Starting phenix.real_space_refine on Tue Jun 17 14:24:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iak_35306/06_2025/8iak_35306.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iak_35306/06_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_35306/06_2025/8iak_35306.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iak_35306/06_2025/8iak_35306.map" model { file = "/net/cci-nas-00/data/ceres_data/8iak_35306/06_2025/8iak_35306.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iak_35306/06_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-5710/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: 15.61, per 1000 atoms: 0.77 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: 4.89 Conformation dependent library (CDL) restraints added in 2.4 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: 2.46 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: 6.70 Time building geometry restraints manager: 5.81 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: 0.11 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: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.790 Check model and map are aligned: 0.150 Set scattering table: 0.230 Process input model: 49.310 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.980 ------------------------------------------------------------------------------- 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 : 2.491 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: 0.3010 time to fit residues: 124.6669 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 : 2.072 ------------------------------------------------------------------------------- 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 = 0.135482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.105674 restraints weight = 28657.494| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.86 r_work: 0.3067 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- 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= 0.173 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 : 2.309 Fit side-chains REVERT: A 79 LYS cc_start: 0.7629 (tppt) cc_final: 0.7299 (tptm) REVERT: E 79 LYS cc_start: 0.7678 (tppt) cc_final: 0.7360 (tptm) outliers start: 22 outliers final: 16 residues processed: 227 average time/residue: 0.3195 time to fit residues: 113.5818 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 : 2.466 ------------------------------------------------------------------------------- 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: 0.9980 chunk 191 optimal weight: 6.9990 chunk 181 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 161 optimal weight: 0.0870 chunk 233 optimal weight: 7.9990 chunk 196 optimal weight: 0.0980 chunk 127 optimal weight: 10.0000 chunk 58 optimal weight: 0.1980 chunk 230 optimal weight: 0.0870 chunk 193 optimal weight: 0.4980 overall best weight: 0.1936 ------------------------------------------------------------------------------- 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 = 0.3679 r_free = 0.3679 target = 0.141727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.113395 restraints weight = 28315.212| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.80 r_work: 0.3160 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20614 Z= 0.102 Angle : 0.513 8.007 27958 Z= 0.270 Chirality : 0.040 0.185 3166 Planarity : 0.004 0.045 3552 Dihedral : 4.611 64.827 2758 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.22 % Favored : 95.62 % Rotamer: Outliers : 0.89 % Allowed : 8.21 % Favored : 90.90 % 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: 0.75 (0.17), residues: 2514 helix: 2.00 (0.15), residues: 1212 sheet: 0.15 (0.32), residues: 266 loop : -1.29 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 74 HIS 0.003 0.001 HIS A 61 PHE 0.034 0.001 PHE G 62 TYR 0.012 0.001 TYR F 186 ARG 0.003 0.000 ARG F 135 Details of bonding type rmsd hydrogen bonds : bond 0.03581 ( 1007) hydrogen bonds : angle 4.30277 ( 2877) covalent geometry : bond 0.00204 (20612) covalent geometry : angle 0.51308 (27958) Misc. bond : bond 0.00016 ( 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 260 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 240 time to evaluate : 2.512 Fit side-chains REVERT: A 348 ASP cc_start: 0.7818 (m-30) cc_final: 0.7443 (m-30) REVERT: B 119 ASP cc_start: 0.8122 (t0) cc_final: 0.7675 (t0) REVERT: D 168 ILE cc_start: 0.7616 (mm) cc_final: 0.7404 (mm) REVERT: F 119 ASP cc_start: 0.8140 (t0) cc_final: 0.7696 (t0) REVERT: F 204 ILE cc_start: 0.8794 (mm) cc_final: 0.8529 (mm) REVERT: H 173 TYR cc_start: 0.6621 (p90) cc_final: 0.6373 (p90) outliers start: 20 outliers final: 5 residues processed: 252 average time/residue: 0.4250 time to fit residues: 175.8413 Evaluate side-chains 218 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 213 time to evaluate : 2.