Starting phenix.real_space_refine on Sun Jun 15 04:46:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j35_61106/06_2025/9j35_61106.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j35_61106/06_2025/9j35_61106.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j35_61106/06_2025/9j35_61106.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j35_61106/06_2025/9j35_61106.map" model { file = "/net/cci-nas-00/data/ceres_data/9j35_61106/06_2025/9j35_61106.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j35_61106/06_2025/9j35_61106.cif" } resolution = 2.71 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= 0.002 sd= 0.102 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 100 5.16 5 C 11008 2.51 5 N 2840 2.21 5 O 3012 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 150 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16960 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4240 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 19, 'TRANS': 503} Chain breaks: 1 Chain: "B" Number of atoms: 4240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4240 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 19, 'TRANS': 503} Chain breaks: 1 Chain: "C" Number of atoms: 4240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4240 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 19, 'TRANS': 503} Chain breaks: 1 Chain: "D" Number of atoms: 4240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4240 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 19, 'TRANS': 503} Chain breaks: 1 Time building chain proxies: 9.76, per 1000 atoms: 0.58 Number of scatterers: 16960 At special positions: 0 Unit cell: (109.044, 110.908, 139.8, 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 100 16.00 O 3012 8.00 N 2840 7.00 C 11008 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 310 " distance=2.04 Simple disulfide: pdb=" SG CYS A 292 " - pdb=" SG CYS A 333 " distance=2.04 Simple disulfide: pdb=" SG CYS A 297 " - pdb=" SG CYS A 303 " distance=1.34 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 310 " distance=2.04 Simple disulfide: pdb=" SG CYS B 292 " - pdb=" SG CYS B 333 " distance=2.04 Simple disulfide: pdb=" SG CYS B 297 " - pdb=" SG CYS B 303 " distance=2.03 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 310 " distance=2.04 Simple disulfide: pdb=" SG CYS C 292 " - pdb=" SG CYS C 333 " distance=2.04 Simple disulfide: pdb=" SG CYS C 297 " - pdb=" SG CYS C 303 " distance=1.34 Simple disulfide: pdb=" SG CYS D 129 " - pdb=" SG CYS D 310 " distance=2.03 Simple disulfide: pdb=" SG CYS D 292 " - pdb=" SG CYS D 333 " distance=2.04 Simple disulfide: pdb=" SG CYS D 297 " - pdb=" SG CYS D 303 " distance=1.46 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: 3.67 Conformation dependent library (CDL) restraints added in 2.0 seconds 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4000 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 16 sheets defined 57.2% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'A' and resid 94 through 99 Processing helix chain 'A' and resid 104 through 111 removed outlier: 3.637A pdb=" N LEU A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A 111 " --> pdb=" O CYS A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 119 removed outlier: 3.561A pdb=" N PHE A 117 " --> pdb=" O ASP A 114 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR A 119 " --> pdb=" O PHE A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 159 removed outlier: 3.776A pdb=" N ALA A 137 " --> pdb=" O ASP A 133 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER A 141 " --> pdb=" O ALA A 137 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG A 144 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A 149 " --> pdb=" O THR A 145 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N PHE A 150 " --> pdb=" O PHE A 146 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA A 153 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N HIS A 154 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N MET A 155 " --> pdb=" O TYR A 151 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ALA A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 191 removed outlier: 4.094A pdb=" N ALA A 184 " --> pdb=" O PRO A 180 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LYS A 185 " --> pdb=" O ALA A 181 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLN A 189 " --> pdb=" O LYS A 185 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG A 190 " --> pdb=" O ARG A 186 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TRP A 191 " --> pdb=" O TYR A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 204 through 212 removed outlier: 3.679A pdb=" N TRP A 208 " --> pdb=" O GLN A 204 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE A 210 " --> pdb=" O VAL A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 225 Processing helix chain 'A' and resid 226 through 233 Processing helix chain 'A' and resid 234 through 240 Processing helix chain 'A' and resid 241 through 247 Processing helix chain 'A' and resid 266 through 294 removed outlier: 3.914A pdb=" N TYR A 270 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET A 271 " --> pdb=" O LEU A 267 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA A 279 " --> pdb=" O HIS A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 323 removed outlier: 3.516A pdb=" N TRP A 321 " --> pdb=" O GLY A 317 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG A 323 " --> pdb=" O ALA A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 332 removed outlier: 3.758A pdb=" N VAL A 328 " --> pdb=" O ALA A 324 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N LYS A 330 " --> pdb=" O GLU A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 348 No H-bonds generated for 'chain 'A' and resid 346 through 348' Processing helix chain 'A' and resid 349 through 355 removed outlier: 3.518A pdb=" N LEU A 353 " --> pdb=" O TYR A 349 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER A 355 " --> pdb=" O GLN A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 380 removed outlier: 3.657A pdb=" N LYS A 366 " --> pdb=" O ASN A 362 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N CYS A 370 " --> pdb=" O LYS A 366 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR A 380 " --> pdb=" O GLN A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 421 removed outlier: 3.514A pdb=" N ILE A 394 " --> pdb=" O TYR A 390 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 405 " --> pdb=" O ALA A 401 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA A 409 " --> pdb=" O LEU A 405 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN A 414 " --> pdb=" O LEU A 410 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET A 415 " --> pdb=" O LEU A 411 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER A 421 " --> pdb=" O THR A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 444 removed outlier: 3.642A pdb=" N GLU A 428 " --> pdb=" O ILE A 424 