Starting phenix.real_space_refine on Tue May 20 13:55:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iak_35306/05_2025/8iak_35306.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iak_35306/05_2025/8iak_35306.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/8iak_35306/05_2025/8iak_35306.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iak_35306/05_2025/8iak_35306.map" model { file = "/net/cci-nas-00/data/ceres_data/8iak_35306/05_2025/8iak_35306.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iak_35306/05_2025/8iak_35306.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 12952 2.51 5 N 3356 2.21 5 O 3730 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 220 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 20154 Number of models: 1 Model: "" Number of chains: 5 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: 1231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1231 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 6, 'TRANS': 142} Chain: "C" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 576 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain breaks: 1 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Restraints were copied for chains: G, F, E, H Time building chain proxies: 14.79, per 1000 atoms: 0.73 Number of scatterers: 20154 At special positions: 0 Unit cell: (171.72, 109.08, 123.12, 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 3730 8.00 N 3356 7.00 C 12952 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: 4.91 Conformation dependent library (CDL) restraints added in 2.5 seconds 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4760 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 16 sheets defined 53.8% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.26 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 Processing helix chain 'A' and resid 157 through 160 removed outlier: 3.846A pdb=" N ALA A 160 " --> pdb=" O GLN A 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 157 through 160' Processing helix chain 'A' and resid 161 through 175 Processing helix chain 'A' and resid 189 through 204 removed outlier: 3.835A 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 225 Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 239 through 250 removed outlier: 4.166A 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: 3.701A pdb=" N LEU A 306 " --> pdb=" O PRO A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 339 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 406 removed outlier: 3.891A pdb=" N VAL A 393 " --> pdb=" O PRO A 389 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASN A 406 " --> pdb=" O LEU A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 426 Processing helix chain 'A' and resid 450 through 459 removed outlier: 3.586A 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 removed outlier: 3.710A pdb=" N GLU A 486 " --> pdb=" O ILE A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 554 Processing helix chain 'B' and resid 19 through 28 Processing helix chain 'B' and resid 57 through 85 removed outlier: 3.852A pdb=" N SER B 61 " --> pdb=" O PRO B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 94 removed outlier: 3.684A pdb=" N LYS B 89 " --> pdb=" O GLN B 86 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LEU B 91 " --> pdb=" O ASN B 88 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ASP B 92 " --> pdb=" O LYS B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 116 Processing helix chain 'B' and resid 118 through 122 Processing helix chain 'B' and resid 173 through 186 removed outlier: 3.662A pdb=" N ASP B 177 " --> pdb=" O GLY B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 215 removed outlier: 3.703A pdb=" N ILE B 204 " --> pdb=" O THR B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 233 removed outlier: 4.358A pdb=" N PHE B 233 " --> pdb=" O ASN B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 236 No H-bonds generated for 'chain 'B' and resid 234 through 236' Processing helix chain 'B' and resid 250 through 261 removed outlier: 3.550A pdb=" N ARG B 254 " --> pdb=" O HIS B 250 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER B 260 " --> pdb=" O GLY B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 286 removed outlier: 3.771A 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 350 removed outlier: 3.615A pdb=" N ILE B 349 " --> pdb=" O GLY B 345 " (cutoff:3.500A) 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 415 removed outlier: 3.700A pdb=" N LEU B 403 " --> pdb=" O PRO B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 444 removed outlier: 3.509A pdb=" N GLU B 424 " --> pdb=" O GLY B 420 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG B 434 " --> pdb=" O ALA B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 476 removed outlier: 4.034A 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 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 81 through 99 removed outlier: 3.788A pdb=" N ILE D 85 " --> pdb=" O TRP D 81 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE D 88 " --> pdb=" O HIS D 84 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU D 91 " --> pdb=" O VAL D 87 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY D 99 " --> pdb=" O TYR D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 122 Processing helix chain 'D' and resid 141 through 148 removed outlier: 6.069A pdb=" N ASN D 146 " --> pdb=" O GLU D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 174 Proline residue: D 162 - end of helix removed outlier: 4.380A pdb=" N GLN D 171 " --> pdb=" O LEU D 167 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N TYR D 172 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TYR D 173 " --> pdb=" O SER D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 191 Processing helix chain 'D' and resid 192 through 196 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 74 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 Processing helix chain 'E' and resid 157 through 160 removed outlier: 3.845A pdb=" N ALA E 160 " --> pdb=" O GLN E 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 157 through 160' Processing helix chain 'E' and resid 161 through 175 Processing helix chain 'E' and resid 189 through 204 removed outlier: 3.835A 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 225 Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 239 through 