Starting phenix.real_space_refine on Wed Jun 18 06:47:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z1c_39722/06_2025/8z1c_39722.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z1c_39722/06_2025/8z1c_39722.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z1c_39722/06_2025/8z1c_39722.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z1c_39722/06_2025/8z1c_39722.map" model { file = "/net/cci-nas-00/data/ceres_data/8z1c_39722/06_2025/8z1c_39722.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z1c_39722/06_2025/8z1c_39722.cif" } resolution = 3.15 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= 0.010 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: 4 Type Number sf(0) Gaussians S 78 5.16 5 C 13128 2.51 5 N 3618 2.21 5 O 3978 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 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: 20802 Number of models: 1 Model: "" Number of chains: 6 Chain: "E" Number of atoms: 3467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3467 Classifications: {'peptide': 460} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 443} Chain: "F" Number of atoms: 3467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3467 Classifications: {'peptide': 460} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 443} Chain: "D" Number of atoms: 3467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3467 Classifications: {'peptide': 460} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 443} Chain: "A" Number of atoms: 3467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3467 Classifications: {'peptide': 460} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 443} Chain: "B" Number of atoms: 3467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3467 Classifications: {'peptide': 460} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 443} Chain: "C" Number of atoms: 3467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3467 Classifications: {'peptide': 460} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 443} Time building chain proxies: 13.78, per 1000 atoms: 0.66 Number of scatterers: 20802 At special positions: 0 Unit cell: (116.63, 119.84, 113.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 78 16.00 O 3978 8.00 N 3618 7.00 C 13128 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: 5.33 Conformation dependent library (CDL) restraints added in 3.0 seconds 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4920 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 17 sheets defined 51.6% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.07 Creating SS restraints... Processing helix chain 'E' and resid 7 through 23 Processing helix chain 'E' and resid 24 through 30 removed outlier: 4.207A pdb=" N GLN E 28 " --> pdb=" O SER E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 40 removed outlier: 4.080A pdb=" N LYS E 35 " --> pdb=" O PRO E 31 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA E 36 " --> pdb=" O GLU E 32 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA E 38 " --> pdb=" O ARG E 34 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL E 39 " --> pdb=" O LYS E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 103 removed outlier: 3.889A pdb=" N PHE E 101 " --> pdb=" O PHE E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 141 Processing helix chain 'E' and resid 142 through 144 No H-bonds generated for 'chain 'E' and resid 142 through 144' Processing helix chain 'E' and resid 158 through 174 Processing helix chain 'E' and resid 197 through 213 removed outlier: 4.148A pdb=" N VAL E 202 " --> pdb=" O GLY E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 244 removed outlier: 3.691A pdb=" N LEU E 238 " --> pdb=" O GLN E 234 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS E 239 " --> pdb=" O TYR E 235 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLU E 242 " --> pdb=" O LEU E 238 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU E 243 " --> pdb=" O LYS E 239 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLY E 244 " --> pdb=" O VAL E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 281 Processing helix chain 'E' and resid 284 through 290 removed outlier: 3.526A pdb=" N LEU E 288 " --> pdb=" O GLN E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 297 Processing helix chain 'E' and resid 305 through 309 Processing helix chain 'E' and resid 326 through 337 Processing helix chain 'E' and resid 350 through 364 removed outlier: 4.094A pdb=" N ALA E 363 " --> pdb=" O ALA E 359 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASN E 364 " --> pdb=" O HIS E 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 379 Processing helix chain 'E' and resid 381 through 396 Processing helix chain 'E' and resid 400 through 422 removed outlier: 3.635A pdb=" N THR E 422 " --> pdb=" O ASN E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 436 through 456 removed outlier: 3.884A pdb=" N GLY E 440 " --> pdb=" O SER E 436 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS E 448 " --> pdb=" O ALA E 444 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 23 Processing helix chain 'F' and resid 24 through 30 removed outlier: 4.314A pdb=" N GLN F 28 " --> pdb=" O SER F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 41 removed outlier: 4.226A pdb=" N LYS F 35 " --> pdb=" O PRO F 31 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA F 36 " --> pdb=" O GLU F 32 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA F 38 " --> pdb=" O ARG F 34 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL F 39 " --> pdb=" O LYS F 35 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER F 41 " --> pdb=" O LEU F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 106 removed outlier: 3.887A pdb=" N PHE F 101 " --> pdb=" O PHE F 97 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR F 106 " --> pdb=" O LYS F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 142 Processing helix chain 'F' and resid 158 through 174 Processing helix chain 'F' and resid 192 through 194 No H-bonds generated for 'chain 'F' and resid 192 through 194' Processing helix chain 'F' and resid 195 through 213 removed outlier: 3.672A pdb=" N VAL F 201 " --> pdb=" O THR F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 231 through 239 removed outlier: 3.743A pdb=" N LYS F 239 " --> pdb=" O TYR F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 244 removed outlier: 3.534A pdb=" N LEU F 243 " --> pdb=" O VAL F 240 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 281 Processing helix chain 'F' and resid 286 through 291 Processing helix chain 'F' and resid 291 through 296 Processing helix chain 'F' and resid 326 through 337 Processing helix chain 'F' and resid 350 through 363 Processing helix chain 'F' and resid 380 through 395 removed outlier: 3.509A pdb=" N ALA F 384 " --> pdb=" O ALA F 380 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 408 Processing helix chain 'F' and resid 412 through 423 Processing helix chain 'F' and resid 436 through 457 removed outlier: 3.918A pdb=" N GLY F 440 " --> pdb=" O SER F 436 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS F 448 " --> pdb=" O ALA F 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 23 Processing helix chain 'D' and resid 25 through 30 Processing helix chain 'D' and resid 32 through 41 removed outlier: 4.212A pdb=" N ALA D 36 " --> pdb=" O GLU D 32 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA D 38 " --> pdb=" O ARG D 34 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER D 41 " --> pdb=" O LEU D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 106 removed outlier: 3.878A pdb=" N PHE D 101 " --> pdb=" O PHE D 97 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR D 106 " --> pdb=" O LYS D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 141 Processing helix chain 'D' and resid 142 through 144 No H-bonds generated for 'chain 'D' and resid 142 through 144' Processing helix chain 'D' and resid 158 through 174 removed outlier: 3.576A pdb=" N LYS D 171 " --> pdb=" O GLY D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 213 removed outlier: 4.228A pdb=" N VAL D 201 " --> pdb=" O THR D 197 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N VAL D 202 " --> pdb=" O GLY D 198 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR D 213 " --> pdb=" O ILE D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 244 Processing helix chain 'D' and resid 268 through 281 removed outlier: 3.632A pdb=" N ASP D 281 " --> pdb=" O ALA D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 291 removed outlier: 4.219A pdb=" N LEU D 288 " --> pdb=" O GLN D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 296 Processing helix chain 'D' and resid 305 through 309 removed outlier: 4.066A pdb=" N VAL D 308 " --> pdb=" O ARG D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 337 Processing helix chain 'D' and resid 350 through 363 removed outlier: 3.784A pdb=" N GLU D 362 " --> pdb=" O GLU D 358 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ALA D 363 " --> pdb=" O ALA D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 379 removed