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU A 437 " --> pdb=" O ARG A 433 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN A 438 " --> pdb=" O ARG A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 465 removed outlier: 3.895A pdb=" N GLU A 451 " --> pdb=" O GLN A 447 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG A 452 " --> pdb=" O ASP A 448 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR A 456 " --> pdb=" O ARG A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 474 Processing helix chain 'A' and resid 477 through 494 removed outlier: 3.561A pdb=" N ASP A 483 " --> pdb=" O ASP A 479 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU A 490 " --> pdb=" O ARG A 486 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ALA A 491 " --> pdb=" O HIS A 487 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N LEU A 492 " --> pdb=" O LEU A 488 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL A 493 " --> pdb=" O CYS A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 501 removed outlier: 3.951A pdb=" N SER A 501 " --> pdb=" O PRO A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 511 removed outlier: 3.709A pdb=" N ILE A 510 " --> pdb=" O LEU A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 577 removed outlier: 3.921A pdb=" N THR A 573 " --> pdb=" O GLU A 569 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASP A 577 " --> pdb=" O THR A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 612 removed outlier: 4.395A pdb=" N PHE A 609 " --> pdb=" O GLU A 605 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL A 610 " --> pdb=" O GLU A 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 101 removed outlier: 3.671A pdb=" N LEU B 97 " --> pdb=" O ASP B 93 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS B 101 " --> pdb=" O LEU B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 111 removed outlier: 3.713A pdb=" N LEU B 109 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL B 111 " --> pdb=" O CYS B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 119 removed outlier: 3.536A pdb=" N PHE B 117 " --> pdb=" O ASP B 114 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR B 119 " --> pdb=" O PHE B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 147 removed outlier: 3.725A pdb=" N ALA B 137 " --> pdb=" O ASP B 133 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE B 138 " --> pdb=" O ARG B 134 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR B 139 " --> pdb=" O LYS B 135 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER B 141 " --> pdb=" O ALA B 137 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG B 144 " --> pdb=" O ALA B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 182 through 188 Processing helix chain 'B' and resid 192 through 197 Processing helix chain 'B' and resid 204 through 212 removed outlier: 3.568A pdb=" N TRP B 208 " --> pdb=" O GLN B 204 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE B 210 " --> pdb=" O VAL B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 225 No H-bonds generated for 'chain 'B' and resid 223 through 225' Processing helix chain 'B' and resid 226 through 233 removed outlier: 3.554A pdb=" N VAL B 230 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 240 removed outlier: 3.743A pdb=" N PHE B 238 " --> pdb=" O TYR B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 246 removed outlier: 3.575A pdb=" N SER B 246 " --> pdb=" O LEU B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 294 removed outlier: 3.694A pdb=" N TYR B 270 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET B 271 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU B 272 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS B 275 " --> pdb=" O MET B 271 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR B 282 " --> pdb=" O GLY B 278 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU B 283 " --> pdb=" O ALA B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 323 removed outlier: 3.590A pdb=" N TRP B 321 " --> pdb=" O GLY B 317 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ARG B 323 " --> pdb=" O ALA B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 332 removed outlier: 3.790A pdb=" N VAL B 328 " --> pdb=" O ALA B 324 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N LYS B 330 " --> pdb=" O GLU B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 348 No H-bonds generated for 'chain 'B' and resid 346 through 348' Processing helix chain 'B' and resid 349 through 355 removed outlier: 3.515A pdb=" N LEU B 353 " --> pdb=" O TYR B 349 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER B 355 " --> pdb=" O GLN B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 380 removed outlier: 3.657A pdb=" N LYS B 366 " --> pdb=" O ASN B 362 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N CYS B 370 " --> pdb=" O LYS B 366 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR B 380 " --> pdb=" O GLN B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 421 removed outlier: 3.523A pdb=" N PHE B 396 " --> pdb=" O MET B 392 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B 405 " --> pdb=" O ALA B 401 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA B 409 " --> pdb=" O LEU B 405 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN B 414 " --> pdb=" O LEU B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 444 removed outlier: 3.640A pdb=" N GLU B 428 " --> pdb=" O ILE B 424 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU B 437 " --> pdb=" O ARG B 433 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN B 438 " --> pdb=" O ARG B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 465 removed outlier: 3.895A pdb=" N GLU B 451 " --> pdb=" O GLN B 447 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG B 452 " --> pdb=" O ASP B 448 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR B 456 " --> pdb=" O ARG B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 474 Processing helix chain 'B' and resid 477 through 494 removed outlier: 3.550A pdb=" N ASP B 483 " --> pdb=" O ASP B 479 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU B 490 " --> pdb=" O ARG B 486 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ALA B 491 " --> pdb=" O HIS B 487 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N LEU B 492 " --> pdb=" O LEU B 488 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL B 493 " --> pdb=" O CYS B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 501 removed outlier: 3.967A pdb=" N SER B 501 " --> pdb=" O PRO B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 511 Processing helix chain 'B' and resid 569 through 577 removed outlier: 3.765A pdb=" N THR B 573 " --> pdb=" O GLU B 569 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP B 577 " --> pdb=" O THR B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 612 removed outlier: 4.439A pdb=" N PHE B 609 " --> pdb=" O GLU B 605 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL B 610 " --> pdb=" O GLU B 