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v9a_31813/06_2025/7v9a_31813.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v9a_31813/06_2025/7v9a_31813.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7v9a_31813/06_2025/7v9a_31813.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v9a_31813/06_2025/7v9a_31813.map" model { file = "/net/cci-nas-00/data/ceres_data/7v9a_31813/06_2025/7v9a_31813.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v9a_31813/06_2025/7v9a_31813.cif" } resolution = 3.94 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= 0.004 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 146 5.49 5 S 86 5.16 5 C 10128 2.51 5 N 2999 2.21 5 O 3517 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 112 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: 16876 Number of models: 1 Model: "" Number of chains: 10 Chain: "B" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2938 Classifications: {'peptide': 377} Link IDs: {'PTRANS': 25, 'TRANS': 351} Chain: "C" Number of atoms: 3118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3118 Classifications: {'peptide': 393} Link IDs: {'PTRANS': 16, 'TRANS': 376} Chain: "D" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 940 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 9, 'TRANS': 107} Chain: "E" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1031 Classifications: {'peptide': 129} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 119} Chain: "F" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 526 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 5, 'TRANS': 56} Chain: "G" Number of atoms: 2762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2762 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 13, 'TRANS': 335} Chain: "H" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 9, 'TRANS': 88} Chain: "I" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1065 Classifications: {'peptide': 134} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 123} Chain: "J" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 541 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 5, 'TRANS': 58} Chain: "R" Number of atoms: 3144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3144 Classifications: {'RNA': 146} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 7, 'rna3p_pur': 70, 'rna3p_pyr': 57} Link IDs: {'rna2p': 19, 'rna3p': 126} Chain breaks: 2 Time building chain proxies: 11.07, per 1000 atoms: 0.66 Number of scatterers: 16876 At special positions: 0 Unit cell: (183.7, 96.8, 132, 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 86 16.00 P 146 15.00 O 3517 8.00 N 2999 7.00 C 10128 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: 4.39 Conformation dependent library (CDL) restraints added in 2.0 seconds 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3200 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 21 sheets defined 24.7% alpha, 23.0% beta 16 base pairs and 57 stacking pairs defined. Time for finding SS restraints: 5.06 Creating SS restraints... Processing helix chain 'B' and resid 200 through 206 removed outlier: 4.259A pdb=" N GLY B 206 " --> pdb=" O LEU B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 498 Processing helix chain 'C' and resid 53 through 57 removed outlier: 3.700A pdb=" N LYS C 57 " --> pdb=" O LEU C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 89 Processing helix chain 'C' and resid 101 through 114 Processing helix chain 'C' and resid 139 through 141 No H-bonds generated for 'chain 'C' and resid 139 through 141' Processing helix chain 'C' and resid 142 through 148 removed outlier: 3.785A pdb=" N SER C 148 " --> pdb=" O LYS C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 176 removed outlier: 3.910A pdb=" N LEU C 169 " --> pdb=" O GLY C 165 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU C 176 " --> pdb=" O ALA C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 238 removed outlier: 3.535A pdb=" N LEU C 229 " --> pdb=" O TYR C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 276 removed outlier: 3.525A pdb=" N VAL C 266 " --> pdb=" O THR C 262 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TRP C 271 " --> pdb=" O LEU C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 286 removed outlier: 3.746A pdb=" N VAL C 285 " --> pdb=" O TYR C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 295 removed outlier: 3.632A pdb=" N LEU C 293 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR C 294 " --> pdb=" O LYS C 291 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N SER C 295 " --> pdb=" O LEU C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 312 Processing helix chain 'C' and resid 351 through 356 Processing helix chain 'C' and resid 385 through 396 Processing helix chain 'C' and resid 409 through 414 removed outlier: 3.538A pdb=" N LYS C 413 " --> pdb=" O PRO C 409 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 30 Processing helix chain 'E' and resid 42 through 58 removed outlier: 4.232A pdb=" N LYS E 56 " --> pdb=" O LYS E 52 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN E 57 " --> pdb=" O LYS E 53 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS E 58 " --> pdb=" O ALA E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 74 removed outlier: 3.736A pdb=" N LYS E 73 " --> pdb=" O LYS E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 101 Processing helix chain 'E' and resid 111 through 120 Processing helix chain 'E' and resid 134 through 137 removed outlier: 4.139A pdb=" N GLU E 137 " --> pdb=" O GLU E 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 134 through 137' Processing helix chain 'E' and resid 138 through 148 removed outlier: 3.624A pdb=" N CYS E 142 " --> pdb=" O ALA E 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 53 removed outlier: 3.713A pdb=" N ARG F 45 " --> pdb=" O TYR F 41 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE F 52 " --> pdb=" O ILE F 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 