250 removed outlier: 4.166A 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: 3.700A pdb=" N LEU E 306 " --> pdb=" O PRO E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 339 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 406 removed outlier: 3.890A pdb=" N VAL E 393 " --> pdb=" O PRO E 389 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASN E 406 " --> pdb=" O LEU E 402 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 426 Processing helix chain 'E' and resid 450 through 459 removed outlier: 3.586A 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 removed outlier: 3.710A pdb=" N GLU E 486 " --> pdb=" O ILE E 482 " (cutoff:3.500A) Processing helix chain 'E' and resid 534 through 554 Processing helix chain 'F' and resid 19 through 28 Processing helix chain 'F' and resid 57 through 85 removed outlier: 3.852A pdb=" N SER F 61 " --> pdb=" O PRO F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 94 removed outlier: 3.684A pdb=" N LYS F 89 " --> pdb=" O GLN F 86 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LEU F 91 " --> pdb=" O ASN F 88 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ASP F 92 " --> pdb=" O LYS F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 116 Processing helix chain 'F' and resid 118 through 122 Processing helix chain 'F' and resid 173 through 186 removed outlier: 3.662A pdb=" N ASP F 177 " --> pdb=" O GLY F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 215 removed outlier: 3.703A pdb=" N ILE F 204 " --> pdb=" O THR F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 233 removed outlier: 4.358A pdb=" N PHE F 233 " --> pdb=" O ASN F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 236 No H-bonds generated for 'chain 'F' and resid 234 through 236' Processing helix chain 'F' and resid 250 through 261 removed outlier: 3.551A pdb=" N ARG F 254 " --> pdb=" O HIS F 250 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER F 260 " --> pdb=" O GLY F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 286 removed outlier: 3.771A 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 350 removed outlier: 3.615A pdb=" N ILE F 349 " --> pdb=" O GLY F 345 " (cutoff:3.500A) 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 415 removed outlier: 3.699A pdb=" N LEU F 403 " --> pdb=" O PRO F 399 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 444 removed outlier: 3.509A pdb=" N GLU F 424 " --> pdb=" O GLY F 420 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG F 434 " --> pdb=" O ALA F 430 " (cutoff:3.500A) Processing helix chain 'F' and resid 464 through 476 removed outlier: 4.035A 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 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 81 through 99 removed outlier: 3.788A pdb=" N ILE H 85 " --> pdb=" O TRP H 81 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE H 88 " --> pdb=" O HIS H 84 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU H 91 " --> pdb=" O VAL H 87 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY H 99 " --> pdb=" O TYR H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 122 Processing helix chain 'H' and resid 141 through 148 removed outlier: 6.069A pdb=" N ASN H 146 " --> pdb=" O GLU H 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 152 through 174 Proline residue: H 162 - end of helix removed outlier: 4.380A pdb=" N GLN H 171 " --> pdb=" O LEU H 167 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N TYR H 172 " --> pdb=" O ILE H 168 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TYR H 173 " --> pdb=" O SER H 169 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 191 Processing helix chain 'H' and resid 192 through 196 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 74 Processing sheet with id=AA1, first strand: chain 'A' and resid 123 through 124 removed outlier: 7.229A pdb=" N ILE A 135 " --> pdb=" O THR A 145 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N THR A 145 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N LEU A 506 " --> pdb=" O ASN A 146 " (cutoff:3.500A) removed outlier: 6.632A 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: 3.932A pdb=" N PHE A 364 " --> pdb=" O GLY A 352 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LYS A 286 " --> pdb=" O ARG A 316 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N PHE A 318 " --> pdb=" O LYS A 286 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ILE A 288 " --> pdb=" O PHE A 318 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ASP A 320 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N THR A 290 " --> pdb=" O ASP A 320 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL A 231 " --> pdb=" O PHE A 287 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N VAL A 289 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL A 233 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 8.951A pdb=" N GLU A 291 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 435 through 436 Processing sheet with id=AA4, first strand: chain 'A' and resid 444 through 445 removed outlier: 3.530A pdb=" N THR A 508 " --> pdb=" O LYS A 526 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 126 through 127 removed outlier: 4.086A pdb=" N ARG B 135 " --> pdb=" O THR B 127 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N ALA B 479 " --> pdb=" O PRO B 156 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N MET B 158 " --> pdb=" O ALA B 479 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 140 through 142 removed outlier: 3.707A pdb=" N TYR B 147 " --> pdb=" O HIS B 142 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 218 through 222 removed outlier: 7.867A pdb=" N GLU B 302 " --> pdb=" O ASP B 246 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE B 267 " --> pdb=" O SER B 245 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 455 through 459 removed outlier: 3.617A pdb=" N ARG B 494 " --> pdb=" O VAL B 483 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 123 through 124 removed outlier: 7.229A pdb=" N ILE E 135 " --> pdb=" O THR E 145 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N THR E 145 " --> pdb=" O ILE E 135 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N LEU E 506 " --> pdb=" O ASN E 146 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N PHE E 148 " --> pdb=" O LEU E 506 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 207 through 211 removed outlier: 3.932A