Starting phenix.real_space_refine on Wed Jun 18 02:15:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iaj_35304/06_2025/8iaj_35304.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iaj_35304/06_2025/8iaj_35304.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iaj_35304/06_2025/8iaj_35304.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iaj_35304/06_2025/8iaj_35304.map" model { file = "/net/cci-nas-00/data/ceres_data/8iaj_35304/06_2025/8iaj_35304.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iaj_35304/06_2025/8iaj_35304.cif" } resolution = 3.1 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 114 5.16 5 C 13350 2.51 5 N 3470 2.21 5 O 3832 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 209 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 20768 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 3861 Classifications: {'peptide': 495} Link IDs: {'PTRANS': 24, 'TRANS': 470} Chain: "B" Number of atoms: 4394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 555, 4394 Classifications: {'peptide': 555} Link IDs: {'PTRANS': 29, 'TRANS': 525} Chain: "D" Number of atoms: 1484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1484 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 8, 'TRANS': 173} Chain: "C" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 584 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain breaks: 1 Chain: "E" Number of atoms: 3861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 3861 Classifications: {'peptide': 495} Link IDs: {'PTRANS': 24, 'TRANS': 470} Chain: "F" Number of atoms: 4394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 555, 4394 Classifications: {'peptide': 555} Link IDs: {'PTRANS': 29, 'TRANS': 525} Chain: "H" Number of atoms: 1484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1484 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 8, 'TRANS': 173} Chain: "G" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 584 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain breaks: 1 Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'PLP': 1, 'Z1T': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'PLP': 1, 'Z1T': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 14.81, per 1000 atoms: 0.71 Number of scatterers: 20768 At special positions: 0 Unit cell: (171.72, 106.92, 124.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 114 16.00 P 2 15.00 O 3832 8.00 N 3470 7.00 C 13350 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.05 Conformation dependent library (CDL) restraints added in 3.1 seconds 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4888 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 14 sheets defined 51.5% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.23 Creating SS restraints... Processing helix chain 'A' and resid 60 through 77 Processing helix chain 'A' and resid 89 through 100 Processing helix chain 'A' and resid 115 through 120 removed outlier: 3.558A pdb=" N ALA A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 175 Processing helix chain 'A' and resid 189 through 204 removed outlier: 3.700A pdb=" N TYR A 193 " --> pdb=" O GLN A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'A' and resid 217 through 222 Processing helix chain 'A' and resid 223 through 225 No H-bonds generated for 'chain 'A' and resid 223 through 225' Processing helix chain 'A' and resid 239 through 250 removed outlier: 3.980A pdb=" N ARG A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 279 Processing helix chain 'A' and resid 302 through 314 removed outlier: 3.589A pdb=" N LEU A 306 " --> pdb=" O PRO A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 339 removed outlier: 3.527A pdb=" N HIS A 338 " --> pdb=" O GLY A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 347 Processing helix chain 'A' and resid 368 through 379 Processing helix chain 'A' and resid 379 through 384 Processing helix chain 'A' and resid 389 through 405 removed outlier: 3.744A pdb=" N VAL A 393 " --> pdb=" O PRO A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 427 removed outlier: 4.028A pdb=" N ASP A 427 " --> pdb=" O SER A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 459 removed outlier: 3.706A pdb=" N ARG A 454 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 476 Processing helix chain 'A' and resid 482 through 504 Processing helix chain 'A' and resid 534 through 554 Processing helix chain 'B' and resid 19 through 28 removed outlier: 3.533A pdb=" N GLN B 23 " --> pdb=" O PRO B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 85 removed outlier: 3.898A pdb=" N SER B 61 " --> pdb=" O PRO B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 116 removed outlier: 3.510A pdb=" N ARG B 112 " --> pdb=" O SER B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 122 removed outlier: 3.574A pdb=" N PHE B 122 " --> pdb=" O ASP B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 186 removed outlier: 3.823A pdb=" N ASP B 177 " --> pdb=" O GLY B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 215 removed outlier: 3.662A pdb=" N ILE B 204 " --> pdb=" O THR B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 237 removed outlier: 4.614A pdb=" N PHE B 233 " --> pdb=" O ASN B 229 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ASN B 234 " --> pdb=" O ALA B 230 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA B 235 " --> pdb=" O ASN B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 261 removed outlier: 3.553A pdb=" N ARG B 254 " --> pdb=" O HIS B 250 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER B 260 " --> pdb=" O GLY B 256 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY B 261 " --> pdb=" O VAL B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 286 removed outlier: 3.634A pdb=" N LEU B 275 " --> pdb=" O ASP B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 325 Processing helix chain 'B' and resid 345 through 351 Processing helix chain 'B' and resid 378 through 389 Processing helix chain 'B' and resid 390 through 395 Processing helix chain 'B' and resid 399 through 414 removed outlier: 3.516A pdb=" N LEU B 403 " --> pdb=" O PRO B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 444 removed outlier: 4.724A pdb=" N THR B 423 " --> pdb=" O PRO B 419 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG B 434 " --> pdb=" O ALA B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 476 removed outlier: 4.049A pdb=" N ALA B 468 " --> pdb=" O SER B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 522 Processing helix chain 'B' and resid 528 through 532 removed outlier: 3.869A pdb=" N SER B 531 " --> pdb=" O SER B 528 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER B 532 " --> pdb=" O GLY B 529 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 528 through 532' Processing helix chain 'B' and resid 541 through 553 Proline residue: B 550 - end of helix Processing helix chain 'D' and resid 57 through 66 Processing helix chain 'D' and resid 73 through 77 Processing helix chain 'D' and resid 79 through 98 removed outlier: 4.056A pdb=" N ILE D 88 " --> pdb=" O HIS D 84 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL D 89 " --> pdb=" O ILE D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 123 removed outlier: 3.933A pdb=" N LEU D 123 " --> pdb=" O ILE D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 145 removed outlier: 3.580A pdb=" N ILE D 145 " --> pdb=" O MET D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 148 No H-bonds generated for 'chain 'D' and resid 146 through 148' Processing helix chain 'D' and resid 152 through 170 Proline residue: D 162 - end of helix Processing helix chain 'D' and resid 176 through 191 Processing helix chain 'C' and resid 13 through 22 Processing helix chain 'C' and resid 27 through 45 Processing helix chain 'C' and resid 53 through 75 Processing helix chain 'E' and resid 61 through 77 Processing helix chain 'E' and resid 89 through 100 Processing helix chain 'E' and resid 115 through 120 removed outlier: 3.558A pdb=" N ALA E 119 " --> pdb=" O SER E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 175 Processing helix chain 'E' and resid 189 through 204 removed outlier: 3.700A pdb=" N TYR E 193 " --> pdb=" O GLN E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 216 Processing helix chain 'E' and resid 217 through 222 Processing helix chain 'E' and resid 223 through 225 No H-bonds generated for 'chain 'E' and resid 223 through 225' Processing helix chain 'E' and resid 239 through 250 removed outlier: 3.980A pdb=" N ARG E 250 " --> pdb=" O LEU E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 279 Processing helix chain 'E' and resid 302 through 314 removed outlier: 3.589A pdb=" N LEU E 306 " --> pdb=" O PRO E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 339 removed outlier: 3.527A pdb=" N HIS E 338 " --> pdb=" O GLY E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 347 Processing helix chain 'E' and resid 368 through 379 Processing helix chain 'E' and resid 379 through 384 Processing helix chain 'E' and resid 389 through 405 removed outlier: 3.743A pdb=" N VAL E 393 " --> pdb=" O PRO E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 427 removed outlier: 4.028A pdb=" N ASP E 427 " --> pdb=" O SER E 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 450 through 459 removed outlier: 3.706A pdb=" N ARG E 454 " --> pdb=" O THR E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 461 through 476 Processing helix chain 'E' and resid 482 through 504 Processing helix chain 'E' and resid 534 through 554 Processing helix chain 'F' and resid 19 through 28 removed outlier: 3.533A pdb=" N GLN F 23 " --> pdb=" O PRO F 19 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 85 removed outlier: 3.899A pdb=" N SER F 61 " --> pdb=" O PRO F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 116 removed outlier: 3.510A pdb=" N ARG F 112 " --> pdb=" O SER F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 122 removed outlier: 3.574A pdb=" N PHE F 122 " --> pdb=" O ASP F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 186 removed outlier: 3.824A pdb=" N ASP F 177 " --> pdb=" O GLY F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 215 removed outlier: 3.662A pdb=" N ILE F 204 " --> pdb=" O THR F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 237 removed outlier: 4.615A pdb=" N PHE F 233 " --> pdb=" O ASN F 229 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ASN F 234 " --> pdb=" O ALA F 230 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA F 235 " --> pdb=" O ASN F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 261 removed outlier: 3.553A pdb=" N ARG F 254 " --> pdb=" O HIS F 250 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER F 260 " --> pdb=" O GLY F 256 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY F 261 " --> pdb=" O VAL F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 286 removed outlier: 3.634A pdb=" N LEU F 275 " --> pdb=" O ASP F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 325 Processing helix chain 'F' and resid 345 through 351 Processing helix chain 'F' and resid 378 through 389 Processing helix chain 'F' and resid 390 through 395 Processing helix chain 'F' and resid 399 through 414 removed outlier: 3.516A pdb=" N LEU F 403 " --> pdb=" O PRO F 399 " (cutoff:3.500A) Processing helix chain 'F' and resid 419 through 444 removed outlier: 4.724A pdb=" N THR F 423 " --> pdb=" O PRO F 419 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG F 434 " --> pdb=" O ALA F 430 " (cutoff:3.500A) Processing helix chain 'F' and resid 464 through 476 removed outlier: 4.049A pdb=" N ALA F 468 " --> pdb=" O SER F 464 " (cutoff:3.500A) Processing helix chain 'F' and resid 504 through 522 Processing helix chain 'F' and resid 528 through 532 removed outlier: 3.869A pdb=" N SER F 531 " --> pdb=" O SER F 528 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER F 532 " --> pdb=" O GLY F 529 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 528 through 532' Processing helix chain 'F' and resid 541 through 553 Proline residue: F 550 - end of helix Processing helix chain 'H' and resid 57 through 66 Processing helix chain 'H' and resid 73 through 77 Processing helix chain 'H' and resid 79 through 98 removed outlier: 4.056A pdb=" N ILE H 88 " --> pdb=" O HIS H 84 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL H 89 " --> pdb=" O ILE H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 123 removed outlier: 3.933A pdb=" N LEU H 123 " --> pdb=" O ILE H 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 145 removed outlier: 3.580A pdb=" N ILE H 145 " --> pdb=" O MET H 141 " (cutoff:3.500A) Processing helix chain 'H' and resid 146 through 148 No H-bonds generated for 'chain 'H' and resid 146 through 148' Processing helix chain 'H' and resid 152 through 170 Proline residue: H 162 - end of helix Processing helix chain 'H' and resid 176 through 191 Processing helix chain 'G' and resid 13 through 22 Processing helix chain 'G' and resid 27 through 45 Processing helix chain 'G' and resid 53 through 75 Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 135 removed outlier: 6.913A pdb=" N ILE A 135 " --> pdb=" O THR A 145 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N THR A 145 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N LEU A 506 " --> pdb=" O ASN A 146 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N PHE A 148 " --> pdb=" O LEU A 506 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 207 through 211 removed outlier: 3.602A pdb=" N GLY A 207 " --> pdb=" O GLY A 367 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE A 364 " --> pdb=" O GLY A 352 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LYS A 286 " --> pdb=" O ARG A 316 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N PHE A 318 " --> pdb=" O LYS A 286 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ILE A 288 " --> pdb=" O PHE A 318 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ASP A 320 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N THR A 290 " --> pdb=" O ASP A 320 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL A 231 " --> pdb=" O PHE A 287 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N VAL A 289 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL A 