57 removed outlier: 4.096A pdb=" N LYS G 57 " --> pdb=" O LEU G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 89 Processing helix chain 'G' and resid 101 through 114 removed outlier: 3.660A pdb=" N ALA G 107 " --> pdb=" O HIS G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 141 No H-bonds generated for 'chain 'G' and resid 139 through 141' Processing helix chain 'G' and resid 142 through 148 removed outlier: 3.735A pdb=" N SER G 148 " --> pdb=" O LYS G 144 " (cutoff:3.500A) Processing helix chain 'G' and resid 165 through 176 removed outlier: 4.085A pdb=" N LEU G 169 " --> pdb=" O GLY G 165 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU G 176 " --> pdb=" O ALA G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 226 through 237 Processing helix chain 'G' and resid 263 through 276 Processing helix chain 'G' and resid 279 through 284 Processing helix chain 'G' and resid 288 through 292 removed outlier: 3.702A pdb=" N LYS G 291 " --> pdb=" O PRO G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 303 through 312 removed outlier: 4.360A pdb=" N ASN G 307 " --> pdb=" O ASP G 303 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ALA G 308 " --> pdb=" O SER G 304 " (cutoff:3.500A) Processing helix chain 'G' and resid 351 through 356 Processing helix chain 'G' and resid 385 through 395 Processing helix chain 'H' and resid 148 through 151 removed outlier: 3.809A pdb=" N LEU H 151 " --> pdb=" O PRO H 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 148 through 151' Processing helix chain 'I' and resid 20 through 30 Processing helix chain 'I' and resid 40 through 56 removed outlier: 4.128A pdb=" N LYS I 56 " --> pdb=" O LYS I 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 74 removed outlier: 3.788A pdb=" N LYS I 73 " --> pdb=" O LYS I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 101 Processing helix chain 'I' and resid 111 through 119 removed outlier: 3.502A pdb=" N ALA I 118 " --> pdb=" O LEU I 114 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY I 119 " --> pdb=" O GLY I 115 " (cutoff:3.500A) Processing helix chain 'I' and resid 136 through 147 removed outlier: 3.999A pdb=" N GLU I 141 " --> pdb=" O GLU I 137 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 53 removed outlier: 3.911A pdb=" N ILE J 46 " --> pdb=" O SER J 42 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR J 47 " --> pdb=" O ARG J 43 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 155 through 160 removed outlier: 3.513A pdb=" N ARG B 155 " --> pdb=" O TRP B 518 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N LEU B 516 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLY B 159 " --> pdb=" O LEU B 514 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU B 514 " --> pdb=" O GLY B 159 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY B 466 " --> pdb=" O ALA B 479 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 173 through 177 removed outlier: 3.582A pdb=" N ASN B 187 " --> pdb=" O LYS B 173 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU B 185 " --> pdb=" O CYS B 175 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N TRP B 177 " --> pdb=" O CYS B 183 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N CYS B 183 " --> pdb=" O TRP B 177 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU B 218 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ASN B 197 " --> pdb=" O PRO B 216 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 226 through 231 removed outlier: 7.140A pdb=" N SER B 248 " --> pdb=" O TYR B 227 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N TYR B 229 " --> pdb=" O ALA B 246 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ALA B 246 " --> pdb=" O TYR B 229 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N TRP B 231 " --> pdb=" O TYR B 244 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N TYR B 244 " --> pdb=" O TRP B 231 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE B 254 " --> pdb=" O SER B 267 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N SER B 267 " --> pdb=" O ILE B 254 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ILE B 256 " --> pdb=" O ARG B 265 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 283 through 285 removed outlier: 3.646A pdb=" N CYS B 284 " --> pdb=" O PHE B 293 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE B 293 " --> pdb=" O CYS B 284 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 328 through 333 removed outlier: 3.521A pdb=" N LEU B 351 " --> pdb=" O ALA B 361 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA B 361 " --> pdb=" O LEU B 351 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 370 through 373 removed outlier: 6.711A pdb=" N GLY B 385 " --> pdb=" O THR B 371 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N LEU B 373 " --> pdb=" O PHE B 383 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N PHE B 383 " --> pdb=" O LEU B 373 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER B 384 " --> pdb=" O LEU B 393 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU B 393 " --> pdb=" O SER B 384 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ALA B 386 " --> pdb=" O GLU B 391 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N GLU B 391 " --> pdb=" O ALA B 386 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N TRP B 405 " --> pdb=" O CYS B 394 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 419 through 421 removed outlier: 3.565A pdb=" N VAL B 429 " --> pdb=" O ASP B 420 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LEU B 455 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ASP B 441 " --> pdb=" O PRO B 453 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 63 through 64 removed outlier: 3.581A pdb=" N TYR C 323 " --> pdb=" O ASN C 63 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL C 300 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N TYR C 323 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ARG C 298 " --> pdb=" O TYR C 