outlier: 3.626A pdb=" N ALA D 378 " --> pdb=" O PRO D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 395 Processing helix chain 'D' and resid 400 through 422 removed outlier: 3.524A pdb=" N THR D 422 " --> pdb=" O ASN D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 457 removed outlier: 4.098A pdb=" N LYS D 448 " --> pdb=" O ALA D 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 7 through 23 Processing helix chain 'A' and resid 25 through 30 Processing helix chain 'A' and resid 32 through 42 removed outlier: 3.604A pdb=" N ALA A 36 " --> pdb=" O GLU A 32 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA A 38 " --> pdb=" O ARG A 34 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL A 39 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N SER A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL A 42 " --> pdb=" O ALA A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 106 removed outlier: 3.872A pdb=" N PHE A 101 " --> pdb=" O PHE A 97 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A 106 " --> pdb=" O LYS A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 141 removed outlier: 3.560A pdb=" N THR A 138 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU A 139 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 144 No H-bonds generated for 'chain 'A' and resid 142 through 144' Processing helix chain 'A' and resid 158 through 174 Processing helix chain 'A' and resid 192 through 194 No H-bonds generated for 'chain 'A' and resid 192 through 194' Processing helix chain 'A' and resid 195 through 213 Processing helix chain 'A' and resid 229 through 241 removed outlier: 4.420A pdb=" N ALA A 233 " --> pdb=" O SER A 229 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N TYR A 235 " --> pdb=" O ASN A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 281 Processing helix chain 'A' and resid 286 through 291 Processing helix chain 'A' and resid 291 through 298 Processing helix chain 'A' and resid 305 through 310 removed outlier: 4.178A pdb=" N VAL A 310 " --> pdb=" O TRP A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 337 removed outlier: 3.679A pdb=" N GLY A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 363 Processing helix chain 'A' and resid 381 through 395 Processing helix chain 'A' and resid 400 through 408 Processing helix chain 'A' and resid 412 through 423 Processing helix chain 'A' and resid 437 through 456 removed outlier: 4.602A pdb=" N ILE A 443 " --> pdb=" O THR A 439 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ALA A 444 " --> pdb=" O GLY A 440 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LYS A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 23 removed outlier: 3.501A pdb=" N ASN B 23 " --> pdb=" O SER B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 30 removed outlier: 3.959A pdb=" N GLN B 28 " --> pdb=" O SER B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 41 removed outlier: 3.652A pdb=" N ALA B 36 " --> pdb=" O GLU B 32 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA B 38 " --> pdb=" O ARG B 34 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL B 39 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 106 removed outlier: 3.879A pdb=" N PHE B 101 " --> pdb=" O PHE B 97 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR B 106 " --> pdb=" O LYS B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 142 Processing helix chain 'B' and resid 158 through 174 Processing helix chain 'B' and resid 192 through 194 No H-bonds generated for 'chain 'B' and resid 192 through 194' Processing helix chain 'B' and resid 195 through 213 Processing helix chain 'B' and resid 231 through 242 removed outlier: 4.064A pdb=" N GLU B 242 " --> pdb=" O LEU B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 281 removed outlier: 3.619A pdb=" N ILE B 272 " --> pdb=" O THR B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 296 Processing helix chain 'B' and resid 326 through 337 removed outlier: 3.617A pdb=" N GLY B 337 " --> pdb=" O LEU B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 363 Processing helix chain 'B' and resid 381 through 395 Processing helix chain 'B' and resid 400 through 408 Processing helix chain 'B' and resid 412 through 423 Processing helix chain 'B' and resid 436 through 457 removed outlier: 3.844A pdb=" N GLY B 440 " --> pdb=" O SER B 436 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYS B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 23 removed outlier: 3.539A pdb=" N ASN C 23 " --> pdb=" O SER C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 