233 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 8.942A pdb=" N GLU A 291 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 444 through 447 removed outlier: 4.012A pdb=" N LEU A 447 " --> pdb=" O LEU A 525 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 126 through 127 removed outlier: 4.142A pdb=" N ARG B 135 " --> pdb=" O THR B 127 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP B 138 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ALA B 153 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N ILE B 140 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N SER B 151 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N HIS B 142 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N THR B 149 " --> pdb=" O HIS B 142 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ALA B 479 " --> pdb=" O PRO B 156 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N MET B 158 " --> pdb=" O ALA B 479 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 218 through 222 removed outlier: 3.538A pdb=" N ASP B 218 " --> pdb=" O ALA B 377 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N THR B 363 " --> pdb=" O GLU B 332 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP B 246 " --> pdb=" O CYS B 300 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N GLU B 302 " --> pdb=" O ASP B 246 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE B 267 " --> pdb=" O SER B 245 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 455 through 459 removed outlier: 3.702A pdb=" N ARG B 494 " --> pdb=" O VAL B 483 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 50 through 52 Processing sheet with id=AA8, first strand: chain 'E' and resid 132 through 135 removed outlier: 6.913A pdb=" N ILE E 135 " --> pdb=" O THR E 145 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N THR E 145 " --> pdb=" O ILE E 135 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N LEU E 506 " --> pdb=" O ASN E 146 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N PHE E 148 " --> pdb=" O LEU E 506 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 207 through 211 removed outlier: 3.602A pdb=" N GLY E 207 " --> pdb=" O GLY E 367 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE E 364 " --> pdb=" O GLY E 352 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LYS E 286 " --> pdb=" O ARG E 316 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N PHE E 318 " --> pdb=" O LYS E 286 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ILE E 288 " --> pdb=" O PHE E 318 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ASP E 320 " --> pdb=" O ILE E 288 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N THR E 290 " --> pdb=" O ASP E 320 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL E 231 " --> pdb=" O PHE E 287 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N VAL E 289 " --> pdb=" O VAL E 231 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL E 233 " --> pdb=" O VAL E 289 " (cutoff:3.500A) removed outlier: 8.943A pdb=" N GLU E 291 " --> pdb=" O VAL E 233 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 444 through 447 removed outlier: 4.012A pdb=" N LEU E 447 " --> pdb=" O LEU E 525 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 126 through 127 removed outlier: 4.142A pdb=" N ARG F 135 " --> pdb=" O THR F 127 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP F 138 " --> pdb=" O ALA F 153 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ALA F 153 " --> pdb=" O ASP F 138 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N ILE F 140 " --> pdb=" O SER F 151 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N SER F 151 " --> pdb=" O ILE F 140 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N HIS F 142 " --> pdb=" O THR F 149 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N THR F 149 " --> pdb=" O HIS F 142 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ALA F 479 " --> pdb=" O PRO F 156 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N MET F 158 " --> pdb=" O ALA F 479 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 218 through 222 removed outlier: 3.538A pdb=" N ASP F 218 " --> pdb=" O ALA F 377 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N THR F 363 " --> pdb=" O GLU F 332 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP F 246 " --> pdb=" O CYS F 300 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N GLU F 302 " --> pdb=" O ASP F 246 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE F 267 " --> pdb=" O SER F 245 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 455 through 459 removed outlier: 3.702A pdb=" N ARG F 494 " --> pdb=" O VAL F 483 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 50 through 52 985 hydrogen bonds defined for protein. 2889 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: 7.52 Time building geometry restraints manager: 7.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6624 1.34 - 1.47: 5000 1.47 - 1.59: 9432 1.59 - 1.71: 2 1.71 - 1.83: 174 Bond restraints: 21232 Sorted by residual: bond pdb=" C14 Z1T F 602 " pdb=" C15 Z1T F 602 " ideal model delta sigma weight residual 1.329 1.526 -0.197 2.00e-02 2.50e+03 9.68e+01 bond pdb=" C14 Z1T B 602 " pdb=" C15 Z1T B 602 " ideal model delta sigma weight residual 1.329 1.526 -0.197 2.00e-02 2.50e+03 9.68e+01 bond pdb=" C4 PLP F 601 " pdb=" C5 PLP F 601 " ideal model delta sigma weight residual 1.390 1.486 -0.096 2.00e-02 2.50e+03 2.30e+01 bond pdb=" C4 PLP B 601 " pdb=" C5 PLP B 601 " ideal model delta sigma weight residual 1.390 1.486 -0.096 2.00e-02 2.50e+03 2.30e+01 bond pdb=" C2 PLP B 601 " pdb=" C3 PLP B 601 " ideal model delta sigma weight residual 1.390 1.484 -0.094 2.00e-02 2.50e+03 2.23e+01 ... (remaining 21227 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.54: 28668 4.54 - 9.07: 98 9.07 - 13.61: 2 13.61 - 18.15: 0 18.15 - 22.68: 4 Bond angle restraints: 28772 Sorted by residual: angle pdb=" CB MET D 70 " pdb=" CG MET D 70 " pdb=" SD MET D 70 " ideal model delta sigma weight residual 112.70 135.38 -22.68 3.00e+00 1.11e-01 5.72e+01 angle pdb=" CB MET H 70 " pdb=" CG MET H 70 " pdb=" SD MET H 70 " ideal model delta sigma weight residual 112.70 135.38 -22.68 3.00e+00 1.11e-01 5.72e+01 angle pdb=" CB MET H 177 " pdb=" CG MET H 177 " pdb=" SD MET H 177 " ideal model delta sigma weight residual 112.70 133.09 -20.39 3.00e+00 1.11e-01 4.62e+01 angle pdb=" CB MET D 177 " pdb=" CG MET D 177 " pdb=" SD MET D 177 " ideal model delta sigma weight residual 112.70 133.09 -20.39 3.00e+00 1.11e-01 4.62e+01 angle pdb=" N MET B 307 " pdb=" CA MET B 307 " pdb=" C MET B 307 " ideal model delta sigma weight residual 114.64 107.24 7.40 1.52e+00 4.33e-01 2.37e+01 ... (remaining 28767 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.06: 11796 21.06 - 42.12: 862 42.12 - 63.18: 90 63.18 - 84.24: 16 84.24 - 105.30: 6 Dihedral angle restraints: 12770 sinusoidal: 5180 harmonic: 7590 Sorted by residual: dihedral pdb=" CA GLY D 134 " pdb=" C GLY D 134 " pdb=" N ALA D 135 " pdb=" CA ALA D 135 " ideal model delta harmonic sigma weight residual 180.00 150.58 29.42 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA GLY