pdb=" N PHE E 364 " --> pdb=" O GLY E 352 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LYS E 286 " --> pdb=" O ARG E 316 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N PHE E 318 " --> pdb=" O LYS E 286 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ILE E 288 " --> pdb=" O PHE E 318 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N ASP E 320 " --> pdb=" O ILE E 288 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N THR E 290 " --> pdb=" O ASP E 320 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL E 231 " --> pdb=" O PHE E 287 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N VAL E 289 " --> pdb=" O VAL E 231 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL E 233 " --> pdb=" O VAL E 289 " (cutoff:3.500A) removed outlier: 8.951A pdb=" N GLU E 291 " --> pdb=" O VAL E 233 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 435 through 436 Processing sheet with id=AB3, first strand: chain 'E' and resid 444 through 445 removed outlier: 3.530A pdb=" N THR E 508 " --> pdb=" O LYS E 526 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 126 through 127 removed outlier: 4.085A pdb=" N ARG F 135 " --> pdb=" O THR F 127 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N ALA F 479 " --> pdb=" O PRO F 156 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N MET F 158 " --> pdb=" O ALA F 479 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 140 through 142 removed outlier: 3.707A pdb=" N TYR F 147 " --> pdb=" O HIS F 142 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 218 through 222 removed outlier: 7.867A pdb=" N GLU F 302 " --> pdb=" O ASP F 246 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE F 267 " --> pdb=" O SER F 245 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 455 through 459 removed outlier: 3.617A pdb=" N ARG F 494 " --> pdb=" O VAL F 483 " (cutoff:3.500A) 1007 hydrogen bonds defined for protein. 2877 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.16 Time building geometry restraints manager: 5.70 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: 6412 1.34 - 1.46: 4220 1.46 - 1.58: 9804 1.58 - 1.70: 2 1.70 - 1.81: 174 Bond restraints: 20612 Sorted by residual: bond pdb=" C4 PLP F 601 " pdb=" C5 PLP F 601 " ideal model delta sigma weight residual 1.390 1.493 -0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" C4 PLP B 601 " pdb=" C5 PLP B 601 " ideal model delta sigma weight residual 1.390 1.493 -0.103 2.00e-02 2.50e+03 2.64e+01 bond pdb=" C2 PLP B 601 " pdb=" C3 PLP B 601 " ideal model delta sigma weight residual 1.390 1.480 -0.090 2.00e-02 2.50e+03 2.03e+01 bond pdb=" C2 PLP F 601 " pdb=" C3 PLP F 601 " ideal model delta sigma weight residual 1.390 1.480 -0.090 2.00e-02 2.50e+03 2.01e+01 bond pdb=" C3 PLP B 601 " pdb=" C4 PLP B 601 " ideal model delta sigma weight residual 1.390 1.477 -0.087 2.00e-02 2.50e+03 1.90e+01 ... (remaining 20607 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 27525 2.43 - 4.86: 377 4.86 - 7.29: 48 7.29 - 9.72: 4 9.72 - 12.15: 4 Bond angle restraints: 27958 Sorted by residual: angle pdb=" N LYS B 366 " pdb=" CA LYS B 366 " pdb=" C LYS B 366 " ideal model delta sigma weight residual 111.14 121.13 -9.99 1.08e+00 8.57e-01 8.56e+01 angle pdb=" N LYS F 366 " pdb=" CA LYS F 366 " pdb=" C LYS F 366 " ideal model delta sigma weight residual 111.14 121.10 -9.96 1.08e+00 8.57e-01 8.50e+01 angle pdb=" N TYR B 58 " pdb=" CA TYR B 58 " pdb=" C TYR B 58 " ideal model delta sigma weight residual 111.71 118.03 -6.32 1.15e+00 7.56e-01 3.02e+01 angle pdb=" N TYR F 58 " pdb=" CA TYR F 58 " pdb=" C TYR F 58 " ideal model delta sigma weight residual 111.71 117.99 -6.28 1.15e+00 7.56e-01 2.98e+01 angle pdb=" N ILE D 190 " pdb=" CA ILE D 190 " pdb=" C ILE D 190 " ideal model delta sigma weight residual 113.10 108.40 4.70 9.70e-01 1.06e+00 2.35e+01 ... (remaining 27953 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 11242 17.98 - 35.97: 905 35.97 - 53.95: 167 53.95 - 71.94: 22 71.94 - 89.92: 12 Dihedral angle restraints: 12348 sinusoidal: 4954 harmonic: 7394 Sorted by residual: 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 -155.15 -24.85 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA PHE E 256 " pdb=" C PHE E 256 " pdb=" N ASN E 257 " pdb=" CA ASN E 257 " ideal model delta harmonic sigma weight residual -180.00 -155.15 -24.85 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" C5A PLP F 601 " pdb=" O4P PLP F 601 " pdb=" P PLP F 601 " pdb=" O1P PLP F 601 " ideal model delta sinusoidal sigma weight residual 76.43 157.50 -81.07 1 2.00e+01 2.50e-03 2.03e+01 ... (remaining 12345 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 3007 0.093 - 0.186: 155 0.186 - 0.279: 2 0.279 - 0.371: 0 0.371 - 0.464: 2 Chirality restraints: 3166 Sorted by residual: chirality pdb=" CA LYS B 366 " pdb=" N LYS B 366 " pdb=" C LYS B 366 " pdb=" CB LYS B 366 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.39e+00 chirality pdb=" CA LYS F 366 " pdb=" N LYS F 366 " pdb=" C LYS F 366 " pdb=" CB LYS F 366 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.36e+00 chirality pdb=" CA TYR B 58 " pdb=" N TYR B 58 " pdb=" C TYR B 58 " pdb=" CB TYR B 58 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 3163 not shown) Planarity restraints: 3552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG F 112 " 0.012 2.00e-02 2.50e+03 2.45e-02 5.98e+00 pdb=" C ARG F 112 " -0.042 2.00e-02 2.50e+03 pdb=" O ARG F 112 " 0.016 2.00e-02 2.50e+03 pdb=" N ARG F 113 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 112 " -0.012 2.00e-02 2.50e+03 2.43e-02 5.92e+00 pdb=" C ARG B 112 " 0.042 2.00e-02 2.50e+03 pdb=" O ARG B 112 " -0.016 2.00e-02 2.50e+03 pdb=" N ARG B 113 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 111 " -0.011 2.00e-02 2.50e+03 2.12e-02 4.49e+00 pdb=" C VAL B 111 " 0.037 2.00e-02 2.50e+03 pdb=" O VAL B 111 " -0.014 2.00e-02 2.50e+03 pdb=" N ARG B 112 " -0.012 2.00e-02 2.50e+03 ... (remaining 3549 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 279 2.65 - 3.22: 18652 3.22 - 3.78: 28622 3.78 - 4.34: 39942 4.34 - 4.90: 69495 Nonbonded interactions: 156990 Sorted by model distance: nonbonded pdb=" O ASN A 407 " pdb=" N ALA A 409 " model vdw 2.093 3.120 nonbonded pdb=" O ASN E 407 " pdb=" N ALA E 409 " model vdw 2.094 3.120 nonbonded pdb=" OG SER A 417 " pdb=" O SER A 442 " model vdw 2.147 3.040 nonbonded pdb=" OG SER E 417 " pdb=" O SER E 442 " model vdw 2.147 