323 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N LYS C 297 " --> pdb=" O VAL C 334 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE C 336 " --> pdb=" O LYS C 297 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N LEU C 299 " --> pdb=" O ILE C 336 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN C 331 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG C 368 " --> pdb=" O MET C 345 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE C 347 " --> pdb=" O ILE C 366 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE C 366 " --> pdb=" O ILE C 347 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ALA C 364 " --> pdb=" O ILE C 315 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE C 315 " --> pdb=" O ALA C 364 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 91 through 95 removed outlier: 3.587A pdb=" N CYS C 131 " --> pdb=" O ARG C 248 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ARG C 250 " --> pdb=" O CYS C 131 " (cutoff:3.500A) removed outlier: 9.054A pdb=" N ILE C 133 " --> pdb=" O ARG C 250 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLN C 244 " --> pdb=" O ARG C 158 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ARG C 158 " --> pdb=" O GLN C 244 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N LEU C 246 " --> pdb=" O ILE C 156 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ILE C 156 " --> pdb=" O LEU C 246 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ARG C 248 " --> pdb=" O VAL C 154 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL C 154 " --> pdb=" O ARG C 248 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG C 250 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY C 155 " --> pdb=" O PHE C 216 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY C 214 " --> pdb=" O VAL C 157 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU C 213 " --> pdb=" O TYR C 207 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N TYR C 207 " --> pdb=" O LEU C 213 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ILE C 215 " --> pdb=" O ILE C 205 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 119 through 120 removed outlier: 3.587A pdb=" N CYS C 131 " --> pdb=" O ARG C 248 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ARG C 250 " --> pdb=" O CYS C 131 " (cutoff:3.500A) removed outlier: 9.054A pdb=" N ILE C 133 " --> pdb=" O ARG C 250 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N MET C 254 " --> pdb=" O SER C 251 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 71 through 80 removed outlier: 5.767A pdb=" N PHE D 76 " --> pdb=" O LYS D 87 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LYS D 87 " --> pdb=" O PHE D 76 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N HIS D 78 " --> pdb=" O VAL D 85 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL D 85 " --> pdb=" O HIS D 78 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N TYR D 124 " --> pdb=" O ILE D 116 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ILE D 116 " --> pdb=" O TYR D 124 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N SER D 126 " --> pdb=" O ASP D 114 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLY D 111 " --> pdb=" O VAL D 102 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N PHE D 144 " --> pdb=" O LEU D 73 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 94 through 96 removed outlier: 3.881A pdb=" N VAL D 95 " --> pdb=" O LEU D 152 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU D 152 " --> pdb=" O VAL D 95 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'E' and resid 60 through 61 removed outlier: 3.517A pdb=" N VAL E 129 " --> pdb=" O ILE E 78 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE E 78 " --> pdb=" O VAL E 129 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N MET E 79 " --> pdb=" O VAL E 106 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ILE E 108 " --> pdb=" O MET E 79 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU E 81 " --> pdb=" O ILE E 108 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 13 through 16 removed outlier: 3.611A pdb=" N VAL F 14 " --> pdb=" O TYR F 6 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR F 5 " --> pdb=" O CYS F 28 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N CYS F 28 " --> pdb=" O TYR F 5 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 63 through 64 removed outlier: 3.559A pdb=" N TYR G 323 " --> pdb=" O ASN G 63 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 119 through 120 removed outlier: 3.733A pdb=" N GLY G 119 " --> pdb=" O CYS G 135 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU G 132 " --> pdb=" O LEU G 94 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU G 94 " --> pdb=" O LEU G 132 " (cutoff:3.500A) removed outlier: 9.801A pdb=" N VAL G 261 " --> pdb=" O PHE G 91 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ASN G 93 " --> pdb=" O VAL G 261 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 178 through 182 removed outlier: 3.828A pdb=" N ARG G 197 " --> pdb=" O LEU G 180 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU G 201 " --> pdb=" O SER G 219 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLU G 152 " --> pdb=" O VAL G 249 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL G 249 " --> pdb=" O GLU G 152 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU G 245 " --> pdb=" O ILE G 156 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ARG G 158 " --> pdb=" O MET G 243 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N MET G 243 " --> pdb=" O ARG G 158 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N MET G 254 " --> pdb=" O SER G 251 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 298 through 300 removed outlier: 5.841A pdb=" N LEU G 299 " --> pdb=" O ILE G 336 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN G 331 " --> pdb=" O ALA G 348 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N CYS G 344 " --> pdb=" O VAL G 335 