H 134 " pdb=" C GLY H 134 " pdb=" N ALA H 135 " pdb=" CA ALA H 135 " ideal model delta harmonic sigma weight residual 180.00 150.58 29.42 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA PHE A 256 " pdb=" C PHE A 256 " pdb=" N ASN A 257 " pdb=" CA ASN A 257 " ideal model delta harmonic sigma weight residual -180.00 -154.64 -25.36 0 5.00e+00 4.00e-02 2.57e+01 ... (remaining 12767 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2338 0.048 - 0.095: 749 0.095 - 0.143: 153 0.143 - 0.190: 12 0.190 - 0.238: 4 Chirality restraints: 3256 Sorted by residual: chirality pdb=" CA LEU B 91 " pdb=" N LEU B 91 " pdb=" C LEU B 91 " pdb=" CB LEU B 91 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA LEU F 91 " pdb=" N LEU F 91 " pdb=" C LEU F 91 " pdb=" CB LEU F 91 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" C17 Z1T F 602 " pdb=" C16 Z1T F 602 " pdb=" C18 Z1T F 602 " pdb=" N1 Z1T F 602 " both_signs ideal model delta sigma weight residual False 2.47 2.69 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 3253 not shown) Planarity restraints: 3652 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 86 " 0.045 5.00e-02 4.00e+02 6.91e-02 7.65e+00 pdb=" N PRO A 87 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO A 87 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 87 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG E 86 " -0.045 5.00e-02 4.00e+02 6.91e-02 7.65e+00 pdb=" N PRO E 87 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO E 87 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO E 87 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE G 48 " -0.011 2.00e-02 2.50e+03 2.32e-02 5.38e+00 pdb=" C PHE G 48 " 0.040 2.00e-02 2.50e+03 pdb=" O PHE G 48 " -0.015 2.00e-02 2.50e+03 pdb=" N TYR G 49 " -0.014 2.00e-02 2.50e+03 ... (remaining 3649 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 1062 2.72 - 3.27: 20149 3.27 - 3.81: 32021 3.81 - 4.36: 38933 4.36 - 4.90: 70221 Nonbonded interactions: 162386 Sorted by model distance: nonbonded pdb=" CD LYS A 85 " pdb=" OE1 GLN H 55 " model vdw 2.176 3.440 nonbonded pdb=" NH2 ARG A 228 " pdb=" OD2 ASP D 63 " model vdw 2.184 3.120 nonbonded pdb=" NH2 ARG E 228 " pdb=" OD2 ASP H 63 " model vdw 2.184 3.120 nonbonded pdb=" OE1 GLN D 55 " pdb=" CD LYS E 85 " model vdw 2.193 3.440 nonbonded pdb=" OG1 THR F 342 " pdb=" OE2 GLU F 348 " model vdw 2.204 3.040 ... (remaining 162381 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: 0.10 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' 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: 205.900 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: 0.040 Extract box with map and model: 0.890 Check model and map are aligned: 0.160 Set scattering table: 0.220 Process input model: 52.680 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.170 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:3.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 263.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 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 : 0.008 0.463 21234 Z= 0.528 Angle : 0.858 22.682 28772 Z= 0.485 Chirality : 0.047 0.238 3256 Planarity : 0.005 0.069 3652 Dihedral : 13.913 105.296 7882 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.44 % Favored : 92.49 % Rotamer: Outliers : 0.61 % Allowed : 0.78 % Favored : 98.61 % 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: -0.31 (0.16), residues: 2582 helix: 1.50 (0.15), residues: 1218 sheet: -0.46 (0.32), residues: 258 loop : -2.21 (0.16), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 106 HIS 0.004 0.001 HIS G 45 PHE 0.036 0.002 PHE C 62 TYR 0.022 0.002 TYR F 533 ARG 0.007 0.001 ARG D 42 Details of bonding type rmsd hydrogen bonds : bond 0.15985 ( 985) hydrogen bonds : angle 5.88274 ( 2889) covalent geometry : bond 0.00612 (21232) covalent geometry : angle 0.85779 (28772) Misc. bond : bond 0.46243 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 266 time to evaluate : 5.708 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 39 THR cc_start: 0.8399 (p) cc_final: 0.8098 (p) REVERT: F 466 MET cc_start: 0.8273 (ttp) cc_final: 0.7822 (ttp) REVERT: H 39 THR cc_start: 0.8395 (p) cc_final: 0.8078 (p) outliers start: 14 outliers final: 5 residues processed: 270 average time/residue: 0.4952 time to fit residues: 209.3856 Evaluate side-chains 212 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 207 time to evaluate : 2.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain H residue 70 MET Chi-restraints excluded: chain G residue 59 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 5.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.0570 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 10.0000 chunk 149 optimal weight: 1.9990 chunk 232 optimal weight: 0.8980 overall best weight: 0.9300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 237 GLN ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 HIS B 145 ASN ** D 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 GLN E 237 GLN ** E 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 HIS F 145 ASN ** H 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.125658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.099493 restraints weight = 28312.657| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.68 r_work: 0.2969 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21234 Z= 0.125 Angle : 0.576 6.623 28772 Z= 0.306 Chirality : 0.043 0.184 3256 Planarity : 0.005 0.044 3652 Dihedral : 7.383 99.501 2933 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.83 % Allowed : 6.09 % Favored : 93.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.17), residues: 2582 helix: 1.84 (0.15), residues: 1230 sheet: 0.14 (0.31), residues: 280 loop : -2.07 (0.17), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 142 HIS 0.003 0.001 HIS C 45 PHE 0.014 0.001 PHE G 62 TYR 0.014 0.001 TYR B 510 ARG 0.003 0.000 ARG H 174 Details of bonding type rmsd hydrogen bonds : bond 0.04839 ( 985) hydrogen bonds : angle 4.61561 ( 2889) covalent geometry : bond 0.00272 (21232) covalent geometry : angle 0.57624 (28772) Misc. bond : bond 0.00096 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 264 time to evaluate : 5.392 Fit side-chains REVERT: A 94 ASP cc_start: 0.8337 (m-30) cc_final: 0.7918 (m-30) REVERT: A 341 MET cc_start: 0.8514 (mtt) cc_final: 0.8239 (mtp) REVERT: B 466 MET cc_start: 0.8501 (ttp) cc_final: 0.8243 (ttp) REVERT: D 39 THR cc_start: 0.8396 (p) cc_final: 0.8081 (p) REVERT: D 73 THR cc_start: 0.9164 (m) cc_final: 0.8844 (p) REVERT: C 59 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8558 (tp) REVERT: E 94 ASP cc_start: 0.8317 (m-30) cc_final: 0.7880 (m-30) REVERT: E 341 MET cc_start: 0.8527 (mtt) cc_final: 0.8249 (mtp) REVERT: F 466 MET cc_start: 0.8565 (ttp) cc_final: 0.8288 (ttp) REVERT: H 39 THR cc_start: 0.8411 (p) cc_final: 0.8098 (p) REVERT: H 73 THR cc_start: 0.9167 (m) cc_final: 0.8861 (p) REVERT: G 59 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8528 (tp) outliers start: 19 outliers final: 11 residues processed: 275 average time/residue: 0.4799 time to fit residues: 210.6471 Evaluate side-chains 230 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 217 time to evaluate : 4.