30 removed outlier: 3.929A pdb=" N GLN C 28 " --> pdb=" O SER C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 41 removed outlier: 3.617A pdb=" N ALA C 36 " --> pdb=" O GLU C 32 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA C 38 " --> pdb=" O ARG C 34 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL C 39 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N SER C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 106 removed outlier: 3.878A pdb=" N PHE C 101 " --> pdb=" O PHE C 97 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR C 106 " --> pdb=" O LYS C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 142 Processing helix chain 'C' and resid 158 through 174 Processing helix chain 'C' and resid 192 through 194 No H-bonds generated for 'chain 'C' and resid 192 through 194' Processing helix chain 'C' and resid 195 through 214 Processing helix chain 'C' and resid 230 through 239 removed outlier: 4.000A pdb=" N ALA C 236 " --> pdb=" O VAL C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 244 Processing helix chain 'C' and resid 268 through 281 Processing helix chain 'C' and resid 291 through 298 Processing helix chain 'C' and resid 326 through 337 removed outlier: 3.614A pdb=" N GLY C 337 " --> pdb=" O LEU C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 363 Processing helix chain 'C' and resid 380 through 395 Processing helix chain 'C' and resid 400 through 408 Processing helix chain 'C' and resid 412 through 423 Processing helix chain 'C' and resid 436 through 457 removed outlier: 3.988A pdb=" N GLY C 440 " --> pdb=" O SER C 436 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LYS C 448 " --> pdb=" O ALA C 444 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 81 through 83 removed outlier: 6.259A pdb=" N ARG E 82 " --> pdb=" O SER E 117 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N GLY B 115 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N GLY B 80 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N SER B 117 " --> pdb=" O GLY B 80 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ARG B 82 " --> pdb=" O SER B 117 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N TYR B 77 " --> pdb=" O VAL B 150 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N ALA B 152 " --> pdb=" O TYR B 77 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N GLY B 79 " --> pdb=" O ALA B 152 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 77 through 79 removed outlier: 7.125A pdb=" N TYR E 77 " --> pdb=" O VAL E 150 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'E' and resid 246 through 247 removed outlier: 3.991A pdb=" N VAL E 224 " --> pdb=" O ARG E 246 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ARG E 223 " --> pdb=" O VAL E 315 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N LEU E 317 " --> pdb=" O ARG E 223 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ALA E 225 " --> pdb=" O LEU E 317 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ALA E 316 " --> pdb=" O ALA E 342 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE E 341 " --> pdb=" O ALA E 373 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'E' and resid 250 through 251 removed outlier: 3.614A pdb=" N LEU E 250 " --> pdb=" O LEU E 257 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU E 257 " --> pdb=" O LEU E 250 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 149 through 153 removed outlier: 7.076A pdb=" N TYR F 77 " --> pdb=" O VAL F 150 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ALA F 152 " --> pdb=" O TYR F 77 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N GLY F 79 " --> pdb=" O ALA F 152 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N GLY F 115 " --> pdb=" O LYS F 78 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N GLY F 80 " --> pdb=" O GLY F 115 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N SER F 117 " --> pdb=" O GLY F 80 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ARG F 82 " --> pdb=" O SER F 117 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N GLY C 115 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N GLY C 80 " --> pdb=" O GLY C 115 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N SER C 117 " --> pdb=" O GLY C 80 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ARG C 82 " --> pdb=" O SER C 117 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N TYR C 77 " --> pdb=" O VAL C 150 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ALA C 152 " --> pdb=" O TYR C 77 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N