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG G 368 " --> pdb=" O MET G 345 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ILE G 347 " --> pdb=" O ILE G 366 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ILE G 366 " --> pdb=" O ILE G 347 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 71 through 80 removed outlier: 5.278A pdb=" N PHE H 76 " --> pdb=" O LYS H 87 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N LYS H 87 " --> pdb=" O PHE H 76 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N TYR H 124 " --> pdb=" O ILE H 116 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N ILE H 116 " --> pdb=" O TYR H 124 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N SER H 126 " --> pdb=" O ASP H 114 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY H 111 " --> pdb=" O VAL H 102 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N PHE H 144 " --> pdb=" O LEU H 73 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 60 through 61 removed outlier: 3.891A pdb=" N ILE I 78 " --> pdb=" O VAL I 129 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 13 through 16 removed outlier: 3.629A pdb=" N VAL J 14 " --> pdb=" O TYR J 6 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN J 4 " --> pdb=" O THR J 16 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N CYS J 28 " --> pdb=" O TYR J 5 " (cutoff:3.500A) 385 hydrogen bonds defined for protein. 1071 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 42 hydrogen bonds 84 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 57 stacking parallelities Total time for adding SS restraints: 4.81 Time building geometry restraints manager: 4.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4860 1.34 - 1.46: 3643 1.46 - 1.57: 8636 1.57 - 1.69: 289 1.69 - 1.81: 125 Bond restraints: 17553 Sorted by residual: bond pdb=" C LEU H 158 " pdb=" N PRO H 159 " ideal model delta sigma weight residual 1.334 1.354 -0.020 1.11e-02 8.12e+03 3.33e+00 bond pdb=" CA TYR E 91 " pdb=" CB TYR E 91 " ideal model delta sigma weight residual 1.528 1.568 -0.039 2.61e-02 1.47e+03 2.27e+00 bond pdb=" C GLY B 444 " pdb=" N PRO B 445 " ideal model delta sigma weight residual 1.335 1.354 -0.018 1.36e-02 5.41e+03 1.79e+00 bond pdb=" N LEU G 54 " pdb=" CA LEU G 54 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.29e-02 6.01e+03 1.70e+00 bond pdb=" N LEU C 54 " pdb=" CA LEU C 54 " ideal model delta sigma weight residual 1.459 1.474 -0.015 1.16e-02 7.43e+03 1.65e+00 ... (remaining 17548 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 23566 1.36 - 2.73: 714 2.73 - 4.09: 134 4.09 - 5.46: 35 5.46 - 6.82: 9 Bond angle restraints: 24458 Sorted by residual: angle pdb=" CA ASP D 91 " pdb=" C ASP D 91 " pdb=" N GLU D 92 " ideal model delta sigma weight residual 118.81 113.40 5.41 1.15e+00 7.56e-01 2.21e+01 angle pdb=" N VAL C 239 " pdb=" CA VAL C 239 " pdb=" C VAL C 239 " ideal model delta sigma weight residual 113.71 109.66 4.05 9.50e-01 1.11e+00 1.82e+01 angle pdb=" N VAL G 239 " pdb=" CA VAL G 239 " pdb=" C VAL G 239 " ideal model delta sigma weight residual 113.71 109.85 3.86 9.50e-01 1.11e+00 1.65e+01 angle pdb=" C PRO C 53 " pdb=" N LEU C 54 " pdb=" CA LEU C 54 " ideal model delta sigma weight residual 120.79 126.37 -5.58 1.39e+00 5.18e-01 1.61e+01 angle pdb=" N VAL C 363 " pdb=" CA VAL C 363 " pdb=" C VAL C 363 " ideal model delta sigma weight residual 113.53 109.70 3.83 9.80e-01 1.04e+00 1.53e+01 ... (remaining 24453 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.19: 10279 34.19 - 68.38: 550 68.38 - 102.57: 77 102.57 - 136.76: 1 136.76 - 170.96: 6 Dihedral angle restraints: 10913 sinusoidal: 5927 harmonic: 4986 Sorted by residual: dihedral pdb=" C4' C R 398 " pdb=" C3' C R 398 " pdb=" C2' C R 398 " pdb=" C1' C R 398 " ideal model delta sinusoidal sigma weight residual -35.00 33.12 -68.12 1 8.00e+00 1.56e-02 9.41e+01 dihedral pdb=" C5' C R 398 " pdb=" C4' C R 398 " pdb=" C3' C R 398 " pdb=" O3' C R 398 " ideal model delta sinusoidal sigma weight residual 147.00 81.29 65.71 1 8.00e+00 1.56e-02 8.83e+01 dihedral pdb=" O4' C R 398 " pdb=" C4' C R 398 " pdb=" C3' C R 398 " pdb=" C2' C R 398 " ideal model delta sinusoidal sigma weight residual 24.00 -34.36 58.36 1 8.00e+00 1.56e-02 7.13e+01 ... (remaining 10910 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2519 0.055 - 0.111: 262 0.111 - 0.166: 23 0.166 - 0.222: 0 0.222 - 0.277: 2 Chirality restraints: 2806 Sorted by residual: chirality pdb=" C3' C R 398 " pdb=" C4' C R 398 " pdb=" O3' C R 398 " pdb=" C2' C R 398 " both_signs ideal model delta sigma weight residual False -2.74 -2.47 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" C2' C R 398 " pdb=" C3' C R 398 " pdb=" O2' C R 398 " pdb=" C1' C R 398 " both_signs ideal model delta sigma weight residual False -2.52 -2.75 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" P C R 394 " pdb=" OP1 C R 394 " pdb=" OP2 C R 394 " pdb=" O5' C R 394 " both_signs ideal model delta sigma weight residual True 2.41 -2.56 -0.15 2.00e-01 2.50e+01 5.90e-01 ... (remaining 2803 not shown) Planarity restraints: 2586 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU H 158 " -0.027 5.00e-02 4.00e+02 4.06e-02 2.64e+00 pdb=" N PRO H 159 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO H 159 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO H 159 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP G 52 " 0.025 5.00e-02 4.00e+02 3.85e-02 2.37e+00 pdb=" N PRO G 53 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO G 53 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO G 53 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 500 " 0.025 5.00e-02 4.00e+02 3.71e-02 2.20e+00 pdb=" N PRO B 501 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 501 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 501 " 0.021 5.00e-02 4.00e+02 ... (remaining 2583 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3643 2.79 - 3.32: 13897 3.32 - 3.84: 26781 3.84 - 4.37: 30435 4.37 - 4.90: 51103 Nonbonded interactions: 