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 375 ILE Chi-restraints excluded: chain G residue 59 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 61 optimal weight: 1.9990 chunk 142 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 166 optimal weight: 3.9990 chunk 159 optimal weight: 0.8980 chunk 134 optimal weight: 5.9990 chunk 230 optimal weight: 0.0370 chunk 202 optimal weight: 7.9990 chunk 71 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 overall best weight: 1.3864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 55 GLN ** 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 = 0.3418 r_free = 0.3418 target = 0.124570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.099228 restraints weight = 28258.966| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.57 r_work: 0.2926 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21234 Z= 0.129 Angle : 0.556 7.272 28772 Z= 0.295 Chirality : 0.042 0.180 3256 Planarity : 0.005 0.050 3652 Dihedral : 7.169 96.875 2927 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.13 % Allowed : 8.74 % Favored : 90.13 % 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: 0.36 (0.17), residues: 2582 helix: 1.99 (0.15), residues: 1218 sheet: 0.28 (0.32), residues: 280 loop : -1.94 (0.17), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 142 HIS 0.003 0.001 HIS G 45 PHE 0.017 0.001 PHE E 256 TYR 0.015 0.001 TYR B 510 ARG 0.002 0.000 ARG H 174 Details of bonding type rmsd hydrogen bonds : bond 0.04780 ( 985) hydrogen bonds : angle 4.40134 ( 2889) covalent geometry : bond 0.00297 (21232) covalent geometry : angle 0.55630 (28772) Misc. bond : bond 0.00080 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 230 time to evaluate : 2.435 Fit side-chains REVERT: A 85 LYS cc_start: 0.8578 (tppt) cc_final: 0.8299 (mmtp) REVERT: A 98 ASP cc_start: 0.8169 (m-30) cc_final: 0.7881 (m-30) REVERT: B 271 ASP cc_start: 0.8310 (t0) cc_final: 0.8103 (t0) REVERT: B 396 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.7790 (pp20) REVERT: B 520 ASP cc_start: 0.8107 (t0) cc_final: 0.7677 (m-30) REVERT: D 39 THR cc_start: 0.8341 (p) cc_final: 0.8023 (p) REVERT: C 59 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8632 (tp) REVERT: E 85 LYS cc_start: 0.8600 (tppt) cc_final: 0.8321 (mmtp) REVERT: E 98 ASP cc_start: 0.8173 (m-30) cc_final: 0.7894 (m-30) REVERT: F 271 ASP cc_start: 0.8310 (t0) cc_final: 0.8103 (t0) REVERT: F 396 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.7769 (pp20) REVERT: F 483 VAL cc_start: 0.8649 (m) cc_final: 0.8416 (t) REVERT: F 520 ASP cc_start: 0.8110 (t0) cc_final: 0.7684 (m-30) REVERT: H 39 THR cc_start: 0.8358 (p) cc_final: 0.8039 (p) REVERT: G 59 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8627 (tp) outliers start: 26 outliers final: 21 residues processed: 245 average time/residue: 0.3765 time to fit residues: 145.2929 Evaluate side-chains 249 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 224 time to evaluate : 3.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 514 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 396 GLU Chi-restraints excluded: chain H residue 98 PHE Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain G residue 59 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 91 optimal weight: 6.9990 chunk 216 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 160 optimal weight: 0.0020 chunk 191 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 144 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 overall best weight: 1.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 GLN ** E 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.125715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.098976 restraints weight = 28576.463| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 1.75 r_work: 0.2948 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 21234 Z= 0.125 Angle : 0.540 7.001 28772 Z= 0.286 Chirality : 0.042 0.178 3256 Planarity : 0.005 0.052 3652 Dihedral : 7.107 94.804 2927 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.43 % Allowed : 9.87 % Favored : 88.70 % 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: 0.49 (0.17), residues: 2582 helix: 1.98 (0.15), residues: 1232 sheet: 0.57 (0.33), residues: 256 loop : -1.79 (0.17), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 142 HIS 0.003 0.001 HIS A 374 PHE 0.016 0.001 PHE A 256 TYR 0.015 0.001 TYR B 510 ARG 0.003 0.000 ARG H 174 Details of bonding type rmsd hydrogen bonds : bond 0.04506 ( 985) hydrogen bonds : angle 4.29116 ( 2889) covalent geometry : bond 0.00290 (21232) covalent geometry : angle 0.53953 (28772) Misc. bond : bond 0.00067 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 222 time to evaluate : 2.373 Fit side-chains REVERT: A 94 ASP cc_start: 0.8034 (m-30) cc_final: 0.7739 (m-30) REVERT: A 98 ASP cc_start: 0.8180 (m-30) cc_final: 0.7806 (m-30) REVERT: A 308 LYS cc_start: 0.8579 (ttmt) cc_final: 0.8311 (ttmm) REVERT: B 271 ASP cc_start: 0.8337 (t0) cc_final: 0.8075 (t0) REVERT: B 396 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.7750 (pp20) REVERT: B 520 ASP cc_start: 0.8167 (t0) cc_final: 0.7676 (m-30) REVERT: D 39 THR cc_start: 0.8259 (p) cc_final: 0.7930 (p) REVERT: D 42 ARG cc_start: 0.7613 (ttm110) cc_final: 0.7035 (mtm180) REVERT: C 59 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8546 (tp) REVERT: E 94 ASP cc_start: 0.8026 (m-30) cc_final: 0.7738 (m-30) REVERT: E 98 ASP cc_start: 0.8177 (m-30) cc_final: 0.7800 (m-30) REVERT: E 308 LYS cc_start: 0.8640 (ttmt) cc_final: 0.8191 (ttmm) REVERT: F 116 MET cc_start: 0.8560 (mmm) cc_final: 0.8185 (mmm) REVERT: F 271 ASP cc_start: 0.8326 (t0) cc_final: 0.8044 (t0) REVERT: F 396 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.7737 (pp20) REVERT: F 520 ASP cc_start: 0.8165 (t0) cc_final: 0.7674 (m-30) REVERT: H 39 THR cc_start: 0.8278 (p) cc_final: 0.7948 (p) REVERT: H 42 ARG cc_start: 0.7645 (ttm110) cc_final: 0.7049 (mtm180) REVERT: G 59 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8560 (tp) outliers start: 33 outliers final: 22 residues processed: 244 average time/residue: 0.4117 time to fit residues: 156.3451 Evaluate side-chains 244 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 218 time to evaluate : 2.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 514 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 396 GLU Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain H residue 98 PHE Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain G residue 59 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 215 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 210 optimal weight: 6.9990 chunk 75 optimal weight: 0.9980 chunk 20 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 216 optimal weight: 0.