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 98 Processing helix chain 'C' and resid 104 through 111 removed outlier: 3.630A pdb=" N LEU C 109 " --> pdb=" O ALA C 105 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL C 111 " --> pdb=" O CYS C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 119 removed outlier: 3.578A pdb=" N PHE C 117 " --> pdb=" O ASP C 114 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR C 119 " --> pdb=" O PHE C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 144 removed outlier: 3.726A pdb=" N ALA C 137 " --> pdb=" O ASP C 133 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER C 141 " --> pdb=" O ALA C 137 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG C 144 " --> pdb=" O ALA C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 154 Processing helix chain 'C' and resid 179 through 191 removed outlier: 4.311A pdb=" N ALA C 184 " --> pdb=" O PRO C 180 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS C 185 " --> pdb=" O ALA C 181 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG C 186 " --> pdb=" O GLN C 182 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLN C 189 " --> pdb=" O LYS C 185 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG C 190 " --> pdb=" O ARG C 186 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TRP C 191 " --> pdb=" O TYR C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 197 Processing helix chain 'C' and resid 201 through 212 removed outlier: 3.839A pdb=" N ILE C 205 " --> pdb=" O PRO C 201 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL C 206 " --> pdb=" O LEU C 202 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL C 207 " --> pdb=" O PRO C 203 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TRP C 208 " --> pdb=" O GLN C 204 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE C 210 " --> pdb=" O VAL C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 225 Processing helix chain 'C' and resid 226 through 233 Processing helix chain 'C' and resid 234 through 240 Processing helix chain 'C' and resid 241 through 252 removed outlier: 3.572A pdb=" N SER C 246 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLU C 247 " --> pdb=" O PRO C 243 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU C 248 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG C 250 " --> pdb=" O SER C 246 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N THR C 251 " --> pdb=" O GLU C 247 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA C 252 " --> pdb=" O LEU C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 294 removed outlier: 3.756A pdb=" N TYR C 270 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET C 271 " --> pdb=" O LEU C 267 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU C 272 " --> pdb=" O LEU C 268 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N HIS C 275 " --> pdb=" O MET C 271 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE C 276 " --> pdb=" O LEU C 272 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA C 279 " --> pdb=" O HIS C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 322 removed outlier: 3.533A pdb=" N TRP C 321 " --> pdb=" O GLY C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 332 removed outlier: 3.788A pdb=" N VAL C 328 " --> pdb=" O ALA C 324 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N LYS C 330 " --> pdb=" O GLU C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 348 No H-bonds generated for 'chain 'C' and resid 346 through 348' Processing helix chain 'C' and resid 349 through 355 removed outlier: 3.521A pdb=" N LEU C 353 " --> pdb=" O TYR C 349 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER C 355 " --> pdb=" O GLN C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 380 removed outlier: 3.658A pdb=" N LYS C 366 " --> pdb=" O ASN C 362 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS C 370 " --> pdb=" O LYS C 366 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR C 380 " --> pdb=" O GLN C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 423 removed outlier: 3.755A pdb=" N LEU C 405 " --> pdb=" O ALA C 401 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE C 406 " --> pdb=" O ILE C 402 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN C 416 " --> pdb=" O ILE C 412 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR C 417 " --> pdb=" O GLY C 413 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TYR C 418 " --> pdb=" O ASN C 414 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU C 422 " --> pdb=" O TYR C 418 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR C 423 " --> pdb=" O LEU C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 444 removed outlier: 3.649A pdb=" N GLU C 437 " --> pdb=" O ARG C 433 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN C 438 " --> pdb=" O ARG C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 465 removed outlier: 3.714A pdb=" N ARG C 452 " --> pdb=" O ASP C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 474 Processing helix chain 'C' and resid 477 through 494 removed outlier: 6.122A pdb=" N ALA C 491 " --> pdb=" O HIS C 487 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N LEU C 492 " --> pdb=" O LEU C 488 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL C 493 " --> pdb=" O CYS C 489 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG C 494 " --> pdb=" O LEU C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 502 Processing helix chain 'C' and resid 503 through 508 Processing helix chain 'C' and resid 569 through 576 removed outlier: 3.963A pdb=" N THR C 573 " --> pdb=" O GLU C 569 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TRP C 574 " --> pdb=" O GLU C 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 612 removed outlier: 4.464A pdb=" N PHE C 609 " --> pdb=" O GLU C 605 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL C 610 " --> pdb=" O GLU C 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 99 removed outlier: 3.902A pdb=" N TYR D 98 " --> pdb=" O LYS D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 111 removed outlier: 3.604A pdb=" N LEU D 109 " --> pdb=" O ALA D 105 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL D 111 " --> pdb=" O CYS D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 119 removed outlier: 3.574A pdb=" N PHE D 117 " --> pdb=" O ASP D 114 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR D 119 " --> pdb=" O PHE D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 148 removed outlier: 3.752A pdb=" N ALA D 137 " --> pdb=" O ASP D 133 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE D 138 " --> pdb=" O ARG D 134 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR D 139 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER D 141 " --> pdb=" O ALA D 137 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG D 144 " --> pdb=" O ALA D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 157 removed outlier: 3.842A pdb=" N ALA D 153 " --> pdb=" O VAL D 149 