125859 Sorted by model distance: nonbonded pdb=" O LYS G 291 " pdb=" OG1 THR G 294 " model vdw 2.260 3.040 nonbonded pdb=" OD2 ASP B 422 " pdb=" OG1 THR B 424 " model vdw 2.285 3.040 nonbonded pdb=" O GLY C 383 " pdb=" OG SER C 387 " model vdw 2.290 3.040 nonbonded pdb=" OD1 ASP B 180 " pdb=" OG SER B 182 " model vdw 2.292 3.040 nonbonded pdb=" O ASP G 85 " pdb=" OG1 THR G 89 " model vdw 2.295 3.040 ... (remaining 125854 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 Found NCS groups: ncs_group { reference = (chain 'C' and resid 47 through 395) selection = chain 'G' } ncs_group { reference = chain 'E' selection = (chain 'I' and resid 22 through 150) } ncs_group { reference = chain 'F' selection = (chain 'J' and resid 1 through 62) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.700 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: 0.660 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 41.630 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.060 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5619 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 : 0.002 0.039 17553 Z= 0.126 Angle : 0.579 6.823 24458 Z= 0.353 Chirality : 0.035 0.277 2806 Planarity : 0.004 0.041 2586 Dihedral : 18.983 170.955 7713 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.05 (0.16), residues: 1705 helix: -1.49 (0.23), residues: 379 sheet: -2.27 (0.27), residues: 301 loop : -3.49 (0.14), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 52 HIS 0.002 0.000 HIS H 78 PHE 0.009 0.001 PHE B 419 TYR 0.008 0.001 TYR E 91 ARG 0.002 0.000 ARG C 141 Details of bonding type rmsd hydrogen bonds : bond 0.23041 ( 425) hydrogen bonds : angle 8.42022 ( 1155) covalent geometry : bond 0.00202 (17553) covalent geometry : angle 0.57914 (24458) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 319 time to evaluate : 1.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 80 LYS cc_start: 0.8330 (mptt) cc_final: 0.8024 (mmtm) REVERT: D 146 ILE cc_start: 0.7064 (tt) cc_final: 0.6297 (tt) REVERT: G 133 ILE cc_start: 0.5893 (mm) cc_final: 0.5673 (mm) outliers start: 0 outliers final: 0 residues processed: 319 average time/residue: 0.4105 time to fit residues: 175.0570 Evaluate side-chains 140 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 152 optimal weight: 9.9990 chunk 137 optimal weight: 0.0670 chunk 76 optimal weight: 8.9990 chunk 46 optimal weight: 0.9980 chunk 92 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 86 optimal weight: 0.9980 chunk 105 optimal weight: 9.9990 chunk 164 optimal weight: 5.9990 overall best weight: 2.0122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 252 ASN ** B 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 ASN C 93 ASN C 147 GLN C 160 HIS C 244 GLN C 276 HIS ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN G 244 GLN G 307 ASN G 331 GLN H 64 GLN I 31 GLN I 68 GLN J 59 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.115021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.095491 restraints weight = 67088.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.095517 restraints weight = 58137.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.096179 restraints weight = 44812.427| |-----------------------------------------------------------------------------| r_work (final): 0.4082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6276 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17553 Z= 0.144 Angle : 0.622 8.598 24458 Z= 0.306 Chirality : 0.040 0.257 2806 Planarity : 0.005 0.075 2586 Dihedral : 20.159 171.454 4258 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 2.25 % Allowed : 13.52 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % 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: -3.17 (0.18), residues: 1705 helix: -0.43 (0.26), residues: 376 sheet: -1.96 (0.25), residues: 352 loop : -2.97 (0.16), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 380 HIS 0.006 0.001 HIS E 132 PHE 0.019 0.002 PHE C 181 TYR 0.013 0.001 TYR E 139 ARG 0.012 0.001 ARG G 227 Details of bonding type rmsd hydrogen bonds : bond 0.04129 ( 425) hydrogen bonds : angle 5.35406 ( 1155) covalent geometry : bond 0.00317 (17553) covalent geometry : angle 0.62201 (24458) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 156 time to evaluate : 1.693 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: C 88 ARG cc_start: 0.7430 (mmt-90) cc_final: 0.7222 (mmt90) REVERT: C 94 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7639 (tp) REVERT: D 133 MET cc_start: 0.5126 (mmm) cc_final: 0.4822 (mmt) REVERT: D 146 ILE cc_start: 0.7503 (tt) cc_final: 0.7218 (tt) REVERT: E 79 MET cc_start: 0.5638 (mmp) cc_final: 0.5428 (mmp) REVERT: G 227 ARG cc_start: 0.6728 (ttt180) cc_final: 0.6343 (ttt90) REVERT: G 254 MET cc_start: 0.5891 (mmm) cc_final: 0.5561 (mmm) REVERT: G 345 MET cc_start: 0.4991 (ptp) cc_final: 0.4745 (mtp) REVERT: G 371 MET cc_start: 0.5317 (mmm) cc_final: 0.5111 (mtt) REVERT: H 115 GLU cc_start: 0.7934 (pp20) cc_final: 0.7460 (pp20) REVERT: H 133 MET cc_start: 0.6486 (OUTLIER) cc_final: 0.6209 (mmt) outliers start: 34 outliers final: 22 residues processed: 178 average time/residue: 0.3454 time to fit residues: 89.2518 Evaluate side-chains 152 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 1.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 311 TYR Chi-restraints excluded: chain C residue 323 TYR Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 48 TYR Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain G residue 224 THR Chi-restraints excluded: chain G residue 327 ILE Chi-restraints excluded: chain H residue 133 MET Chi-restraints excluded: chain J residue 2 PHE Chi-restraints excluded: chain J residue 3 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 31 optimal weight: 0.9990 chunk 168 optimal weight: 30.0000 chunk 68 optimal weight: 4.9990 chunk 151 optimal weight: 5.9990 chunk 87 optimal weight: 9.9990 chunk 38 optimal weight: 7.9990 chunk 67 optimal weight: 0.9980 chunk 40 optimal weight: 8.9990 chunk 50 optimal weight: 0.0030 chunk 122 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 overall best weight: 2.