GLY C 79 " --> pdb=" O ALA C 152 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 223 through 224 Processing sheet with id=AA7, first strand: chain 'F' and resid 258 through 259 removed outlier: 3.576A pdb=" N ILE F 258 " --> pdb=" O THR F 299 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 149 through 153 removed outlier: 6.981A pdb=" N TYR D 77 " --> pdb=" O VAL D 150 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N ALA D 152 " --> pdb=" O TYR D 77 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N GLY D 79 " --> pdb=" O ALA D 152 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N GLY D 115 " --> pdb=" O LYS D 78 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N GLY D 80 " --> pdb=" O GLY D 115 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N SER D 117 " --> pdb=" O GLY D 80 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ARG D 82 " --> pdb=" O SER D 117 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N GLY A 115 " --> pdb=" O LYS A 78 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N GLY A 80 " --> pdb=" O GLY A 115 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N SER A 117 " --> pdb=" O GLY A 80 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ARG A 82 " --> pdb=" O SER A 117 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N TYR A 77 " --> pdb=" O VAL A 150 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ALA A 152 " --> pdb=" O TYR A 77 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLY A 79 " --> pdb=" O ALA A 152 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 223 through 224 removed outlier: 3.533A pdb=" N VAL D 224 " --> pdb=" O ARG D 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 257 through 259 removed outlier: 3.521A pdb=" N ILE D 258 " --> pdb=" O THR D 299 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 315 through 316 removed outlier: 5.926A pdb=" N ALA D 316 " --> pdb=" O ALA D 342 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 223 through 224 Processing sheet with id=AB4, first strand: chain 'A' and resid 257 through 258 removed outlier: 3.529A pdb=" N ILE A 258 " --> pdb=" O THR A 299 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 246 through 247 removed outlier: 6.296A pdb=" N ARG B 223 " --> pdb=" O VAL B 315 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N LEU B 317 " --> pdb=" O ARG B 223 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ALA B 225 " --> pdb=" O LEU B 317 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 255 through 259 removed outlier: 3.614A pdb=" N LEU B 301 " --> pdb=" O SER B 256 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 224 through 226 Processing sheet with id=AB8, first strand: chain 'C' and resid 255 through 258 removed outlier: 3.869A pdb=" N SER C 256 " --> pdb=" O LEU C 301 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU C 301 " --> pdb=" O SER C 256 " (cutoff:3.500A) 1010 hydrogen bonds defined for protein. 2967 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.62 Time building geometry restraints manager: 6.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 4637 1.33 - 1.47: 7444 1.47 - 1.61: 9015 1.61 - 1.75: 0 1.75 - 1.88: 126 Bond restraints: 21222 Sorted by residual: bond pdb=" CA SER A 117 " pdb=" CB SER A 117 " ideal model delta sigma weight residual 1.533 1.460 0.073 1.65e-02 3.67e+03 1.95e+01 bond pdb=" CA SER E 117 " pdb=" CB SER E 117 " ideal model delta sigma weight residual 1.532 1.458 0.074 1.68e-02 3.54e+03 1.94e+01 bond pdb=" C THR B 138 " pdb=" O THR B 138 " ideal model delta sigma weight residual 1.236 1.287 -0.050 1.15e-02 7.56e+03 1.92e+01 bond pdb=" CA SER C 117 " pdb=" CB SER C 117 " ideal model delta sigma weight residual 1.533 1.461 0.072 1.65e-02 3.67e+03 1.90e+01 bond pdb=" CA SER F 117 " pdb=" CB SER F 117 " ideal model delta sigma weight residual 1.533 1.463 0.070 1.65e-02 3.67e+03 1.80e+01 ... (remaining 21217 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.06: 28609 4.06 - 8.12: 99 8.12 - 12.18: 7 12.18 - 16.25: 0 16.25 - 20.31: 1 Bond angle restraints: 28716 Sorted by residual: angle pdb=" N PRO F 269 " pdb=" CD PRO F 269 " pdb=" CG PRO F 269 " ideal model delta sigma weight residual 103.20 82.89 20.31 1.50e+00 4.44e-01 1.83e+02 angle pdb=" N PRO A 374 " pdb=" CD PRO A 374 " pdb=" CG PRO A 374 " ideal model delta sigma weight residual 103.20 91.87 11.33 1.50e+00 4.44e-01 5.71e+01 angle pdb=" N PRO F 306 " pdb=" CD PRO F 306 " pdb=" CG PRO F 306 " ideal model delta sigma weight residual 103.20 93.15 10.05 1.50e+00 4.44e-01 4.49e+01 