3.040 nonbonded pdb=" OH TYR E 460 " pdb=" OE1 GLU E 488 " model vdw 2.169 3.040 ... (remaining 156985 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 'B' selection = chain 'F' } ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'H' } 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: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.800 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 46.180 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 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 : 0.005 0.103 20614 Z= 0.239 Angle : 0.742 12.150 27958 Z= 0.443 Chirality : 0.046 0.464 3166 Planarity : 0.004 0.053 3552 Dihedral : 13.482 89.920 7588 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.17 % Favored : 93.60 % Rotamer: Outliers : 1.34 % Allowed : 1.07 % Favored : 97.59 % 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: -0.07 (0.17), residues: 2514 helix: 1.42 (0.15), residues: 1182 sheet: -0.30 (0.36), residues: 216 loop : -1.66 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 294 HIS 0.003 0.001 HIS C 45 PHE 0.019 0.001 PHE E 256 TYR 0.019 0.001 TYR B 533 ARG 0.009 0.001 ARG D 174 Details of bonding type rmsd hydrogen bonds : bond 0.17581 ( 1007) hydrogen bonds : angle 6.09063 ( 2877) covalent geometry : bond 0.00490 (20612) covalent geometry : angle 0.74218 (27958) Misc. bond : bond 0.06686 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 245 time to evaluate : 2.455 Fit side-chains REVERT: A 79 LYS cc_start: 0.7206 (tppt) cc_final: 0.6936 (tptm) REVERT: A 477 GLN cc_start: 0.7479 (mt0) cc_final: 0.7269 (mt0) REVERT: E 79 LYS cc_start: 0.7233 (tppt) cc_final: 0.6968 (tptm) REVERT: E 477 GLN cc_start: 0.7466 (mt0) cc_final: 0.7253 (mt0) outliers start: 30 outliers final: 10 residues processed: 264 average time/residue: 0.3027 time to fit residues: 124.9174 Evaluate side-chains 198 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 188 time to evaluate : 2.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 407 ASN Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 475 GLN Chi-restraints excluded: chain B residue 530 LYS Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain E residue 407 ASN Chi-restraints excluded: chain F residue 138 ASP Chi-restraints excluded: chain F residue 475 GLN Chi-restraints excluded: chain F residue 530 LYS Chi-restraints excluded: chain H residue 130 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 3.9990 chunk 187 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 126 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 194 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 118 optimal weight: 9.9990 chunk 144 optimal weight: 8.9990 chunk 225 optimal weight: 10.0000 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 78 HIS B 143 ASN B 475 GLN F 78 HIS F 143 ASN F 475 GLN G 60 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.135502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.105707 restraints weight = 28658.901| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.85 r_work: 0.3067 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20614 Z= 0.172 Angle : 0.630 9.379 27958 Z= 0.334 Chirality : 0.044 0.166 3166 Planarity : 0.005 0.044 3552 Dihedral : 5.386 69.620 2780 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.93 % Favored : 93.91 % Rotamer: Outliers : 0.98 % Allowed : 7.18 % Favored : 91.84 % 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: 0.32 (0.17), residues: 2514 helix: 1.68 (0.15), residues: 1212 sheet: 0.18 (0.34), residues: 244 loop : -1.58 (0.18), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 294 HIS 0.003 0.001 HIS G 45 PHE 0.020 0.002 PHE A 256 TYR 0.018 0.002 TYR E 453 ARG 0.003 0.000 ARG D 174 Details of bonding type rmsd hydrogen bonds : bond 0.05663 ( 1007) hydrogen bonds : angle 4.70779 ( 2877) covalent geometry : bond 0.00412 (20612) covalent geometry : angle 0.62957 (27958) Misc. bond : bond 0.00022 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 212 time to evaluate : 2.253 Fit side-chains REVERT: A 79 LYS cc_start: 0.7630 (tppt) cc_final: 0.7302 (tptm) REVERT: E 79 LYS cc_start: 0.7677 (tppt) cc_final: 0.7360 (tptm) outliers start: 22 outliers final: 16 residues processed: 227 average time/residue: 0.2990 time to fit residues: 106.4210 Evaluate side-chains 225 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 209 time to evaluate : 2.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain D residue 125 LYS Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain H residue 125 LYS Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 56 SER Chi-restraints excluded: chain G residue 66 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 14 optimal weight: 1.9990 chunk 191 optimal weight: 5.9990 chunk 181 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 161 optimal weight: 4.9990 chunk 233 optimal weight: 7.9990 chunk 196 optimal weight: 0.0670 chunk 127 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 230 optimal weight: 0.5980 chunk 193 optimal weight: 0.8980 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 HIS E 421 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.139735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.111366 restraints weight = 28351.092| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.81 r_work: 0.3127 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20614 Z= 0.105 Angle : 0.526 8.322 27958 Z= 0.277 Chirality : 0.041 0.181 3166 Planarity : 0.004 0.045 3552 Dihedral : 4.667 66.501 2758 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.65 % Favored : 95.19 % Rotamer: Outliers : 1.12 % Allowed : 8.16 % Favored : 90.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.17), residues: 2514 helix: 2.01 (0.15), residues: 1202 sheet: 0.14 (0.32), residues: 266 loop : -1.35 (0.19), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 294 HIS 0.003 0.001 HIS A 61 PHE 0.032 0.001 PHE G 62 TYR 0.012 0.001 TYR A 453 ARG 0.003 0.000 ARG D 174 Details of bonding type rmsd hydrogen bonds : bond 0.03964 ( 1007) hydrogen bonds : angle 4.33390 ( 2877) covalent geometry : bond 0.00226 (20612) covalent geometry : angle 0.52558 (27958) Misc. bond : bond 0.00012 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 234 time to evaluate : 2.114 Fit side-chains REVERT: A 79 LYS cc_start: 0.7495 (tppt) cc_final: 0.7273 (tptm) REVERT: A 348 ASP cc_start: 0.7926 (m-30) cc_final: 0.7559 (m-30) REVERT: B 119 ASP cc_start: 0.8130 (t0) cc_final: 0.7682 (t0) REVERT: D 168 ILE cc_start: 0.7668 (mm) cc_final: 0.7452 (mm) REVERT: E 79 LYS cc_start: 0.7505 (tppt) cc_final: 0.7293 (tptm) REVERT: F 119 ASP cc_start: 0.8151 (t0) cc_final: 0.7702 (t0) REVERT: F 204 ILE cc_start: 0.8824 (mm) cc_final: 0.8555 (mm) REVERT: H 118 TYR cc_start: 0.8849 (t80) cc_final: 0.8554 (t80) REVERT: H 173 TYR cc_start: 0.6544 (p90) cc_final: 0.6342 (p90) outliers start: 25 outliers final: 9 residues processed: 249 average time/residue: 0.2939 time to fit residues: 115.6705 Evaluate side-chains 223 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 214 time to evaluate : 2.