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 GLN ** E 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.122689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.095049 restraints weight = 28344.315| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 1.78 r_work: 0.2898 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 21234 Z= 0.182 Angle : 0.599 7.888 28772 Z= 0.316 Chirality : 0.044 0.173 3256 Planarity : 0.005 0.056 3652 Dihedral : 7.208 94.901 2926 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 1.70 % Allowed : 11.04 % Favored : 87.26 % 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: 0.35 (0.17), residues: 2582 helix: 1.87 (0.15), residues: 1226 sheet: 0.43 (0.33), residues: 254 loop : -1.82 (0.17), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 142 HIS 0.005 0.001 HIS E 374 PHE 0.021 0.002 PHE E 256 TYR 0.019 0.002 TYR B 510 ARG 0.003 0.000 ARG H 174 Details of bonding type rmsd hydrogen bonds : bond 0.05508 ( 985) hydrogen bonds : angle 4.34142 ( 2889) covalent geometry : bond 0.00447 (21232) covalent geometry : angle 0.59892 (28772) Misc. bond : bond 0.00084 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 217 time to evaluate : 3.614 Fit side-chains REVERT: A 85 LYS cc_start: 0.8613 (tppt) cc_final: 0.8251 (tppt) REVERT: B 396 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.7745 (pp20) REVERT: D 39 THR cc_start: 0.8278 (p) cc_final: 0.7943 (p) REVERT: C 59 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8558 (tp) REVERT: E 85 LYS cc_start: 0.8614 (tppt) cc_final: 0.8253 (tppt) REVERT: F 271 ASP cc_start: 0.8362 (t0) cc_final: 0.8143 (t0) REVERT: F 396 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.7731 (pp20) REVERT: H 39 THR cc_start: 0.8294 (p) cc_final: 0.7953 (p) REVERT: G 59 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8579 (tp) outliers start: 39 outliers final: 25 residues processed: 244 average time/residue: 0.4344 time to fit residues: 166.8005 Evaluate side-chains 241 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 212 time to evaluate : 2.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 514 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 375 ILE Chi-restraints excluded: chain F residue 396 GLU Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain H residue 98 PHE Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain G residue 59 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 99 optimal weight: 2.9990 chunk 188 optimal weight: 2.9990 chunk 161 optimal weight: 0.7980 chunk 165 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 65 optimal weight: 0.9980 chunk 36 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 141 optimal weight: 0.7980 chunk 155 optimal weight: 8.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 GLN E 375 GLN ** E 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 171 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.125030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.097586 restraints weight = 28082.544| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 1.78 r_work: 0.2915 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21234 Z= 0.129 Angle : 0.550 10.048 28772 Z= 0.288 Chirality : 0.042 0.177 3256 Planarity : 0.005 0.057 3652 Dihedral : 7.072 93.939 2926 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.70 % Allowed : 11.70 % Favored : 86.61 % 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: 0.48 (0.17), residues: 2582 helix: 1.96 (0.15), residues: 1234 sheet: 0.46 (0.33), residues: 256 loop : -1.75 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 142 HIS 0.004 0.001 HIS E 374 PHE 0.018 0.001 PHE C 62 TYR 0.016 0.001 TYR B 510 ARG 0.002 0.000 ARG D 174 Details of bonding type rmsd hydrogen bonds : bond 0.04604 ( 985) hydrogen bonds : angle 4.25821 ( 2889) covalent geometry : bond 0.00304 (21232) covalent geometry : angle 0.54950 (28772) Misc. bond : bond 0.00064 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 216 time to evaluate : 2.413 Fit side-chains REVERT: B 139 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.7763 (mtm180) REVERT: B 323 LYS cc_start: 0.8402 (tttt) cc_final: 0.8157 (tttp) REVERT: B 396 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.7703 (pp20) REVERT: D 39 THR cc_start: 0.8238 (p) cc_final: 0.7906 (p) REVERT: C 14 THR cc_start: 0.7854 (p) cc_final: 0.7595 (p) REVERT: C 59 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8498 (tp) REVERT: E 125 MET cc_start: 0.7429 (mtm) cc_final: 0.7075 (mtm) REVERT: F 116 MET cc_start: 0.8561 (mmm) cc_final: 0.8153 (mmm) REVERT: F 139 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.7789 (mtm180) REVERT: F 396 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.7696 (pp20) REVERT: H 39 THR cc_start: 0.8239 (p) cc_final: 0.7888 (p) REVERT: G 14 THR cc_start: 0.7844 (p) cc_final: 0.7578 (p) REVERT: G 59 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8487 (tp) outliers start: 39 outliers final: 25 residues processed: 248 average time/residue: 0.3189 time to fit residues: 123.5100 Evaluate side-chains 243 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 212 time to evaluate : 2.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 514 LEU Chi-restraints excluded: chain F residue 139 ARG Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain F residue 396 GLU Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain H residue 98 PHE Chi-restraints excluded: chain H residue 205 SER Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain G residue 59 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 129 optimal weight: 6.9990 chunk 135 optimal weight: 6.9990 chunk 191 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 195 optimal weight: 8.9990 chunk 212 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 GLN D 171 GLN E 130 GLN ** E 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 477 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.120767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.093195 restraints weight = 28271.709| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 1.78 r_work: 0.2878 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 21234 Z= 0.233 Angle : 0.664 9.409 28772 Z= 0.347 Chirality : 0.046 0.186 3256 Planarity : 0.005 0.062 3652 Dihedral : 7.365 95.038 2926 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.13 % Allowed : 11.96 % Favored : 85.91 % 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: 0.20 (0.17), residues: 2582 helix: 1.66 (0.15), residues: 1238 sheet: 0.36 (0.33), residues: 254 loop : -1.82 (0.17), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 142 HIS 0.006 0.001 HIS A 374 PHE 0.024 0.002 PHE A 256 TYR 0.020 0.002 TYR B 510 ARG 0.003 0.001 ARG D 174 Details of bonding type rmsd hydrogen bonds : bond 0.06264 ( 985) hydrogen bonds : angle 4.44631 ( 2889) covalent geometry : bond 0.00580 (21232) covalent geometry : angle 0.66359 (28772) Misc. bond : bond 0.00089 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 208 time to evaluate : 2.501 Fit side-chains REVERT: B 116 MET cc_start: 0.8631 (mmm) cc_final: 0.8306 (mmp) REVERT: B 139 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.7537 (mtm180) REVERT: B 396 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.7835 (pp20) REVERT: B 520 ASP cc_start: 0.8186 (t0) cc_final: 0.7845 (m-30) REVERT: D 39 THR cc_start: 0.8303 (p) cc_final: 0.7928 (p) REVERT: C 59 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8606 (tp) REVERT: E 125 MET cc_start: 0.7833 (mtm) cc_final: 0.7241 (mtm) REVERT: F 139 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.7551 (mtm180) REVERT: F 396 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.7832 (pp20) REVERT: F 520 ASP cc_start: 0.8183 (t0) cc_final: 0.7845 (m-30) REVERT: H 39 THR cc_start: 0.8282 (p) cc_final: 0.7917 (p) REVERT: G 14 THR cc_start: 0.7889 (p) cc_final: 0.7597 (p) REVERT: G 59 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8586 (tp) outliers start: 49 outliers final: 28 residues processed: 247 average time/residue: 0.3247 time to fit residues: 124.6130 Evaluate side-chains 238 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 204 time to evaluate : 2.