angle pdb=" CA PRO D 429 " pdb=" N PRO D 429 " pdb=" CD PRO D 429 " ideal model delta sigma weight residual 112.00 103.73 8.27 1.40e+00 5.10e-01 3.49e+01 angle pdb=" CB ARG D 170 " pdb=" CG ARG D 170 " pdb=" CD ARG D 170 " ideal model delta sigma weight residual 111.30 100.77 10.53 2.30e+00 1.89e-01 2.10e+01 ... (remaining 28711 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 10963 17.57 - 35.14: 1167 35.14 - 52.71: 269 52.71 - 70.28: 115 70.28 - 87.85: 14 Dihedral angle restraints: 12528 sinusoidal: 4782 harmonic: 7746 Sorted by residual: dihedral pdb=" CA ASP F 410 " pdb=" C ASP F 410 " pdb=" N ILE F 411 " pdb=" CA ILE F 411 " ideal model delta harmonic sigma weight residual 180.00 156.19 23.81 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA ASP B 410 " pdb=" C ASP B 410 " pdb=" N ILE B 411 " pdb=" CA ILE B 411 " ideal model delta harmonic sigma weight residual 180.00 156.87 23.13 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA GLU D 44 " pdb=" C GLU D 44 " pdb=" N ARG D 45 " pdb=" CA ARG D 45 " ideal model delta harmonic sigma weight residual 180.00 157.21 22.79 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 12525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2105 0.066 - 0.131: 835 0.131 - 0.197: 147 0.197 - 0.262: 23 0.262 - 0.328: 10 Chirality restraints: 3120 Sorted by residual: chirality pdb=" CA LEU C 172 " pdb=" N LEU C 172 " pdb=" C LEU C 172 " pdb=" CB LEU C 172 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.69e+00 chirality pdb=" CA ASN B 174 " pdb=" N ASN B 174 " pdb=" C ASN B 174 " pdb=" CB ASN B 174 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CB VAL E 52 " pdb=" CA VAL E 52 " pdb=" CG1 VAL E 52 " pdb=" CG2 VAL E 52 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.30 2.00e-01 2.50e+01 2.32e+00 ... (remaining 3117 not shown) Planarity restraints: 3786 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 170 " 0.374 9.50e-02 1.11e+02 1.68e-01 1.73e+01 pdb=" NE ARG F 170 " -0.020 2.00e-02 2.50e+03 pdb=" CZ ARG F 170 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG F 170 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG F 170 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 170 " -0.345 9.50e-02 1.11e+02 1.55e-01 1.46e+01 pdb=" NE ARG C 170 " 0.020 2.00e-02 2.50e+03 pdb=" CZ ARG C 170 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG C 170 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 170 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 170 " 0.322 9.50e-02 1.11e+02 1.45e-01 1.30e+01 pdb=" NE ARG D 170 " -0.021 2.00e-02 2.50e+03 pdb=" CZ ARG D 170 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG D 170 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG D 170 " 0.008 2.00e-02 2.50e+03 ... (remaining 3783 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 562 2.69 - 3.24: 21712 3.24 - 3.79: 34863 3.79 - 4.35: 47019 4.35 - 4.90: 76097 Nonbonded interactions: 180253 Sorted by model distance: nonbonded pdb=" O GLY B 375 " pdb=" ND2 ASN B 379 " model vdw 2.137 3.120 nonbonded pdb=" OE1 GLN F 456 " pdb=" NH1 ARG D 170 " model vdw 2.154 3.120 nonbonded pdb=" O GLY A 375 " pdb=" ND2 ASN A 379 " model vdw 2.170 3.120 nonbonded pdb=" O VAL D 383 " pdb=" OG SER D 386 " model vdw 2.175 3.040 nonbonded pdb=" NH1 ARG E 170 " pdb=" OE1 GLN D 456 " model vdw 2.197 3.120 ... (remaining 180248 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.230 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: 0.030 Extract box with map and model: 0.820 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 49.250 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6271 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 : 0.009 0.082 21222 Z= 0.559 Angle : 1.007 20.307 28716 Z= 0.647 Chirality : 0.071 0.328 3120 Planarity : 0.011 0.168 3786 Dihedral : 16.339 87.846 7608 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.79 % Favored : 92.03 % Rotamer: Outliers : 1.14 % Allowed : 21.37 % Favored : 77.49 % 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: -1.12 (0.16), residues: 2748 helix: 0.49 (0.14), residues: 1296 sheet: -1.49 (0.29), residues: 318 loop : -1.96 (0.17), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.008 TRP E 176 HIS 0.019 0.004 HIS D 143 PHE 0.043 0.007 PHE A 66 TYR 0.034 0.007 TYR B 14 ARG 0.028 0.004 ARG D 130 Details of bonding type rmsd hydrogen bonds : bond 0.13593 ( 1010) hydrogen bonds : angle 5.89080 ( 2967) covalent geometry : bond 0.00892 (21222) covalent geometry : angle 1.00660 (28716) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 192 time to evaluate : 2.301 Fit side-chains REVERT: E 433 ILE cc_start: 0.6619 (mp) cc_final: 0.6282 (tp) REVERT: A 26 LEU cc_start: 0.5674 (tt) cc_final: 0.4894 (mm) REVERT: B 172 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8104 (pt) REVERT: C 208 MET cc_start: 0.4031 (ptp) cc_final: 0.3808 (mmt) REVERT: C 288 LEU cc_start: 0.3751 (OUTLIER) cc_final: 0.3514 (tp) outliers start: 24 outliers final: 9 residues processed: 207 average time/residue: 0.3793 time to fit residues: 120.6342 Evaluate side-chains 184 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 173 time to evaluate : 2.