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N HIS D 154 " --> pdb=" O PHE D 150 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N MET D 155 " --> pdb=" O TYR D 151 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA D 156 " --> pdb=" O LEU D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 188 Processing helix chain 'D' and resid 192 through 197 removed outlier: 3.795A pdb=" N LEU D 197 " --> pdb=" O ILE D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 212 removed outlier: 3.774A pdb=" N TRP D 208 " --> pdb=" O GLN D 204 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE D 210 " --> pdb=" O VAL D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 225 Processing helix chain 'D' and resid 226 through 233 Processing helix chain 'D' and resid 234 through 240 Processing helix chain 'D' and resid 241 through 249 removed outlier: 3.698A pdb=" N SER D 246 " --> pdb=" O LEU D 242 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLU D 247 " --> pdb=" O PRO D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 294 removed outlier: 3.915A pdb=" N TYR D 270 " --> pdb=" O TYR D 266 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N MET D 271 " --> pdb=" O LEU D 267 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU D 272 " --> pdb=" O LEU D 268 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA D 279 " --> pdb=" O HIS D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 322 removed outlier: 3.536A pdb=" N TRP D 321 " --> pdb=" O GLY D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 332 removed outlier: 3.921A pdb=" N VAL D 328 " --> pdb=" O ALA D 324 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N LYS D 330 " --> pdb=" O GLU D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 348 No H-bonds generated for 'chain 'D' and resid 346 through 348' Processing helix chain 'D' and resid 349 through 355 removed outlier: 3.517A pdb=" N LEU D 353 " --> pdb=" O TYR D 349 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER D 355 " --> pdb=" O GLN D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 379 removed outlier: 3.652A pdb=" N LYS D 366 " --> pdb=" O ASN D 362 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS D 370 " --> pdb=" O LYS D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 421 removed outlier: 3.528A pdb=" N LEU D 405 " --> pdb=" O ALA D 401 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA D 409 " --> pdb=" O LEU D 405 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN D 414 " --> pdb=" O LEU D 410 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN D 416 " --> pdb=" O ILE D 412 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER D 421 " --> pdb=" O THR D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 444 Processing helix chain 'D' and resid 446 through 465 removed outlier: 3.870A pdb=" N GLU D 451 " --> pdb=" O GLN D 447 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG D 452 " --> pdb=" O ASP D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 474 Processing helix chain 'D' and resid 477 through 494 removed outlier: 3.518A pdb=" N ARG D 486 " --> pdb=" O ARG D 482 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N HIS D 487 " --> pdb=" O ASP D 483 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU D 488 " --> pdb=" O ILE D 484 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU D 490 " --> pdb=" O ARG D 486 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ALA D 491 " --> pdb=" O HIS D 487 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N LEU D 492 " --> pdb=" O LEU D 488 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL D 493 " --> pdb=" O CYS D 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 577 removed outlier: 3.921A pdb=" N THR D 573 " --> pdb=" O GLU D 569 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASP D 577 " --> pdb=" O THR D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 604 through 612 removed outlier: 4.395A pdb=" N PHE D 609 " --> pdb=" O GLU D 605 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL D 610 " --> pdb=" O GLU D 606 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 121 through 124 Processing sheet with id=AA2, first strand: chain 'A' and resid 163 through 165 removed outlier: 3.647A pdb=" N TYR A 163 " --> pdb=" O VAL A 177 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 515 through 519 removed outlier: 6.598A pdb=" N GLU A 598 " --> pdb=" O ILE A 539 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 524 through 526 removed outlier: 6.648A pdb=" N VAL A 591 " --> pdb=" O LEU A 525 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 121 through 124 Processing sheet with id=AA6, first strand: chain 'B' and resid 163 through 165 removed outlier: 3.684A pdb=" N TYR B 163 " --> pdb=" O VAL B 177 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 515 through 519 removed outlier: 6.588A pdb=" N GLU B 598 " --> pdb=" O ILE B 539 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 524 through 526 removed outlier: 6.649A pdb=" N VAL B 591 " --> pdb=" O LEU B 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 121 through 124 Processing sheet with id=AB1, first strand: chain 'C' and resid 163 through 165 Processing sheet with id=AB2, first strand: chain 'C' and resid 515 through 519 removed outlier: 6.586A pdb=" N GLU C 598 " --> pdb=" O ILE C 539 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 524 through 526 removed outlier: 6.574A pdb=" N VAL C 591 " --> pdb=" O LEU C 525 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU C 561 " --> pdb=" O LEU C 543 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 121 through 124 Processing sheet with id=AB5, first strand: chain 'D' and resid 163 through 165 removed outlier: 3.773A pdb=" N TYR D 163 " --> pdb=" O VAL D 177 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 515 through 519 removed outlier: 6.597A pdb=" N GLU D 598 " --> pdb=" O ILE D 539 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 524 through 526 removed outlier: 6.648A pdb=" N VAL D 591 " --> pdb=" O LEU D 525 " (cutoff:3.500A) 691 hydrogen bonds defined for protein. 1944 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: 4.76 Time building geometry restraints manager: 4.