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 515 GLN C 93 ASN C 120 HIS ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 63 ASN G 242 GLN G 331 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.111082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.091278 restraints weight = 66612.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.091025 restraints weight = 58903.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.091710 restraints weight = 50053.983| |-----------------------------------------------------------------------------| r_work (final): 0.4008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6457 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17553 Z= 0.135 Angle : 0.580 8.743 24458 Z= 0.286 Chirality : 0.039 0.165 2806 Planarity : 0.004 0.072 2586 Dihedral : 20.118 169.239 4258 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.92 % Allowed : 17.03 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % 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: -2.80 (0.18), residues: 1705 helix: -0.20 (0.26), residues: 384 sheet: -1.74 (0.26), residues: 338 loop : -2.71 (0.17), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 257 HIS 0.007 0.001 HIS E 132 PHE 0.013 0.001 PHE D 76 TYR 0.012 0.002 TYR H 149 ARG 0.008 0.001 ARG G 227 Details of bonding type rmsd hydrogen bonds : bond 0.03832 ( 425) hydrogen bonds : angle 4.94262 ( 1155) covalent geometry : bond 0.00301 (17553) covalent geometry : angle 0.58049 (24458) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 140 time to evaluate : 1.733 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 515 GLN cc_start: 0.5233 (OUTLIER) cc_final: 0.4158 (mp10) REVERT: D 133 MET cc_start: 0.5663 (mmm) cc_final: 0.5371 (mmt) REVERT: E 128 MET cc_start: 0.4737 (OUTLIER) cc_final: 0.4439 (ttt) REVERT: F 5 TYR cc_start: 0.7099 (OUTLIER) cc_final: 0.6774 (p90) REVERT: G 345 MET cc_start: 0.5625 (ptp) cc_final: 0.5338 (mtp) REVERT: G 371 MET cc_start: 0.5551 (mmm) cc_final: 0.5164 (mtt) REVERT: H 115 GLU cc_start: 0.8120 (pp20) cc_final: 0.7824 (pp20) REVERT: H 124 TYR cc_start: 0.8252 (m-80) cc_final: 0.7987 (m-80) outliers start: 44 outliers final: 26 residues processed: 167 average time/residue: 0.2953 time to fit residues: 73.1895 Evaluate side-chains 140 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 111 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 515 GLN Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 323 TYR Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 48 TYR Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 128 MET Chi-restraints excluded: chain F residue 5 TYR Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 327 ILE Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain J residue 2 PHE Chi-restraints excluded: chain J residue 3 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 157 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 chunk 178 optimal weight: 10.0000 chunk 146 optimal weight: 0.0060 chunk 180 optimal weight: 10.0000 chunk 47 optimal weight: 7.9990 chunk 175 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 chunk 80 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 overall best weight: 4.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 515 GLN C 270 GLN ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 HIS G 259 HIS G 331 GLN I 59 GLN J 44 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.105058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.085641 restraints weight = 67337.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.085225 restraints weight = 73515.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.085849 restraints weight = 64105.427| |-----------------------------------------------------------------------------| r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6702 moved from start: 0.5464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.140 17553 Z= 0.213 Angle : 0.735 10.580 24458 Z= 0.369 Chirality : 0.043 0.179 2806 Planarity : 0.005 0.043 2586 Dihedral : 20.353 172.739 4258 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 4.17 % Allowed : 19.42 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % 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: -2.78 (0.18), residues: 1705 helix: -0.36 (0.26), residues: 382 sheet: -1.65 (0.26), residues: 340 loop : -2.65 (0.17), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP B 517 HIS 0.011 0.002 HIS B 376 PHE 0.022 0.002 PHE F 52 TYR 0.017 0.002 TYR G 153 ARG 0.011 0.001 ARG G 227 Details of bonding type rmsd hydrogen bonds : bond 0.05050 ( 425) hydrogen bonds : angle 5.37923 ( 1155) covalent geometry : bond 0.00474 (17553) covalent geometry : angle 0.73488 (24458) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 118 time to evaluate : 1.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 235 MET cc_start: 0.5087 (tpt) cc_final: 0.4740 (tpt) REVERT: B 250 ARG cc_start: 0.7900 (ttt180) cc_final: 0.7570 (ttt90) REVERT: D 133 MET cc_start: 0.5964 (mmm) cc_final: 0.5250 (mmt) REVERT: G 136 ILE cc_start: 0.4898 (OUTLIER) cc_final: 0.4673 (mm) REVERT: G 227 ARG cc_start: 0.6505 (ttt180) cc_final: 0.5593 (ttm-80) REVERT: G 345 MET cc_start: 0.5979 (ptp) cc_final: 0.5666 (mtp) REVERT: G 371 MET cc_start: 0.5524 (mmm) cc_final: 0.5231 (mtt) REVERT: H 124 TYR cc_start: 0.8330 (m-80) cc_final: 0.8044 (m-80) outliers start: 63 outliers final: 46 residues processed: 170 average time/residue: 0.2756 time to fit residues: 73.0561 Evaluate side-chains 147 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 100 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 515 GLN Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 316 MET Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 323 TYR Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 48 TYR Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 136 ILE Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 327 ILE Chi-restraints excluded: chain G residue 333 ILE Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain J residue 2 PHE Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 12 ASP Chi-restraints excluded: chain J residue 56 MET Chi-restraints excluded: chain J residue 64 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 24 optimal weight: 10.0000 chunk 99 optimal weight: 1.9990 chunk 153 optimal weight: 0.9990 chunk 156 optimal weight: 2.9990 chunk 178 optimal weight: 10.0000 chunk 129 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 128 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 chunk 9 optimal weight: 20.0000 chunk 56 optimal weight: 6.