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain D residue 125 LYS Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain H residue 125 LYS Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain G residue 56 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 224 optimal weight: 0.8980 chunk 109 optimal weight: 6.9990 chunk 80 optimal weight: 0.7980 chunk 125 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 chunk 135 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 chunk 156 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 238 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 77 GLN C 60 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.135743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.106950 restraints weight = 28687.200| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.83 r_work: 0.3056 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20614 Z= 0.175 Angle : 0.592 8.674 27958 Z= 0.311 Chirality : 0.043 0.166 3166 Planarity : 0.005 0.043 3552 Dihedral : 4.812 71.960 2758 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.69 % Favored : 94.15 % Rotamer: Outliers : 1.92 % Allowed : 9.14 % Favored : 88.94 % 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: 0.70 (0.17), residues: 2514 helix: 2.03 (0.15), residues: 1206 sheet: 0.20 (0.35), residues: 234 loop : -1.36 (0.19), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 294 HIS 0.003 0.001 HIS G 45 PHE 0.035 0.002 PHE C 62 TYR 0.018 0.001 TYR F 510 ARG 0.004 0.000 ARG H 174 Details of bonding type rmsd hydrogen bonds : bond 0.05137 ( 1007) hydrogen bonds : angle 4.39127 ( 2877) covalent geometry : bond 0.00428 (20612) covalent geometry : angle 0.59209 (27958) Misc. bond : bond 0.00007 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 209 time to evaluate : 2.223 Fit side-chains REVERT: A 79 LYS cc_start: 0.7535 (tppt) cc_final: 0.7292 (tptm) REVERT: B 18 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7938 (pp) REVERT: B 119 ASP cc_start: 0.8161 (t0) cc_final: 0.7690 (t0) REVERT: B 366 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8004 (mttt) REVERT: B 530 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8748 (ttmp) REVERT: E 79 LYS cc_start: 0.7580 (tppt) cc_final: 0.7348 (tptm) REVERT: F 18 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7866 (pp) REVERT: F 119 ASP cc_start: 0.8211 (t0) cc_final: 0.7758 (t0) REVERT: F 366 LYS cc_start: 0.9149 (OUTLIER) cc_final: 0.8010 (mttt) REVERT: F 472 MET cc_start: 0.8928 (mtp) cc_final: 0.8696 (mtt) REVERT: F 530 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8715 (ttmp) outliers start: 43 outliers final: 29 residues processed: 239 average time/residue: 0.3151 time to fit residues: 116.1125 Evaluate side-chains 240 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 205 time to evaluate : 2.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 356 ASP Chi-restraints excluded: chain B residue 366 LYS Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 530 LYS Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 125 LYS Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain E residue 273 GLU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 224 MET Chi-restraints excluded: chain F residue 308 GLU Chi-restraints excluded: chain F residue 356 ASP Chi-restraints excluded: chain F residue 366 LYS Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain F residue 530 LYS Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 125 LYS Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 56 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 177 optimal weight: 6.9990 chunk 239 optimal weight: 5.9990 chunk 131 optimal weight: 0.7980 chunk 232 optimal weight: 4.9990 chunk 133 optimal weight: 0.9990 chunk 200 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 140 optimal weight: 0.8980 chunk 8 optimal weight: 7.9990 chunk 213 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.136312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.106672 restraints weight = 28577.309| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.84 r_work: 0.3080 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20614 Z= 0.149 Angle : 0.569 8.576 27958 Z= 0.299 Chirality : 0.042 0.173 3166 Planarity : 0.004 0.046 3552 Dihedral : 4.784 72.341 2758 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.45 % Favored : 94.39 % Rotamer: Outliers : 2.10 % Allowed : 9.90 % Favored : 88.00 % 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: 0.76 (0.17), residues: 2514 helix: 2.06 (0.15), residues: 1206 sheet: 0.33 (0.33), residues: 242 loop : -1.35 (0.19), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 294 HIS 0.003 0.001 HIS G 45 PHE 0.038 0.001 PHE C 62 TYR 0.016 0.001 TYR F 510 ARG 0.004 0.000 ARG H 174 Details of bonding type rmsd hydrogen bonds : bond 0.04743 ( 1007) hydrogen bonds : angle 4.32903 ( 2877) covalent geometry : bond 0.00359 (20612) covalent geometry : angle 0.56908 (27958) Misc. bond : bond 0.00004 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 208 time to evaluate : 2.168 Fit side-chains REVERT: A 79 LYS cc_start: 0.7509 (tppt) cc_final: 0.7273 (tptm) REVERT: B 18 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7883 (pp) REVERT: B 119 ASP cc_start: 0.8122 (t0) cc_final: 0.7656 (t0) REVERT: B 366 LYS cc_start: 0.9122 (OUTLIER) cc_final: 0.7984 (mttt) REVERT: B 530 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8690 (ttmp) REVERT: E 79 LYS cc_start: 0.7566 (tppt) cc_final: 0.7338 (tptm) REVERT: F 18 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7860 (pp) REVERT: F 119 ASP cc_start: 0.8166 (t0) cc_final: 0.7705 (t0) REVERT: F 366 LYS cc_start: 0.9126 (OUTLIER) cc_final: 0.7987 (mttt) REVERT: F 472 MET cc_start: 0.8903 (mtp) cc_final: 0.8673 (mtt) REVERT: F 530 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8768 (ttmp) outliers start: 47 outliers final: 31 residues processed: 237 average time/residue: 0.2984 time to fit residues: 110.3156 Evaluate side-chains 239 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 202 time to evaluate : 2.