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 2703 1.28 - 1.42: 4617 1.42 - 1.55: 9867 1.55 - 1.69: 17 1.69 - 1.82: 144 Bond restraints: 17348 Sorted by residual: bond pdb=" C LEU A 411 " pdb=" N ILE A 412 " ideal model delta sigma weight residual 1.335 1.588 -0.253 1.20e-02 6.94e+03 4.45e+02 bond pdb=" N PRO B 236 " pdb=" CD PRO B 236 " ideal model delta sigma weight residual 1.473 1.227 0.246 1.40e-02 5.10e+03 3.08e+02 bond pdb=" C LEU B 411 " pdb=" N ILE B 412 " ideal model delta sigma weight residual 1.335 1.541 -0.206 1.20e-02 6.94e+03 2.94e+02 bond pdb=" C LEU B 378 " pdb=" N SER B 379 " ideal model delta sigma weight residual 1.334 1.566 -0.232 1.49e-02 4.50e+03 2.43e+02 bond pdb=" C MET D 512 " pdb=" N ARG D 513 " ideal model delta sigma weight residual 1.333 1.567 -0.234 1.51e-02 4.39e+03 2.40e+02 ... (remaining 17343 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.50: 23306 5.50 - 11.01: 186 11.01 - 16.51: 9 16.51 - 22.02: 4 22.02 - 27.52: 3 Bond angle restraints: 23508 Sorted by residual: angle pdb=" CA LEU D 378 " pdb=" C LEU D 378 " pdb=" N SER D 379 " ideal model delta sigma weight residual 118.14 142.73 -24.59 1.31e+00 5.83e-01 3.52e+02 angle pdb=" O LEU D 378 " pdb=" C LEU D 378 " pdb=" N SER D 379 " ideal model delta sigma weight residual 122.43 97.37 25.06 1.34e+00 5.57e-01 3.50e+02 angle pdb=" C LEU D 378 " pdb=" N SER D 379 " pdb=" CA SER D 379 " ideal model delta sigma weight residual 121.66 149.18 -27.52 1.76e+00 3.23e-01 2.44e+02 angle pdb=" O LEU B 378 " pdb=" C LEU B 378 " pdb=" N SER B 379 " ideal model delta sigma weight residual 122.27 103.72 18.55 1.23e+00 6.61e-01 2.28e+02 angle pdb=" CA LEU B 378 " pdb=" C LEU B 378 " pdb=" N SER B 379 " ideal model delta sigma weight residual 117.72 136.95 -19.23 1.31e+00 5.83e-01 2.16e+02 ... (remaining 23503 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 9217 17.87 - 35.74: 966 35.74 - 53.61: 180 53.61 - 71.48: 35 71.48 - 89.35: 10 Dihedral angle restraints: 10408 sinusoidal: 4240 harmonic: 6168 Sorted by residual: dihedral pdb=" C TYR B 234 " pdb=" N TYR B 234 " pdb=" CA TYR B 234 " pdb=" CB TYR B 234 " ideal model delta harmonic sigma weight residual -122.60 -102.43 -20.17 0 2.50e+00 1.60e-01 6.51e+01 dihedral pdb=" C GLN B 233 " pdb=" N GLN B 233 " pdb=" CA GLN B 233 " pdb=" CB GLN B 233 " ideal model delta harmonic sigma weight residual -122.60 -105.50 -17.10 0 2.50e+00 1.60e-01 4.68e+01 dihedral pdb=" CA ASP B 148 " pdb=" C ASP B 148 " pdb=" N VAL B 149 " pdb=" CA VAL B 149 " ideal model delta harmonic sigma weight residual 180.00 152.66 27.34 0 5.00e+00 4.00e-02 2.99e+01 ... (remaining 10405 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 2201 0.084 - 0.167: 393 0.167 - 0.251: 39 0.251 - 0.335: 13 0.335 - 0.419: 6 Chirality restraints: 2652 Sorted by residual: chirality pdb=" CA SER A 379 " pdb=" N SER A 379 " pdb=" C SER A 379 " pdb=" CB SER A 379 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.38e+00 chirality pdb=" CA LEU C 381 " pdb=" N LEU C 381 " pdb=" C LEU C 381 " pdb=" CB LEU C 381 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.21e+00 chirality pdb=" CA SER C 379 " pdb=" N SER C 379 " pdb=" C SER C 379 " pdb=" CB SER C 379 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.96e+00 ... (remaining 2649 not shown) Planarity restraints: 2948 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B 201 " 0.026 2.00e-02 2.50e+03 5.10e-02 2.60e+01 pdb=" C PRO B 201 " -0.088 2.00e-02 2.50e+03 pdb=" O PRO B 201 " 0.033 2.00e-02 2.50e+03 pdb=" N LEU B 202 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 414 " 0.027 2.00e-02 2.50e+03 5.04e-02 2.54e+01 pdb=" C ASN D 414 " -0.087 2.00e-02 2.50e+03 pdb=" O ASN D 414 " 0.030 2.00e-02 2.50e+03 pdb=" N MET D 415 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 235 " 0.071 5.00e-02 4.00e+02 1.04e-01 1.73e+01 pdb=" N PRO A 236 " -0.180 5.00e-02 4.00e+02 pdb=" CA PRO A 236 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 236 " 0.057 5.00e-02 4.00e+02 ... (remaining 2945 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 574 2.71 - 3.26: 14752 3.26 - 3.80: 24301 3.80 - 4.35: 32427 4.35 - 4.90: 54291 Nonbonded interactions: 126345 Sorted by model distance: nonbonded pdb=" O LEU B 200 " pdb=" NE2 GLN B 233 " model vdw 2.161 3.120 nonbonded pdb=" O ALA D 509 " pdb=" NH1 ARG D 513 " model vdw 2.243 3.120 nonbonded pdb=" OG SER B 167 " pdb=" O SER B 168 " model vdw 2.282 3.040 nonbonded pdb=" O GLN C 383 " pdb=" CG GLN C 383 " model vdw 2.312 3.440 nonbonded pdb=" O SER B 522 " pdb=" OG SER B 522 " model vdw 2.314 3.040 ... (remaining 126340 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 2.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.710 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 36.650 Find NCS groups from input model: 0.710 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: 0.000 Load rotamer database and sin/cos tables:11.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 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 : 0.014 0.688 17360 Z= 0.782 Angle : 1.442 41.918 23532 Z= 0.866 Chirality : 0.069 0.419 2652 Planarity : 0.008 0.104 2948 Dihedral : 15.060 89.353 6372 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.42 % Favored : 92.53 % Rotamer: Outliers : 0.76 % Allowed : 5.62 % Favored : 93.63 % Cbeta Deviations : 0.20 % 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: -5.07 (0.13), residues: 2076 helix: -3.36 (0.11), residues: 1236 sheet: -2.45 (0.32), residues: 160 loop : -3.14 (0.17), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.004 TRP C 373 HIS 0.012 0.003 HIS D 275 PHE 0.023 0.003 PHE B 171 TYR 0.033 0.004 TYR D 234 ARG 0.008 0.001 ARG D 169 Details of bonding type rmsd hydrogen bonds : bond 0.28151 ( 691) hydrogen bonds : angle 7.90873 ( 1944) SS BOND : bond 0.32529 ( 12) SS BOND : angle 14.00219 ( 24) covalent geometry : bond 0.01163 (17348) covalent geometry : angle 1.37119 (23508) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 228 time to evaluate : 1.863 Fit side-chains REVERT: A 112 PHE cc_start: 0.7858 (m-80) cc_final: 0.7248 (t80) REVERT: B 112 PHE cc_start: 0.7919 (m-80) cc_final: 0.7325 (t80) REVERT: B 265 TYR cc_start: 0.8322 (t80) cc_final: 0.8106 (t80) REVERT: C 246 SER cc_start: 0.7714 (m) cc_final: 0.7345 (p) REVERT: C 444 MET cc_start: 0.8200 (mmt) cc_final: 0.7783 (mmt) REVERT: D 334 ARG cc_start: 0.8172 (ptt-90) cc_final: 0.7971 (ptt-90) REVERT: D 415 MET cc_start: 0.8112 (tpp) cc_final: 0.7696 (tpp) outliers start: 14 outliers final: 4 residues processed: 240 average time/residue: 1.5438 time to fit residues: 405.7288 Evaluate side-chains 178 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 174 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 TYR Chi-restraints excluded: chain B residue 234 TYR Chi-restraints excluded: chain C residue 234 TYR Chi-restraints excluded: chain D residue 234 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 0.9990 chunk 157 optimal weight: 5.9990 chunk 87 optimal weight: 0.1980 chunk 53 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 chunk 84 optimal weight: 0.6980 chunk 163 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 188 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 275 HIS ** B 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 383 GLN ** C 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 ASN ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.194536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.130704 restraints weight = 17580.481| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.93 r_work: 0.3260 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17360 Z= 0.132 Angle : 0.629 8.152 23532 Z= 0.333 Chirality : 0.040 0.140 2652 Planarity : 0.005 0.066 2948 Dihedral : 6.040 55.630 2316 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.35 % Allowed : 11.50 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -3.37 (0.16), residues: 2076 helix: -1.85 (0.14), residues: 1232 sheet: -2.04 (0.31), residues: 180 loop : -2.70 (0.18), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 281 HIS 0.005 0.001 HIS C 275 PHE 0.014 0.001 PHE B 171 TYR 0.018 0.001 TYR C 187 ARG 0.005 0.000 ARG C 540 Details of bonding type rmsd hydrogen bonds : bond 0.07238 ( 691) hydrogen bonds : angle 4.61742 ( 1944) SS BOND : bond 0.00320 ( 12) SS BOND : angle 1.64402 ( 24) covalent geometry : bond 0.00266 (17348) covalent geometry : angle 0.62747 (23508) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 214 time to evaluate : 1.