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 515 GLN ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 259 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.106204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.087186 restraints weight = 66664.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.086663 restraints weight = 72646.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.087446 restraints weight = 61380.150| |-----------------------------------------------------------------------------| r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6639 moved from start: 0.5578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17553 Z= 0.129 Angle : 0.598 8.655 24458 Z= 0.294 Chirality : 0.040 0.158 2806 Planarity : 0.004 0.043 2586 Dihedral : 20.274 174.779 4258 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 3.98 % Allowed : 21.54 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % 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: -2.49 (0.19), residues: 1705 helix: -0.02 (0.27), residues: 385 sheet: -1.45 (0.27), residues: 329 loop : -2.52 (0.17), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 517 HIS 0.006 0.001 HIS B 376 PHE 0.011 0.001 PHE C 59 TYR 0.009 0.001 TYR E 139 ARG 0.003 0.000 ARG B 409 Details of bonding type rmsd hydrogen bonds : bond 0.03644 ( 425) hydrogen bonds : angle 4.96493 ( 1155) covalent geometry : bond 0.00290 (17553) covalent geometry : angle 0.59836 (24458) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 115 time to evaluate : 1.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 235 MET cc_start: 0.5237 (tpt) cc_final: 0.4682 (tpp) REVERT: B 373 LEU cc_start: 0.6576 (OUTLIER) cc_final: 0.6172 (tp) REVERT: C 392 MET cc_start: 0.7718 (ttp) cc_final: 0.7441 (tmm) REVERT: D 133 MET cc_start: 0.5928 (mmm) cc_final: 0.5543 (mmt) REVERT: G 345 MET cc_start: 0.6016 (ptp) cc_final: 0.5622 (mtp) REVERT: G 371 MET cc_start: 0.5372 (mmm) cc_final: 0.4988 (mtt) REVERT: H 124 TYR cc_start: 0.8158 (m-80) cc_final: 0.7802 (m-80) outliers start: 60 outliers final: 42 residues processed: 164 average time/residue: 0.2856 time to fit residues: 70.9446 Evaluate side-chains 144 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 101 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 316 MET Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 323 TYR Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain D residue 58 PHE Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 48 TYR Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 327 ILE Chi-restraints excluded: chain G residue 333 ILE Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain J residue 2 PHE Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 64 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 104 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 0.3980 chunk 98 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 160 optimal weight: 5.9990 chunk 79 optimal weight: 7.9990 chunk 133 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 GLN ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 GLN G 276 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.105721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.086374 restraints weight = 66779.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.086018 restraints weight = 68972.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.086674 restraints weight = 61639.273| |-----------------------------------------------------------------------------| r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6672 moved from start: 0.5873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17553 Z= 0.124 Angle : 0.586 8.511 24458 Z= 0.289 Chirality : 0.039 0.180 2806 Planarity : 0.004 0.040 2586 Dihedral : 20.267 174.577 4258 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 3.71 % Allowed : 21.94 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % 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: -2.29 (0.19), residues: 1705 helix: 0.07 (0.27), residues: 385 sheet: -1.27 (0.28), residues: 324 loop : -2.37 (0.17), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 517 HIS 0.005 0.001 HIS B 366 PHE 0.015 0.001 PHE H 138 TYR 0.016 0.001 TYR G 225 ARG 0.004 0.000 ARG B 250 Details of bonding type rmsd hydrogen bonds : bond 0.03454 ( 425) hydrogen bonds : angle 4.90337 ( 1155) covalent geometry : bond 0.00280 (17553) covalent geometry : angle 0.58611 (24458) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 110 time to evaluate : 2.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 235 MET cc_start: 0.5120 (tpt) cc_final: 0.4459 (tpp) REVERT: B 373 LEU cc_start: 0.6583 (OUTLIER) cc_final: 0.6175 (tp) REVERT: C 343 ILE cc_start: 0.6566 (mt) cc_final: 0.6350 (mt) REVERT: D 133 MET cc_start: 0.6020 (mmm) cc_final: 0.5543 (mmt) REVERT: E 31 GLN cc_start: 0.5979 (OUTLIER) cc_final: 0.5671 (tp40) REVERT: E 79 MET cc_start: 0.6510 (mmp) cc_final: 0.6301 (mmt) REVERT: G 136 ILE cc_start: 0.4687 (OUTLIER) cc_final: 0.4454 (mm) REVERT: G 227 ARG cc_start: 0.6626 (ttt180) cc_final: 0.5794 (ttm-80) REVERT: G 345 MET cc_start: 0.6065 (ptp) cc_final: 0.5658 (mtp) REVERT: G 371 MET cc_start: 0.5377 (mmm) cc_final: 0.4996 (mtt) REVERT: H 124 TYR cc_start: 0.8204 (m-80) cc_final: 0.7810 (m-80) outliers start: 56 outliers final: 42 residues processed: 158 average time/residue: 0.3485 time to fit residues: 84.7579 Evaluate side-chains 145 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 100 time to evaluate : 2.