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 441 SER Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain D residue 126 ASP Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 416 PHE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 416 PHE Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 379 ASN Chi-restraints excluded: chain C residue 416 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 233 optimal weight: 0.8980 chunk 209 optimal weight: 9.9990 chunk 116 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 chunk 111 optimal weight: 0.0980 chunk 216 optimal weight: 8.9990 chunk 83 optimal weight: 6.9990 chunk 131 optimal weight: 0.9990 chunk 161 optimal weight: 10.0000 chunk 250 optimal weight: 2.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 174 ASN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 379 ASN C 12 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.221063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.184184 restraints weight = 26532.387| |-----------------------------------------------------------------------------| r_work (start): 0.4131 rms_B_bonded: 2.46 r_work: 0.3740 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 21222 Z= 0.129 Angle : 0.543 8.195 28716 Z= 0.285 Chirality : 0.041 0.176 3120 Planarity : 0.003 0.048 3786 Dihedral : 4.651 47.359 2971 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.44 % Favored : 93.38 % Rotamer: Outliers : 2.66 % Allowed : 20.99 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.16), residues: 2748 helix: 0.85 (0.14), residues: 1330 sheet: -1.37 (0.29), residues: 358 loop : -1.67 (0.19), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 371 HIS 0.004 0.001 HIS B 309 PHE 0.021 0.002 PHE C 357 TYR 0.014 0.001 TYR B 77 ARG 0.005 0.001 ARG D 170 Details of bonding type rmsd hydrogen bonds : bond 0.04691 ( 1010) hydrogen bonds : angle 4.85267 ( 2967) covalent geometry : bond 0.00272 (21222) covalent geometry : angle 0.54321 (28716) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 209 time to evaluate : 2.320 Fit side-chains revert: symmetry clash REVERT: E 324 GLU cc_start: 0.5598 (pm20) cc_final: 0.5303 (pm20) REVERT: D 71 ASN cc_start: 0.8610 (OUTLIER) cc_final: 0.8401 (t0) REVERT: B 172 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8369 (pt) REVERT: C 35 LYS cc_start: 0.8278 (tptt) cc_final: 0.8045 (tptt) REVERT: C 208 MET cc_start: 0.4294 (ptp) cc_final: 0.4047 (mmt) REVERT: C 347 MET cc_start: 0.4371 (OUTLIER) cc_final: 0.3344 (ttm) outliers start: 56 outliers final: 23 residues processed: 253 average time/residue: 0.3885 time to fit residues: 151.1702 Evaluate side-chains 201 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 175 time to evaluate : 2.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 415 CYS Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 110 MET Chi-restraints excluded: chain F residue 418 ASN Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 71 ASN Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 371 TRP Chi-restraints excluded: chain B residue 418 ASN Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain C residue 12 GLN Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 418 ASN Chi-restraints excluded: chain C residue 438 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 199 optimal weight: 4.9990 chunk 143 optimal weight: 2.9990 chunk 161 optimal weight: 0.9990 chunk 243 optimal weight: 3.9990 chunk 256 optimal weight: 10.0000 chunk 144 optimal weight: 0.9990 chunk 34 optimal weight: 7.9990 chunk 230 optimal weight: 0.1980 chunk 49 optimal weight: 6.9990 chunk 201 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.220213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.183088 restraints weight = 26281.714| |-----------------------------------------------------------------------------| r_work (start): 0.4131 rms_B_bonded: 2.52 r_work: 0.3729 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 21222 Z= 