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 PHE cc_start: 0.7831 (m-80) cc_final: 0.6924 (t80) REVERT: A 287 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7983 (tt0) REVERT: A 427 GLU cc_start: 0.9167 (mm-30) cc_final: 0.8938 (mm-30) REVERT: A 486 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.7106 (mtm-85) REVERT: B 112 PHE cc_start: 0.7847 (m-80) cc_final: 0.6979 (t80) REVERT: B 155 MET cc_start: 0.6279 (tmm) cc_final: 0.5421 (tmm) REVERT: B 287 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7974 (tt0) REVERT: B 415 MET cc_start: 0.8860 (tpp) cc_final: 0.8568 (tpp) REVERT: C 155 MET cc_start: 0.6619 (tpp) cc_final: 0.6313 (tpp) REVERT: C 287 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7963 (tp30) REVERT: D 108 ILE cc_start: 0.8546 (mt) cc_final: 0.8334 (mm) REVERT: D 235 ILE cc_start: 0.7780 (OUTLIER) cc_final: 0.7483 (mp) REVERT: D 249 LYS cc_start: 0.6105 (tppt) cc_final: 0.5424 (tppt) REVERT: D 287 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7998 (tt0) REVERT: D 334 ARG cc_start: 0.8512 (ptt-90) cc_final: 0.8215 (ptt-90) REVERT: D 381 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8404 (mp) REVERT: D 415 MET cc_start: 0.8778 (tpp) cc_final: 0.8507 (tpp) outliers start: 25 outliers final: 8 residues processed: 229 average time/residue: 1.4633 time to fit residues: 370.3278 Evaluate side-chains 202 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 187 time to evaluate : 2.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 TYR Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 486 ARG Chi-restraints excluded: chain B residue 234 TYR Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 234 TYR Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 234 TYR Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 381 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 103 optimal weight: 8.9990 chunk 58 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 chunk 87 optimal weight: 0.5980 chunk 107 optimal weight: 0.9990 chunk 203 optimal weight: 4.9990 chunk 114 optimal weight: 0.3980 chunk 154 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 GLN ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.194710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.130575 restraints weight = 17455.127| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.93 r_work: 0.3231 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17360 Z= 0.128 Angle : 0.591 8.940 23532 Z= 0.310 Chirality : 0.040 0.139 2652 Planarity : 0.004 0.054 2948 Dihedral : 5.672 57.863 2316 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 2.59 % Allowed : 13.23 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -2.27 (0.18), residues: 2076 helix: -0.96 (0.16), residues: 1180 sheet: -1.05 (0.32), residues: 220 loop : -2.44 (0.19), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 281 HIS 0.006 0.001 HIS D 275 PHE 0.026 0.001 PHE A 150 TYR 0.015 0.001 TYR C 187 ARG 0.007 0.000 ARG C 540 Details of bonding type rmsd hydrogen bonds : bond 0.06875 ( 691) hydrogen bonds : angle 4.21409 ( 1944) SS BOND : bond 0.00320 ( 12) SS BOND : angle 2.11007 ( 24) covalent geometry : bond 0.00274 (17348) covalent geometry : angle 0.58748 (23508) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 191 time to evaluate : 1.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 PHE cc_start: 0.7845 (m-80) cc_final: 0.6928 (t80) REVERT: A 400 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8873 (mt) REVERT: A 415 MET cc_start: 0.8817 (tpp) cc_final: 0.8438 (tpp) REVERT: A 428 GLU cc_start: 0.8972 (tt0) cc_final: 0.8563 (mt-10) REVERT: A 486 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7221 (mtm-85) REVERT: A 533 ASP cc_start: 0.8622 (t0) cc_final: 0.8126 (t0) REVERT: B 112 PHE cc_start: 0.7842 (m-80) cc_final: 0.6987 (t80) REVERT: B 155 MET cc_start: 0.6104 (tmm) cc_final: 0.5253 (mtm) REVERT: B 428 GLU cc_start: 0.8933 (tt0) cc_final: 0.8517 (mt-10) REVERT: B 533 ASP cc_start: 0.8597 (t0) cc_final: 0.8087 (t0) REVERT: B 572 LEU cc_start: 0.7504 (tp) cc_final: 0.7273 (tp) REVERT: C 108 ILE cc_start: 0.8560 (mp) cc_final: 0.8275 (mp) REVERT: C 155 MET cc_start: 0.6573 (tpp) cc_final: 0.6145 (tpp) REVERT: C 287 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7467 (tm-30) REVERT: C 381 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8515 (mp) REVERT: D 108 ILE cc_start: 0.8399 (mt) cc_final: 0.8175 (mm) REVERT: D 235 ILE cc_start: 0.7492 (OUTLIER) cc_final: 0.7239 (mp) REVERT: D 249 LYS cc_start: 0.5935 (tppt) cc_final: 0.5168 (tppt) REVERT: D 334 ARG cc_start: 0.8498 (ptt-90) cc_final: 0.8154 (ptt-90) REVERT: D 381 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8529 (mp) REVERT: D 400 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8890 (mt) REVERT: D 533 ASP cc_start: 0.8604 (t0) cc_final: 0.8395 (t70) outliers start: 48 outliers final: 23 residues processed: 219 average time/residue: 1.5434 time to fit residues: 373.0609 Evaluate side-chains 211 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 181 time to evaluate : 2.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 234 TYR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 486 ARG Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain B residue 234 TYR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 234 TYR Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 234 TYR Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 546 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 73 optimal weight: 4.9990 chunk 168 optimal weight: 0.9990 chunk 162 optimal weight: 6.9990 chunk 83 optimal weight: 0.8980 chunk 191 optimal weight: 4.9990 chunk 104 optimal weight: 9.9990 chunk 183 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 GLN B 275 HIS B 416 GLN ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.190979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.126390 restraints weight = 17471.786| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.14 r_work: 0.3184 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17360 Z= 0.206 Angle : 0.685 9.892 23532 Z= 0.357 Chirality : 0.045 0.150 2652 Planarity : 0.005 0.054 2948 Dihedral : 5.889 58.415 2316 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 