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 356 ASP Chi-restraints excluded: chain B residue 366 LYS Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 530 LYS Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 125 LYS Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 273 GLU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 224 MET Chi-restraints excluded: chain F residue 308 GLU Chi-restraints excluded: chain F residue 356 ASP Chi-restraints excluded: chain F residue 366 LYS Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain F residue 530 LYS Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 125 LYS Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 56 SER Chi-restraints excluded: chain G residue 59 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 46 optimal weight: 0.6980 chunk 75 optimal weight: 6.9990 chunk 120 optimal weight: 8.9990 chunk 103 optimal weight: 0.9990 chunk 180 optimal weight: 4.9990 chunk 236 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 192 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 183 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.136136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.107586 restraints weight = 28649.379| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.84 r_work: 0.3065 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20614 Z= 0.151 Angle : 0.572 8.594 27958 Z= 0.300 Chirality : 0.042 0.172 3166 Planarity : 0.004 0.045 3552 Dihedral : 4.783 72.674 2758 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.65 % Favored : 94.19 % Rotamer: Outliers : 2.01 % Allowed : 11.24 % Favored : 86.75 % 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: 0.78 (0.17), residues: 2514 helix: 2.10 (0.15), residues: 1204 sheet: 0.26 (0.34), residues: 232 loop : -1.34 (0.18), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 294 HIS 0.003 0.001 HIS G 45 PHE 0.035 0.001 PHE C 62 TYR 0.016 0.001 TYR F 510 ARG 0.005 0.000 ARG H 174 Details of bonding type rmsd hydrogen bonds : bond 0.04755 ( 1007) hydrogen bonds : angle 4.31301 ( 2877) covalent geometry : bond 0.00365 (20612) covalent geometry : angle 0.57217 (27958) Misc. bond : bond 0.00006 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 218 time to evaluate : 2.239 Fit side-chains REVERT: A 79 LYS cc_start: 0.7498 (tppt) cc_final: 0.7278 (tptm) REVERT: B 18 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7936 (pp) REVERT: B 119 ASP cc_start: 0.8214 (t0) cc_final: 0.7754 (t0) REVERT: B 278 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8558 (tt) REVERT: B 366 LYS cc_start: 0.9124 (OUTLIER) cc_final: 0.7989 (mttt) REVERT: B 452 ASP cc_start: 0.8143 (m-30) cc_final: 0.7620 (t0) REVERT: D 111 MET cc_start: 0.8056 (mmm) cc_final: 0.7850 (mmm) REVERT: D 118 TYR cc_start: 0.8882 (t80) cc_final: 0.8407 (t80) REVERT: E 79 LYS cc_start: 0.7592 (tppt) cc_final: 0.7358 (tptm) REVERT: F 18 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7963 (pp) REVERT: F 119 ASP cc_start: 0.8219 (t0) cc_final: 0.7754 (t0) REVERT: F 278 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8552 (tt) REVERT: F 366 LYS cc_start: 0.9126 (OUTLIER) cc_final: 0.8023 (mttt) REVERT: F 452 ASP cc_start: 0.8145 (m-30) cc_final: 0.7628 (t0) REVERT: F 472 MET cc_start: 0.8918 (mtp) cc_final: 0.8702 (mtt) REVERT: H 118 TYR cc_start: 0.8847 (t80) cc_final: 0.8363 (t80) outliers start: 45 outliers final: 31 residues processed: 246 average time/residue: 0.3198 time to fit residues: 122.4101 Evaluate side-chains 244 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 207 time to evaluate : 2.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 356 ASP Chi-restraints excluded: chain B residue 366 LYS Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 125 LYS Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain E residue 273 GLU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 224 MET Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 308 GLU Chi-restraints excluded: chain F residue 339 MET Chi-restraints excluded: chain F residue 356 ASP Chi-restraints excluded: chain F residue 366 LYS Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain F residue 398 MET Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 125 LYS Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 56 SER Chi-restraints excluded: chain G residue 59 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 141 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 224 optimal weight: 1.9990 chunk 188 optimal weight: 4.9990 chunk 172 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 244 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 145 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 464 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.132360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.103244 restraints weight = 28763.398| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.84 r_work: 0.3021 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 20614 Z= 0.275 Angle : 0.694 9.146 27958 Z= 0.364 Chirality : 0.047 0.171 3166 Planarity : 0.005 0.051 3552 Dihedral : 5.191 79.327 2758 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.44 % Favored : 93.40 % Rotamer: Outliers : 2.50 % Allowed : 11.73 % Favored : 85.77 % 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: 0.40 (0.17), residues: 2514 helix: 1.72 (0.15), residues: 1218 sheet: 0.03 (0.34), residues: 234 loop : -1.47 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 294 HIS 0.004 0.001 HIS E 295 PHE 0.033 0.002 PHE C 62 TYR 0.023 0.002 TYR F 510 ARG 0.006 0.001 ARG B 139 Details of bonding type rmsd hydrogen bonds : bond 0.06491 ( 1007) hydrogen bonds : angle 4.56556 ( 2877) covalent geometry : bond 0.00689 (20612) covalent geometry : angle 0.69377 (27958) Misc. bond : bond 0.00022 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 200 time to evaluate : 2.356 Fit side-chains REVERT: A 79 LYS cc_start: 0.7642 (tppt) cc_final: 0.7343 (tptm) REVERT: B 18 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8046 (pp) REVERT: B 119 ASP cc_start: 0.8161 (t0) cc_final: 0.7716 (t0) REVERT: B 278 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8543 (tt) REVERT: B 366 LYS cc_start: 0.9206 (OUTLIER) cc_final: 0.8059 (mptt) REVERT: E 79 LYS cc_start: 0.7656 (tppt) cc_final: 0.7354 (tptm) REVERT: F 18 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.8007 (pp) REVERT: F 119 ASP cc_start: 0.8205 (t0) cc_final: 0.7729 (t0) REVERT: F 278 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8540 (tt) REVERT: F 366 LYS cc_start: 0.9206 (OUTLIER) cc_final: 0.8058 (mptt) REVERT: F 472 MET cc_start: 0.8873 (mtp) cc_final: 0.8658 (mtt) REVERT: H 118 TYR cc_start: 0.8850 (t80) cc_final: 0.8370 (t80) outliers start: 56 outliers final: 43 residues processed: 236 average time/residue: 0.2964 time to fit residues: 110.0884 Evaluate side-chains 244 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 195 time to evaluate : 2.