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain F residue 139 ARG Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 332 GLU Chi-restraints excluded: chain F residue 375 ILE Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain F residue 396 GLU Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain H residue 98 PHE Chi-restraints excluded: chain H residue 205 SER Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain G residue 59 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 189 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 214 optimal weight: 0.9980 chunk 167 optimal weight: 3.9990 chunk 173 optimal weight: 6.9990 chunk 86 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 146 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 129 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 GLN ** E 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.123851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.096272 restraints weight = 28222.057| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 1.78 r_work: 0.2917 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21234 Z= 0.140 Angle : 0.570 9.006 28772 Z= 0.300 Chirality : 0.043 0.175 3256 Planarity : 0.005 0.058 3652 Dihedral : 7.167 93.834 2926 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.91 % Allowed : 12.22 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.17), residues: 2582 helix: 1.87 (0.15), residues: 1234 sheet: 0.43 (0.33), residues: 256 loop : -1.79 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 294 HIS 0.004 0.001 HIS E 374 PHE 0.019 0.001 PHE G 62 TYR 0.017 0.001 TYR F 510 ARG 0.003 0.000 ARG A 456 Details of bonding type rmsd hydrogen bonds : bond 0.04917 ( 985) hydrogen bonds : angle 4.31727 ( 2889) covalent geometry : bond 0.00332 (21232) covalent geometry : angle 0.57038 (28772) Misc. bond : bond 0.00064 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 211 time to evaluate : 2.432 Fit side-chains REVERT: B 8 THR cc_start: 0.8465 (OUTLIER) cc_final: 0.8088 (t) REVERT: B 139 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.7708 (mtm180) REVERT: B 323 LYS cc_start: 0.8463 (tttt) cc_final: 0.8228 (tttp) REVERT: B 396 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.7729 (pp20) REVERT: D 39 THR cc_start: 0.8280 (p) cc_final: 0.7917 (p) REVERT: C 14 THR cc_start: 0.7857 (p) cc_final: 0.7569 (p) REVERT: C 59 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8549 (tp) REVERT: E 125 MET cc_start: 0.7771 (mtm) cc_final: 0.7198 (mtm) REVERT: F 8 THR cc_start: 0.8406 (OUTLIER) cc_final: 0.8039 (t) REVERT: F 139 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.7722 (mtm180) REVERT: F 323 LYS cc_start: 0.8459 (tttt) cc_final: 0.8228 (tttp) REVERT: F 396 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.7720 (pp20) REVERT: H 39 THR cc_start: 0.8281 (p) cc_final: 0.7915 (p) REVERT: G 14 THR cc_start: 0.7882 (p) cc_final: 0.7604 (p) REVERT: G 59 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8529 (tp) outliers start: 44 outliers final: 29 residues processed: 245 average time/residue: 0.3334 time to fit residues: 127.3742 Evaluate side-chains 244 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 207 time to evaluate : 2.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 332 GLU Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 514 LEU Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 139 ARG Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 332 GLU Chi-restraints excluded: chain F residue 375 ILE Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain F residue 396 GLU Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain H residue 98 PHE Chi-restraints excluded: chain H residue 205 SER Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain G residue 59 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 158 optimal weight: 6.9990 chunk 196 optimal weight: 0.7980 chunk 162 optimal weight: 2.9990 chunk 104 optimal weight: 7.9990 chunk 112 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 222 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 GLN ** E 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.126116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.098625 restraints weight = 28127.853| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 1.77 r_work: 0.2936 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21234 Z= 0.113 Angle : 0.530 8.847 28772 Z= 0.278 Chirality : 0.041 0.179 3256 Planarity : 0.005 0.055 3652 Dihedral : 7.017 93.508 2926 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.83 % Allowed : 12.43 % Favored : 85.74 % 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: 0.62 (0.17), residues: 2582 helix: 2.05 (0.15), residues: 1234 sheet: 0.56 (0.33), residues: 256 loop : -1.66 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 294 HIS 0.002 0.001 HIS E 374 PHE 0.017 0.001 PHE C 62 TYR 0.013 0.001 TYR B 510 ARG 0.003 0.000 ARG A 456 Details of bonding type rmsd hydrogen bonds : bond 0.04118 ( 985) hydrogen bonds : angle 4.20589 ( 2889) covalent geometry : bond 0.00256 (21232) covalent geometry : angle 0.52959 (28772) Misc. bond : bond 0.00058 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 226 time to evaluate : 2.438 Fit side-chains REVERT: A 308 LYS cc_start: 0.8632 (ttmt) cc_final: 0.8265 (ttmm) REVERT: A 479 ASN cc_start: 0.8024 (t0) cc_final: 0.7779 (t0) REVERT: B 8 THR cc_start: 0.8452 (OUTLIER) cc_final: 0.8086 (t) REVERT: B 116 MET cc_start: 0.8474 (mmm) cc_final: 0.8011 (mmm) REVERT: B 139 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.7925 (mtm180) REVERT: B 323 LYS cc_start: 0.8424 (tttt) cc_final: 0.8194 (tttp) REVERT: B 396 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.7721 (pp20) REVERT: B 548 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.6842 (ttp-110) REVERT: D 39 THR cc_start: 0.8223 (p) cc_final: 0.7866 (p) REVERT: C 14 THR cc_start: 0.7785 (p) cc_final: 0.7583 (p) REVERT: C 59 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8508 (tp) REVERT: E 125 MET cc_start: 0.7758 (mtm) cc_final: 0.7508 (mtm) REVERT: E 308 LYS cc_start: 0.8619 (ttmt) cc_final: 0.8354 (mtpt) REVERT: F 8 THR cc_start: 0.8392 (OUTLIER) cc_final: 0.8025 (t) REVERT: F 139 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.7803 (mtm180) REVERT: F 323 LYS cc_start: 0.8430 (tttt) cc_final: 0.8204 (tttp) REVERT: F 396 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.7693 (pp20) REVERT: F 548 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.6855 (ttp-110) REVERT: H 39 THR cc_start: 0.8222 (p) cc_final: 0.7863 (p) REVERT: G 14 THR cc_start: 0.7888 (p) cc_final: 0.7657 (p) REVERT: G 59 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8486 (tp) outliers start: 42 outliers final: 25 residues processed: 260 average time/residue: 0.3376 time to fit residues: 134.4072 Evaluate side-chains 244 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 209 time to evaluate : 2.