3.73 % Allowed : 13.28 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -2.43 (0.17), residues: 2076 helix: -1.07 (0.15), residues: 1228 sheet: -1.31 (0.32), residues: 180 loop : -2.50 (0.19), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 574 HIS 0.009 0.002 HIS A 275 PHE 0.026 0.002 PHE C 150 TYR 0.016 0.002 TYR B 151 ARG 0.006 0.001 ARG B 540 Details of bonding type rmsd hydrogen bonds : bond 0.08984 ( 691) hydrogen bonds : angle 4.33596 ( 1944) SS BOND : bond 0.00365 ( 12) SS BOND : angle 2.22591 ( 24) covalent geometry : bond 0.00489 (17348) covalent geometry : angle 0.68123 (23508) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 193 time to evaluate : 1.930 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 PHE cc_start: 0.7871 (m-80) cc_final: 0.6945 (t80) REVERT: A 199 VAL cc_start: 0.6970 (OUTLIER) cc_final: 0.6502 (m) REVERT: A 400 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8951 (mt) REVERT: A 415 MET cc_start: 0.8777 (tpp) cc_final: 0.8460 (tpp) REVERT: A 416 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.8436 (tp40) REVERT: A 533 ASP cc_start: 0.8651 (t0) cc_final: 0.8147 (t0) REVERT: B 112 PHE cc_start: 0.7851 (m-80) cc_final: 0.6957 (t80) REVERT: B 155 MET cc_start: 0.6169 (tmm) cc_final: 0.5201 (mtm) REVERT: B 400 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8853 (mt) REVERT: B 415 MET cc_start: 0.8768 (tpp) cc_final: 0.8534 (tpp) REVERT: B 416 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.8543 (tp40) REVERT: B 428 GLU cc_start: 0.8985 (tt0) cc_final: 0.8565 (mt-10) REVERT: B 533 ASP cc_start: 0.8683 (t0) cc_final: 0.8163 (t0) REVERT: C 155 MET cc_start: 0.6533 (tpp) cc_final: 0.6083 (tpp) REVERT: C 287 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7586 (tm-30) REVERT: C 381 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8445 (mp) REVERT: C 400 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8927 (mt) REVERT: D 108 ILE cc_start: 0.8351 (mt) cc_final: 0.8125 (mm) REVERT: D 171 PHE cc_start: 0.6347 (OUTLIER) cc_final: 0.4310 (p90) REVERT: D 189 GLN cc_start: 0.7031 (OUTLIER) cc_final: 0.6201 (tm-30) REVERT: D 235 ILE cc_start: 0.7512 (OUTLIER) cc_final: 0.7240 (mp) REVERT: D 249 LYS cc_start: 0.5909 (tppt) cc_final: 0.5101 (tppt) REVERT: D 330 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8105 (ttpp) REVERT: D 334 ARG cc_start: 0.8483 (ptt-90) cc_final: 0.8139 (ptt-90) REVERT: D 381 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8553 (mp) REVERT: D 400 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8960 (mt) REVERT: D 415 MET cc_start: 0.8767 (tpp) cc_final: 0.8495 (tpp) REVERT: D 495 ARG cc_start: 0.7528 (mmm-85) cc_final: 0.7214 (mmm160) REVERT: D 533 ASP cc_start: 0.8670 (t0) cc_final: 0.8432 (t70) outliers start: 69 outliers final: 34 residues processed: 246 average time/residue: 1.2998 time to fit residues: 357.0208 Evaluate side-chains 238 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 190 time to evaluate : 2.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LYS Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 234 TYR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 234 TYR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 416 GLN Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 567 CYS Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 234 TYR Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 469 GLU Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 171 PHE Chi-restraints excluded: chain D residue 189 GLN Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 234 TYR Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 330 LYS Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain D residue 567 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 9 optimal weight: 0.7980 chunk 99 optimal weight: 0.8980 chunk 111 optimal weight: 0.6980 chunk 185 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 193 optimal weight: 0.5980 chunk 157 optimal weight: 6.9990 chunk 184 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 GLN B 416 GLN ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.194749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.132494 restraints weight = 17661.959| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.38 r_work: 0.3221 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17360 Z= 0.117 Angle : 0.561 9.577 23532 Z= 0.294 Chirality : 0.040 0.137 2652 Planarity : 0.004 0.052 2948 Dihedral : 5.517 59.394 2316 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.43 % Allowed : 15.44 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.71 (0.18), residues: 2076 helix: -0.50 (0.16), residues: 1176 sheet: -0.51 (0.33), residues: 220 loop : -2.32 (0.19), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 281 HIS 0.005 0.001 HIS A 275 PHE 0.024 0.001 PHE A 150 TYR 0.014 0.001 TYR C 187 ARG 0.005 0.000 ARG C 540 Details of bonding type rmsd hydrogen bonds : bond 0.06387 ( 691) hydrogen bonds : angle 4.05120 ( 1944) SS BOND : bond 0.00288 ( 12) SS BOND : angle 1.65881 ( 24) covalent geometry : bond 0.00241 (17348) covalent geometry : angle 0.55871 (23508) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 196 time to evaluate : 1.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 PHE cc_start: 0.7863 (m-80) cc_final: 0.6872 (t80) REVERT: A 199 VAL cc_start: 0.6824 (OUTLIER) cc_final: 0.6418 (m) REVERT: A 416 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.8069 (tp40) REVERT: A 428 GLU cc_start: 0.9013 (tt0) cc_final: 0.8588 (mt-10) REVERT: A 486 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7128 (mtm-85) REVERT: A 533 ASP cc_start: 0.8614 (t0) cc_final: 0.8124 (t0) REVERT: B 112 PHE cc_start: 0.7844 (m-80) cc_final: 0.6910 (t80) REVERT: B 155 MET cc_start: 0.6011 (tmm) cc_final: 0.5125 (mtm) REVERT: B 416 GLN cc_start: 0.8881 (OUTLIER) cc_final: 0.8585 (tp40) REVERT: B 428 GLU cc_start: 0.8921 (tt0) cc_final: 0.8522 (mt-10) REVERT: B 506 LEU cc_start: 0.7532 (tp) cc_final: 0.7247 (mt) REVERT: B 533 ASP cc_start: 0.8621 (t0) cc_final: 0.8121 (t0) REVERT: C 155 MET cc_start: 0.6661 (tpp) cc_final: 0.6176 (tpp) REVERT: C 287 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7480 (tm-30) REVERT: D 108 ILE cc_start: 0.8289 (mt) cc_final: 0.8066 (mm) REVERT: D 171 PHE cc_start: 0.6328 (OUTLIER) cc_final: 0.4133 (p90) REVERT: D 189 GLN cc_start: 0.7021 (OUTLIER) cc_final: 0.6232 (tm-30) REVERT: D 249 LYS cc_start: 0.5760 (tppt) cc_final: 0.4965 (tppt) REVERT: D 334 ARG cc_start: 0.8476 (ptt-90) cc_final: 0.8091 (ptt-90) REVERT: D 381 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8555 (mp) REVERT: D 533 ASP cc_start: 0.8668 (t0) cc_final: 0.8440 (t70) outliers start: 45 outliers final: 25 residues processed: 232 average time/residue: 1.4307 time to fit residues: 366.1237 Evaluate side-chains 222 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 189 time to evaluate : 2.