0.136 Angle : 0.528 8.818 28716 Z= 0.277 Chirality : 0.041 0.196 3120 Planarity : 0.003 0.049 3786 Dihedral : 4.149 39.710 2954 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.80 % Favored : 93.05 % Rotamer: Outliers : 3.18 % Allowed : 20.85 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.16), residues: 2748 helix: 0.93 (0.14), residues: 1342 sheet: -1.47 (0.30), residues: 338 loop : -1.64 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP E 371 HIS 0.005 0.001 HIS D 143 PHE 0.023 0.002 PHE E 357 TYR 0.013 0.001 TYR E 204 ARG 0.003 0.000 ARG B 64 Details of bonding type rmsd hydrogen bonds : bond 0.04570 ( 1010) hydrogen bonds : angle 4.74395 ( 2967) covalent geometry : bond 0.00295 (21222) covalent geometry : angle 0.52761 (28716) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 187 time to evaluate : 2.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 126 ASP cc_start: 0.6727 (m-30) cc_final: 0.6395 (m-30) REVERT: F 306 PRO cc_start: 0.5576 (Cg_exo) cc_final: 0.5361 (Cg_endo) REVERT: F 390 MET cc_start: 0.7517 (ttp) cc_final: 0.7315 (ttm) REVERT: D 324 GLU cc_start: 0.4738 (OUTLIER) cc_final: 0.4516 (pm20) REVERT: D 347 MET cc_start: 0.4146 (OUTLIER) cc_final: 0.3889 (ttm) REVERT: B 172 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8405 (pt) REVERT: B 396 ARG cc_start: 0.7458 (OUTLIER) cc_final: 0.6602 (mtt-85) REVERT: C 35 LYS cc_start: 0.8381 (tptt) cc_final: 0.8117 (tptt) REVERT: C 208 MET cc_start: 0.4283 (ptp) cc_final: 0.3987 (mmt) outliers start: 67 outliers final: 34 residues processed: 239 average time/residue: 0.3225 time to fit residues: 120.4807 Evaluate side-chains 214 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 176 time to evaluate : 2.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 418 ASN Chi-restraints excluded: chain F residue 437 LEU Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 371 TRP Chi-restraints excluded: chain B residue 396 ARG Chi-restraints excluded: chain B residue 418 ASN Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 379 ASN Chi-restraints excluded: chain C residue 416 PHE Chi-restraints excluded: chain C residue 418 ASN Chi-restraints excluded: chain C residue 438 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- 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: 68.8759 > 50: distance: 10 - 152: 22.556 distance: 13 - 149: 21.151 distance: 58 - 80: 11.313 distance: 75 - 80: 13.575 distance: 80 - 81: 16.260 distance: 81 - 82: 17.223 distance: 81 - 84: 11.348 distance: 82 - 83: 20.268 distance: 82 - 87: 10.302 distance: 84 - 85: 22.792 distance: 84 - 86: 29.234 distance: 87 - 88: 5.988 distance: 88 - 89: 14.579 distance: 88 - 91: 25.484 distance: 89 - 90: 11.552 distance: 89 - 95: 53.641 distance: 90 - 116: 39.801 distance: 91 - 92: 20.881 distance: 92 - 93: 3.873 distance: 92 - 94: 23.581 distance: 95 - 96: 30.978 distance: 96 - 97: 25.997 distance: 96 - 99: 27.541 distance: 97 - 98: 7.138 distance: 97 - 100: 30.913 distance: 98 - 121: 36.384 distance: 100 - 101: 27.936 distance: 101 - 102: 12.974 distance: 101 - 104: 6.522 distance: 102 - 103: 14.872 distance: 102 - 105: 4.915 distance: 103 - 129: 40.044 distance: 105 - 106: 13.719 distance: 106 - 107: 4.735 distance: 106 - 109: 23.186 distance: 107 - 108: 20.255 distance: 107 - 116: 7.954 distance: 109 - 110: 17.195 distance: 110 - 111: 11.229 distance: 110 - 112: 21.960 distance: 111 - 113: 19.129 distance: 112 - 114: 18.745 distance: 113 - 115: 16.960 distance: 114 - 115: 7.457 distance: 116 - 117: 39.542 distance: 117 - 118: 13.402 distance: 117 - 120: 35.297 distance: 118 - 119: 15.456 distance: 118 - 121: 16.653 distance: 121 - 122: 27.824 distance: 122 - 123: 28.736 distance: 122 - 125: 30.898 distance: 123 - 124: 19.866 distance: 123 - 129: 16.023 distance: 125 - 126: 10.596 distance: 126 - 127: 31.726 distance: 129 - 130: 20.228 distance: 130 - 131: 35.156 distance: 130 - 133: 24.835 distance: 131 - 132: 6.470 distance: 131 - 138: 33.608 distance: 134 - 135: 39.544 distance: 135 - 136: 37.386 distance: 136 - 137: 32.009 distance: 138 - 139: 39.745 distance: 139 - 140: 41.220 distance: 139 - 142: 9.207 distance: 140 - 141: 13.956 distance: 140 - 149: 35.949 distance: 142 - 143: 4.859 distance: 143 - 144: 32.990 distance: 144 - 146: 12.326 distance: 145 - 147: 39.354 distance: 146 - 148: 15.702 distance: 147 - 148: 10.975 distance: 149 - 150: 14.562 distance: 150 - 151: 34.454 distance: 150 - 153: 17.716 distance: 151 - 152: 27.489 distance: 151 - 156: 16.126 distance: 153 - 154: 23.709 distance: 153 - 155: 13.934