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 323 TYR Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain D residue 58 PHE Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain E residue 31 GLN Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 48 TYR Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 136 ILE Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 327 ILE Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain J residue 2 PHE Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 64 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 169 optimal weight: 40.0000 chunk 142 optimal weight: 0.9990 chunk 179 optimal weight: 20.0000 chunk 54 optimal weight: 9.9990 chunk 141 optimal weight: 3.9990 chunk 49 optimal weight: 9.9990 chunk 50 optimal weight: 4.9990 chunk 158 optimal weight: 4.9990 chunk 139 optimal weight: 7.9990 chunk 5 optimal weight: 0.0870 chunk 85 optimal weight: 0.0870 overall best weight: 2.0342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.104477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.084129 restraints weight = 65915.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.084329 restraints weight = 53657.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.084742 restraints weight = 49524.180| |-----------------------------------------------------------------------------| r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6719 moved from start: 0.6103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17553 Z= 0.123 Angle : 0.588 9.128 24458 Z= 0.289 Chirality : 0.039 0.175 2806 Planarity : 0.004 0.042 2586 Dihedral : 20.226 174.403 4258 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 3.71 % Allowed : 22.66 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % 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: -2.15 (0.19), residues: 1705 helix: 0.17 (0.27), residues: 385 sheet: -1.11 (0.29), residues: 309 loop : -2.29 (0.17), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 257 HIS 0.008 0.001 HIS B 366 PHE 0.010 0.001 PHE H 138 TYR 0.009 0.001 TYR H 145 ARG 0.004 0.000 ARG G 171 Details of bonding type rmsd hydrogen bonds : bond 0.03383 ( 425) hydrogen bonds : angle 4.86893 ( 1155) covalent geometry : bond 0.00281 (17553) covalent geometry : angle 0.58844 (24458) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 105 time to evaluate : 1.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 235 MET cc_start: 0.4873 (tpt) cc_final: 0.4219 (tpp) REVERT: B 373 LEU cc_start: 0.6555 (OUTLIER) cc_final: 0.6157 (tp) REVERT: C 391 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7919 (mm) REVERT: D 133 MET cc_start: 0.6226 (mmm) cc_final: 0.5819 (mmt) REVERT: E 38 LEU cc_start: 0.6771 (OUTLIER) cc_final: 0.6562 (tp) REVERT: G 227 ARG cc_start: 0.6645 (ttt180) cc_final: 0.5924 (ttm-80) REVERT: G 345 MET cc_start: 0.6263 (ptp) cc_final: 0.5861 (mtp) REVERT: G 371 MET cc_start: 0.5565 (mmm) cc_final: 0.5209 (mtt) REVERT: H 124 TYR cc_start: 0.8235 (m-80) cc_final: 0.7872 (m-80) outliers start: 56 outliers final: 45 residues processed: 153 average time/residue: 0.2693 time to fit residues: 64.4121 Evaluate side-chains 144 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 96 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 316 MET Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 323 TYR Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain D residue 58 PHE Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain E residue 31 GLN Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 48 TYR Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 327 ILE Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain J residue 2 PHE Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 64 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- 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: 62.669 > 50: distance: 39 - 44: 7.432 distance: 44 - 45: 33.223 distance: 45 - 46: 40.485 distance: 45 - 48: 37.548 distance: 46 - 47: 7.312 distance: 46 - 50: 12.909 distance: 48 - 49: 38.277 distance: 54 - 55: 14.736 distance: 55 - 56: 9.277 distance: 55 - 57: 8.400 distance: 56 - 58: 18.335 distance: 58 - 60: 3.248 distance: 59 - 60: 17.554 distance: 62 - 63: 54.888 distance: 63 - 64: 44.900 distance: 63 - 67: 32.206 distance: 65 - 66: 33.355 distance: 67 - 68: 24.069 distance: 67 - 73: 15.424 distance: 68 - 69: 31.865 distance: 68 - 71: 31.667 distance: 69 - 70: 32.746 distance: 69 - 74: 3.229 distance: 71 - 72: 3.054 distance: 72 - 73: 3.898 distance: 74 - 75: 18.142 distance: 75 - 76: 40.476 distance: 75 - 78: 26.988 distance: 76 - 77: 13.266 distance: 76 - 82: 25.845 distance: 78 - 79: 26.843 distance: 79 - 80: 25.092 distance: 79 - 81: 17.154 distance: 83 - 84: 20.366 distance: 84 - 85: 10.607 distance: 84 - 86: 46.783 distance: 86 - 87: 12.240 distance: 87 - 88: 18.145 distance: 87 - 90: 17.562 distance: 88 - 89: 52.485 distance: 88 - 92: 20.128 distance: 90 - 91: 30.492 distance: 92 - 93: 16.213 distance: 93 - 96: 15.078 distance: 94 - 101: 16.298 distance: 96 - 97: 40.662 distance: 97 - 98: 26.080 distance: 98 - 99: 21.578 distance: 98 - 100: 19.201 distance: 101 - 102: 23.613 distance: 101 - 140: 22.934 distance: 102 - 103: 21.590 distance: 102 - 105: 30.030 distance: 103 - 104: 6.267 distance: 103 - 109: 40.213 distance: 104 - 137: 31.112 distance: 105 - 106: 12.796 distance: 106 - 107: 29.799 distance: 106 - 108: 13.491 distance: 109 - 110: 10.041 distance: 110 - 111: 23.137 distance: 111 - 112: 31.896 distance: 111 - 120: 20.912 distance: 114 - 115: 24.831 distance: 114 - 116: 10.943 distance: 115 - 117: 15.002 distance: 116 - 118: 36.824 distance: 117 - 119: 18.495 distance: 118 - 119: 22.931