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LYS Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 234 TYR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain A residue 486 ARG Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain B residue 234 TYR Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 416 GLN Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 567 CYS Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 234 TYR Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 469 GLU Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 171 PHE Chi-restraints excluded: chain D residue 189 GLN Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 234 TYR Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain D residue 567 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 122 optimal weight: 0.6980 chunk 140 optimal weight: 1.9990 chunk 107 optimal weight: 0.3980 chunk 183 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 99 optimal weight: 8.9990 chunk 205 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 105 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 168 optimal weight: 3.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 GLN B 416 GLN ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.191242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.133828 restraints weight = 17571.994| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.98 r_work: 0.3230 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17360 Z= 0.193 Angle : 0.663 10.994 23532 Z= 0.343 Chirality : 0.044 0.163 2652 Planarity : 0.004 0.052 2948 Dihedral : 5.725 59.600 2316 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 3.62 % Allowed : 15.28 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.07 (0.18), residues: 2076 helix: -0.78 (0.15), residues: 1224 sheet: -0.91 (0.33), residues: 180 loop : -2.43 (0.20), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 574 HIS 0.009 0.002 HIS A 275 PHE 0.030 0.002 PHE C 150 TYR 0.015 0.002 TYR B 151 ARG 0.006 0.000 ARG C 558 Details of bonding type rmsd hydrogen bonds : bond 0.08549 ( 691) hydrogen bonds : angle 4.21533 ( 1944) SS BOND : bond 0.00345 ( 12) SS BOND : angle 2.37576 ( 24) covalent geometry : bond 0.00457 (17348) covalent geometry : angle 0.65946 (23508) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 189 time to evaluate : 2.020 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 PHE cc_start: 0.7793 (m-80) cc_final: 0.6856 (t80) REVERT: A 199 VAL cc_start: 0.6894 (OUTLIER) cc_final: 0.6456 (m) REVERT: A 400 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8860 (mt) REVERT: A 416 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.7956 (tp40) REVERT: A 428 GLU cc_start: 0.8918 (tt0) cc_final: 0.8681 (mt-10) REVERT: A 533 ASP cc_start: 0.8597 (t0) cc_final: 0.8073 (t0) REVERT: B 112 PHE cc_start: 0.7758 (m-80) cc_final: 0.6843 (t80) REVERT: B 155 MET cc_start: 0.6054 (tmm) cc_final: 0.5100 (mtm) REVERT: B 400 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8788 (mt) REVERT: B 416 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.8530 (tp40) REVERT: B 428 GLU cc_start: 0.8850 (tt0) cc_final: 0.8616 (mt-10) REVERT: B 504 ASP cc_start: 0.7211 (t0) cc_final: 0.6798 (t0) REVERT: B 506 LEU cc_start: 0.7362 (OUTLIER) cc_final: 0.7106 (mp) REVERT: B 533 ASP cc_start: 0.8609 (t0) cc_final: 0.8081 (t0) REVERT: C 287 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7364 (tm-30) REVERT: C 381 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8463 (mp) REVERT: D 108 ILE cc_start: 0.8188 (mt) cc_final: 0.7980 (mm) REVERT: D 171 PHE cc_start: 0.6279 (OUTLIER) cc_final: 0.4235 (p90) REVERT: D 189 GLN cc_start: 0.7052 (OUTLIER) cc_final: 0.6279 (tm-30) REVERT: D 235 ILE cc_start: 0.7535 (OUTLIER) cc_final: 0.7280 (mp) REVERT: D 249 LYS cc_start: 0.5898 (tppt) cc_final: 0.5158 (tppt) REVERT: D 334 ARG cc_start: 0.8402 (ptt-90) cc_final: 0.8027 (ptt-90) REVERT: D 381 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8469 (mp) REVERT: D 400 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8875 (mt) REVERT: D 533 ASP cc_start: 0.8613 (t0) cc_final: 0.8377 (t70) outliers start: 67 outliers final: 39 residues processed: 242 average time/residue: 1.3144 time to fit residues: 353.6853 Evaluate side-chains 240 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 188 time to evaluate : 1.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LYS Chi-restraints excluded: chain A residue 128 LYS Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 234 TYR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain B residue 234 TYR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 416 GLN Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 567 CYS Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 234 TYR Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 469 GLU Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 171 PHE Chi-restraints excluded: chain D residue 189 GLN Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 234 TYR Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 567 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.3102 > 50: distance: 56 - 174: 4.626 distance: 59 - 171: 4.765 distance: 103 - 107: 3.670 distance: 107 - 108: 7.752 distance: 108 - 109: 10.039 distance: 109 - 110: 7.944 distance: 109 - 111: 10.360 distance: 111 - 112: 21.347 distance: 112 - 113: 11.513 distance: 112 - 115: 24.286 distance: 113 - 114: 8.389 distance: 113 - 118: 4.486 distance: 115 - 116: 38.982 distance: 118 - 119: 4.201 distance: 119 - 120: 11.330 distance: 119 - 122: 6.446 distance: 120 - 121: 24.284 distance: 120 - 126: 6.217 distance: 122 - 123: 9.556 distance: 123 - 124: 9.667 distance: 123 - 125: 4.290 distance: 126 - 127: 10.553 distance: 127 - 128: 7.549 distance: 127 - 130: 9.929 distance: 128 - 129: 20.776 distance: 128 - 134: 8.188 distance: 130 - 131: 4.549 distance: 131 - 132: 7.841 distance: 131 - 133: 13.855 distance: 134 - 135: 16.036 distance: 134 - 140: 7.857 distance: 135 - 136: 20.181 distance: 135 - 138: 14.106 distance: 136 - 137: 3.456 distance: 136 - 141: 24.876 distance: 138 - 139: 14.864 distance: 139 - 140: 19.020 distance: 141 - 142: 4.416 distance: 142 - 143: 21.951 distance: 142 - 145: 26.217 distance: 143 - 144: 10.740 distance: 143 - 147: 7.153 distance: 145 - 146: 6.559 distance: 147 - 148: 7.736 distance: 148 - 149: 5.796 distance: 148 - 151: 12.091 distance: 149 - 150: 9.372 distance: 149 - 153: 10.274 distance: 151 - 152: 8.531 distance: 153 - 154: 5.636 distance: 154 - 155: 3.880 distance: 154 - 157: 8.372 distance: 155 - 156: 8.254 distance: 155 - 160: 6.249 distance: 157 - 158: 13.940 distance: 157 - 159: 4.136 distance: 160 - 161: 4.868 distance: 161 - 162: 5.806 distance: 161 - 164: 13.881 distance: 162 - 163: 8.626 distance: 162 - 171: 10.866 distance: 164 - 165: 10.241 distance: 166 - 167: 4.547 distance: 168 - 169: 8.288 distance: 171 - 172: 13.151 distance: 172 - 173: 4.462 distance: 172 - 175: 5.349 distance: 173 - 174: 7.886 distance: 173 - 178: 7.126 distance: 175 - 176: 7.954 distance: 175 - 177: 10.795