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 332 GLU Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 548 ARG Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 514 LEU Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 139 ARG Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 332 GLU Chi-restraints excluded: chain F residue 375 ILE Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain F residue 396 GLU Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 548 ARG Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain H residue 98 PHE Chi-restraints excluded: chain H residue 205 SER Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 59 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 178 optimal weight: 5.9990 chunk 161 optimal weight: 0.7980 chunk 16 optimal weight: 0.0770 chunk 164 optimal weight: 9.9990 chunk 185 optimal weight: 0.3980 chunk 19 optimal weight: 4.9990 chunk 200 optimal weight: 5.9990 chunk 177 optimal weight: 7.9990 chunk 236 optimal weight: 0.9980 chunk 141 optimal weight: 2.9990 chunk 223 optimal weight: 0.7980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 GLN ** E 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 464 GLN H 55 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.128176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.100841 restraints weight = 28126.650| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 1.78 r_work: 0.2973 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 21234 Z= 0.100 Angle : 0.513 8.606 28772 Z= 0.269 Chirality : 0.041 0.180 3256 Planarity : 0.005 0.054 3652 Dihedral : 6.841 92.236 2926 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.57 % Allowed : 12.78 % Favored : 85.65 % 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: 0.83 (0.17), residues: 2582 helix: 2.17 (0.15), residues: 1236 sheet: 0.63 (0.33), residues: 260 loop : -1.49 (0.18), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 294 HIS 0.002 0.000 HIS G 45 PHE 0.018 0.001 PHE C 62 TYR 0.013 0.001 TYR F 147 ARG 0.003 0.000 ARG A 456 Details of bonding type rmsd hydrogen bonds : bond 0.03547 ( 985) hydrogen bonds : angle 4.15034 ( 2889) covalent geometry : bond 0.00213 (21232) covalent geometry : angle 0.51319 (28772) Misc. bond : bond 0.00053 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 230 time to evaluate : 2.273 Fit side-chains REVERT: A 308 LYS cc_start: 0.8583 (ttmt) cc_final: 0.8372 (mtpt) REVERT: A 460 TYR cc_start: 0.7955 (p90) cc_final: 0.7715 (p90) REVERT: B 8 THR cc_start: 0.8416 (OUTLIER) cc_final: 0.8064 (t) REVERT: B 116 MET cc_start: 0.8438 (mmm) cc_final: 0.8086 (mmp) REVERT: B 139 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.8016 (mtm180) REVERT: B 239 LYS cc_start: 0.8365 (ptmm) cc_final: 0.8044 (tttm) REVERT: B 323 LYS cc_start: 0.8403 (tttt) cc_final: 0.8176 (tttp) REVERT: B 396 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.7648 (pp20) REVERT: B 520 ASP cc_start: 0.8164 (t0) cc_final: 0.7664 (m-30) REVERT: B 548 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.6809 (ttp-110) REVERT: D 39 THR cc_start: 0.8354 (p) cc_final: 0.7986 (p) REVERT: D 42 ARG cc_start: 0.7626 (ttm110) cc_final: 0.6989 (mtm180) REVERT: D 56 GLU cc_start: 0.7941 (mp0) cc_final: 0.7725 (mp0) REVERT: C 59 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8385 (tp) REVERT: E 125 MET cc_start: 0.7676 (mtm) cc_final: 0.7373 (mtm) REVERT: E 308 LYS cc_start: 0.8631 (ttmt) cc_final: 0.8373 (mtpt) REVERT: F 8 THR cc_start: 0.8375 (OUTLIER) cc_final: 0.8039 (t) REVERT: F 116 MET cc_start: 0.8459 (mmm) cc_final: 0.8091 (mmp) REVERT: F 139 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.8023 (mtm180) REVERT: F 181 GLU cc_start: 0.8279 (mm-30) cc_final: 0.7891 (mm-30) REVERT: F 239 LYS cc_start: 0.8415 (ptmm) cc_final: 0.8115 (tttm) REVERT: F 323 LYS cc_start: 0.8402 (tttt) cc_final: 0.8175 (tttp) REVERT: F 520 ASP cc_start: 0.8163 (t0) cc_final: 0.7668 (m-30) REVERT: F 548 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.6801 (ttp-110) REVERT: H 39 THR cc_start: 0.8355 (p) cc_final: 0.7975 (p) REVERT: H 42 ARG cc_start: 0.7634 (ttm110) cc_final: 0.6986 (mtm180) REVERT: H 56 GLU cc_start: 0.7944 (mp0) cc_final: 0.7724 (mp0) REVERT: G 59 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8419 (tp) outliers start: 36 outliers final: 19 residues processed: 256 average time/residue: 0.3287 time to fit residues: 129.4955 Evaluate side-chains 241 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 213 time to evaluate : 2.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 548 ARG Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 533 MET Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 139 ARG Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 375 ILE Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 548 ARG Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain G residue 59 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 36 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 chunk 133 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 chunk 245 optimal weight: 7.9990 chunk 121 optimal weight: 2.9990 chunk 26 optimal weight: 0.0770 chunk 69 optimal weight: 0.8980 chunk 109 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.9142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 131 ASN ** 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 = 0.3449 r_free = 0.3449 target = 0.126832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.099597 restraints weight = 28306.381| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.75 r_work: 0.2979 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 21234 Z= 0.105 Angle : 0.518 8.426 28772 Z= 0.272 Chirality : 0.041 0.177 3256 Planarity : 0.005 0.056 3652 Dihedral : 6.827 92.288 2926 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.52 % Allowed : 13.13 % Favored : 85.35 % 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: 0.92 (0.17), residues: 2582 helix: 2.25 (0.15), residues: 1236 sheet: 0.71 (0.33), residues: 256 loop : -1.45 (0.18), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 294 HIS 0.003 0.001 HIS A 374 PHE 0.019 0.001 PHE C 62 TYR 0.013 0.001 TYR B 510 ARG 0.003 0.000 ARG A 456 Details of bonding type rmsd hydrogen bonds : bond 0.03806 ( 985) hydrogen bonds : angle 4.11857 ( 2889) covalent geometry : bond 0.00234 (21232) covalent geometry : angle 0.51837 (28772) Misc. bond : bond 0.00058 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12667.62 seconds wall clock time: 225 minutes 50.29 seconds (13550.29 seconds total)