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 356 ASP Chi-restraints excluded: chain B residue 366 LYS Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 125 LYS Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 273 GLU Chi-restraints excluded: chain E residue 388 LEU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 224 MET Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 308 GLU Chi-restraints excluded: chain F residue 339 MET Chi-restraints excluded: chain F residue 356 ASP Chi-restraints excluded: chain F residue 366 LYS Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 125 LYS Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 165 LEU Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 56 SER Chi-restraints excluded: chain G residue 59 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 172 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 219 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 139 optimal weight: 0.7980 chunk 221 optimal weight: 2.9990 chunk 223 optimal weight: 1.9990 chunk 182 optimal weight: 0.0370 chunk 143 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 208 optimal weight: 0.9980 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.138027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.109907 restraints weight = 28583.005| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.86 r_work: 0.3099 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20614 Z= 0.110 Angle : 0.540 8.089 27958 Z= 0.284 Chirality : 0.041 0.185 3166 Planarity : 0.004 0.041 3552 Dihedral : 4.774 70.402 2758 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.49 % Favored : 95.35 % Rotamer: Outliers : 1.25 % Allowed : 12.67 % Favored : 86.08 % 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: 0.78 (0.17), residues: 2514 helix: 2.07 (0.15), residues: 1204 sheet: 0.06 (0.31), residues: 266 loop : -1.28 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 294 HIS 0.003 0.001 HIS A 61 PHE 0.039 0.001 PHE C 62 TYR 0.015 0.001 TYR F 186 ARG 0.005 0.000 ARG H 174 Details of bonding type rmsd hydrogen bonds : bond 0.04012 ( 1007) hydrogen bonds : angle 4.27977 ( 2877) covalent geometry : bond 0.00239 (20612) covalent geometry : angle 0.54048 (27958) Misc. bond : bond 0.00010 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 225 time to evaluate : 2.144 Fit side-chains REVERT: A 79 LYS cc_start: 0.7530 (tppt) cc_final: 0.7316 (tptm) REVERT: B 18 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8011 (pp) REVERT: B 83 MET cc_start: 0.4739 (mmm) cc_final: 0.3179 (ptm) REVERT: B 119 ASP cc_start: 0.8112 (t0) cc_final: 0.7657 (t0) REVERT: B 366 LYS cc_start: 0.9015 (OUTLIER) cc_final: 0.7850 (mttt) REVERT: B 452 ASP cc_start: 0.8103 (m-30) cc_final: 0.7599 (t0) REVERT: C 5 LYS cc_start: 0.8125 (ttpt) cc_final: 0.7547 (ttpp) REVERT: E 79 LYS cc_start: 0.7548 (tppt) cc_final: 0.7331 (tptm) REVERT: F 18 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7948 (pp) REVERT: F 119 ASP cc_start: 0.8122 (t0) cc_final: 0.7671 (t0) REVERT: F 366 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.7877 (mttt) REVERT: F 452 ASP cc_start: 0.8110 (m-30) cc_final: 0.7605 (t0) outliers start: 28 outliers final: 23 residues processed: 244 average time/residue: 0.2972 time to fit residues: 114.1752 Evaluate side-chains 238 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 211 time to evaluate : 2.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 356 ASP Chi-restraints excluded: chain B residue 366 LYS Chi-restraints excluded: chain D residue 125 LYS Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 273 GLU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 308 GLU Chi-restraints excluded: chain F residue 339 MET Chi-restraints excluded: chain F residue 356 ASP Chi-restraints excluded: chain F residue 366 LYS Chi-restraints excluded: chain H residue 125 LYS Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain G residue 56 SER Chi-restraints excluded: chain G residue 59 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 126 optimal weight: 20.0000 chunk 42 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 181 optimal weight: 0.7980 chunk 221 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 142 optimal weight: 0.6980 chunk 247 optimal weight: 6.9990 chunk 204 optimal weight: 0.6980 chunk 193 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.138652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.109294 restraints weight = 28455.995| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.82 r_work: 0.3121 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 20614 Z= 0.107 Angle : 0.533 7.964 27958 Z= 0.279 Chirality : 0.041 0.182 3166 Planarity : 0.004 0.042 3552 Dihedral : 4.621 69.795 2758 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.81 % Favored : 95.03 % Rotamer: Outliers : 1.16 % Allowed : 12.89 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.17), residues: 2514 helix: 2.18 (0.15), residues: 1206 sheet: 0.39 (0.33), residues: 242 loop : -1.10 (0.19), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 294 HIS 0.003 0.000 HIS A 61 PHE 0.038 0.001 PHE C 62 TYR 0.013 0.001 TYR F 186 ARG 0.007 0.000 ARG D 174 Details of bonding type rmsd hydrogen bonds : bond 0.03814 ( 1007) hydrogen bonds : angle 4.18942 ( 2877) covalent geometry : bond 0.00236 (20612) covalent geometry : angle 0.53281 (27958) Misc. bond : bond 0.00005 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 226 time to evaluate : 2.162 Fit side-chains revert: symmetry clash REVERT: B 18 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8035 (pp) REVERT: B 83 MET cc_start: 0.4634 (mmm) cc_final: 0.3143 (ptm) REVERT: B 107 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7466 (pt0) REVERT: B 119 ASP cc_start: 0.8008 (t0) cc_final: 0.7561 (t0) REVERT: B 366 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.7742 (mttt) REVERT: B 452 ASP cc_start: 0.7987 (m-30) cc_final: 0.7603 (t0) REVERT: F 18 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8054 (pp) REVERT: F 83 MET cc_start: 0.4625 (mmm) cc_final: 0.3088 (ptm) REVERT: F 107 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7461 (pt0) REVERT: F 119 ASP cc_start: 0.8035 (t0) cc_final: 0.7582 (t0) REVERT: F 366 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.7750 (mttt) REVERT: F 452 ASP cc_start: 0.7992 (m-30) cc_final: 0.7599 (t0) REVERT: G 59 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7972 (mt) outliers start: 26 outliers final: 17 residues processed: 243 average time/residue: 0.2967 time to fit residues: 114.0873 Evaluate side-chains 234 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 212 time to evaluate : 2.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 356 ASP Chi-restraints excluded: chain B residue 366 LYS Chi-restraints excluded: chain D residue 125 LYS Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 273 GLU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 308 GLU Chi-restraints excluded: chain F residue 356 ASP Chi-restraints excluded: chain F residue 366 LYS Chi-restraints excluded: chain H residue 125 LYS Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain G residue 56 SER Chi-restraints excluded: chain G residue 59 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 94 optimal weight: 0.2980 chunk 112 optimal weight: 5.9990 chunk 162 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 240 optimal weight: 4.9990 chunk 219 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 161 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.137863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.109594 restraints weight = 28556.096| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.85 r_work: 0.3104 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20614 Z= 0.121 Angle : 0.549 8.012 27958 Z= 0.288 Chirality : 0.041 0.178 3166 Planarity : 0.004 0.043 3552 Dihedral : 4.634 71.112 2758 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.09 % Favored : 94.75 % Rotamer: Outliers : 1.03 % Allowed : 12.85 % Favored : 86.13 % 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: 1.04 (0.17), residues: 2514 helix: 2.17 (0.15), residues: 1216 sheet: 0.40 (0.33), residues: 242 loop : -1.06 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 294 HIS 0.003 0.001 HIS C 45 PHE 0.035 0.001 PHE C 62 TYR 0.013 0.001 TYR B 510 ARG 0.007 0.000 ARG H 174 Details of bonding type rmsd hydrogen bonds : bond 0.04096 ( 1007) hydrogen bonds : angle 4.18752 ( 2877) covalent geometry : bond 0.00282 (20612) covalent geometry : angle 0.54942 (27958) Misc. bond : bond 0.00002 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 214 time to evaluate : 2.157 Fit side-chains revert: symmetry clash REVERT: A 477 GLN cc_start: 0.8292 (mt0) cc_final: 0.7959 (mm-40) REVERT: B 18 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7966 (pp) REVERT: B 83 MET cc_start: 0.4598 (mmm) cc_final: 0.3119 (ptm) REVERT: B 107 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7507 (pt0) REVERT: B 119 ASP cc_start: 0.8035 (t0) cc_final: 0.7587 (t0) REVERT: B 366 LYS cc_start: 0.9053 (OUTLIER) cc_final: 0.7928 (mttt) REVERT: B 452 ASP cc_start: 0.8068 (m-30) cc_final: 0.7652 (t0) REVERT: F 18 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8033 (pp) REVERT: F 107 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7497 (pt0) REVERT: F 119 ASP cc_start: 0.8070 (t0) cc_final: 0.7614 (t0) REVERT: F 366 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.7935 (mttt) REVERT: F 452 ASP cc_start: 0.8035 (m-30) cc_final: 0.7634 (t0) REVERT: F 472 MET cc_start: 0.8850 (mtp) cc_final: 0.8646 (mtp) REVERT: G 59 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.7982 (mt) outliers start: 23 outliers final: 17 residues processed: 231 average time/residue: 0.2817 time to fit residues: 103.7471 Evaluate side-chains 234 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 212 time to evaluate : 2.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 356 ASP Chi-restraints excluded: chain B residue 366 LYS Chi-restraints excluded: chain D residue 125 LYS Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 273 GLU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 308 GLU Chi-restraints excluded: chain F residue 356 ASP Chi-restraints excluded: chain F residue 366 LYS Chi-restraints excluded: chain H residue 125 LYS Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain G residue 56 SER Chi-restraints excluded: chain G residue 59 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 6 optimal weight: 6.9990 chunk 45 optimal weight: 0.5980 chunk 112 optimal weight: 6.9990 chunk 140 optimal weight: 0.5980 chunk 133 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 237 optimal weight: 0.9990 chunk 200 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.139324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.110850 restraints weight = 28581.408| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.82 r_work: 0.3129 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 20614 Z= 0.106 Angle : 0.532 7.784 27958 Z= 0.278 Chirality : 0.041 0.180 3166 Planarity : 0.004 0.041 3552 Dihedral : 4.544 69.437 2758 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.85 % Favored : 94.99 % Rotamer: Outliers : 1.07 % Allowed : 12.62 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.17), residues: 2514 helix: 2.22 (0.15), residues: 1216 sheet: 0.45 (0.32), residues: 242 loop : -1.02 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 294 HIS 0.003 0.000 HIS A 61 PHE 0.039 0.001 PHE C 62 TYR 0.015 0.001 TYR A 485 ARG 0.007 0.000 ARG D 174 Details of bonding type rmsd hydrogen bonds : bond 0.03710 ( 1007) hydrogen bonds : angle 4.14179 ( 2877) covalent geometry : bond 0.00239 (20612) covalent geometry : angle 0.53172 (27958) Misc. bond : bond 0.00004 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10927.91 seconds wall clock time: 189 minutes 36.94 seconds (11376.94 seconds total)