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 125 LYS Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain H residue 125 LYS Chi-restraints excluded: chain H residue 130 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 224 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 125 optimal weight: 7.9990 chunk 96 optimal weight: 0.4980 chunk 135 optimal weight: 5.9990 chunk 155 optimal weight: 0.9990 chunk 156 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 238 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 26 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.139549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.111062 restraints weight = 28515.535| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.81 r_work: 0.3127 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20614 Z= 0.114 Angle : 0.530 10.556 27958 Z= 0.277 Chirality : 0.041 0.175 3166 Planarity : 0.004 0.043 3552 Dihedral : 4.534 66.655 2758 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.65 % Favored : 95.19 % Rotamer: Outliers : 1.38 % Allowed : 9.23 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.17), residues: 2514 helix: 2.13 (0.15), residues: 1216 sheet: 0.42 (0.33), residues: 242 loop : -1.22 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 294 HIS 0.003 0.000 HIS G 45 PHE 0.037 0.001 PHE C 62 TYR 0.014 0.001 TYR B 510 ARG 0.005 0.000 ARG H 174 Details of bonding type rmsd hydrogen bonds : bond 0.03943 ( 1007) hydrogen bonds : angle 4.22677 ( 2877) covalent geometry : bond 0.00261 (20612) covalent geometry : angle 0.52983 (27958) Misc. bond : bond 0.00004 ( 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 247 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 216 time to evaluate : 2.101 Fit side-chains REVERT: B 18 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7828 (pp) REVERT: B 119 ASP cc_start: 0.8131 (t0) cc_final: 0.7682 (t0) REVERT: B 366 LYS cc_start: 0.9066 (OUTLIER) cc_final: 0.7773 (mttt) REVERT: B 472 MET cc_start: 0.8910 (mtp) cc_final: 0.8651 (mtt) REVERT: B 530 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8573 (ttmp) REVERT: D 168 ILE cc_start: 0.7618 (mm) cc_final: 0.7372 (mm) REVERT: F 18 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7807 (pp) REVERT: F 119 ASP cc_start: 0.8160 (t0) cc_final: 0.7702 (t0) REVERT: F 204 ILE cc_start: 0.8800 (mm) cc_final: 0.8533 (mm) REVERT: F 366 LYS cc_start: 0.9069 (OUTLIER) cc_final: 0.7800 (mttt) REVERT: F 472 MET cc_start: 0.8913 (mtp) cc_final: 0.8663 (mtt) REVERT: F 530 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8632 (ttmp) REVERT: H 173 TYR cc_start: 0.6715 (p90) cc_final: 0.6471 (p90) outliers start: 31 outliers final: 18 residues processed: 239 average time/residue: 0.3174 time to fit residues: 117.9833 Evaluate side-chains 231 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 207 time to evaluate : 2.295 ------------------------------------------------------------------------------- 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 187 SER 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 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 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 187 SER Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 356 ASP Chi-restraints excluded: chain F residue 366 LYS 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 177 optimal weight: 9.9990 chunk 239 optimal weight: 10.0000 chunk 131 optimal weight: 1.9990 chunk 232 optimal weight: 4.9990 chunk 133 optimal weight: 3.9990 chunk 200 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 140 optimal weight: 0.7980 chunk 8 optimal weight: 7.9990 chunk 213 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 60 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.136915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.107386 restraints weight = 28539.679| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.81 r_work: 0.3081 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20614 Z= 0.150 Angle : 0.569 8.524 27958 Z= 0.298 Chirality : 0.042 0.164 3166 Planarity : 0.004 0.041 3552 Dihedral : 4.701 71.480 2758 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.41 % Favored : 94.43 % Rotamer: Outliers : 1.83 % Allowed : 9.63 % Favored : 88.54 % 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: 0.90 (0.17), residues: 2514 helix: 2.14 (0.15), residues: 1216 sheet: 0.29 (0.35), residues: 234 loop : -1.23 (0.19), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 294 HIS 0.003 0.001 HIS C 45 PHE 0.038 0.002 PHE C 62 TYR 0.016 0.001 TYR B 510 ARG 0.005 0.000 ARG D 174 Details of bonding type rmsd hydrogen bonds : bond 0.04749 ( 1007) hydrogen bonds : angle 4.28710 ( 2877) covalent geometry : bond 0.00364 (20612) covalent geometry : angle 0.56900 (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 252 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 211 time to evaluate : 2.143 Fit side-chains REVERT: B 18 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7893 (pp) REVERT: B 119 ASP cc_start: 0.8102 (t0) cc_final: 0.7637 (t0) REVERT: B 366 LYS cc_start: 0.9129 (OUTLIER) cc_final: 0.8000 (mttt) REVERT: B 452 ASP cc_start: 0.8138 (m-30) cc_final: 0.7457 (t0) REVERT: B 472 MET cc_start: 0.8910 (mtp) cc_final: 0.8678 (mtt) REVERT: B 530 LYS cc_start: 0.8969 (OUTLIER) cc_final: 0.8665 (ttmp) REVERT: F 18 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7845 (pp) REVERT: F 119 ASP cc_start: 0.8141 (t0) cc_final: 0.7664 (t0) REVERT: F 366 LYS cc_start: 0.9135 (OUTLIER) cc_final: 0.8010 (mttt) REVERT: F 452 ASP cc_start: 0.8107 (m-30) cc_final: 0.7466 (t0) REVERT: F 472 MET cc_start: 0.8914 (mtp) cc_final: 0.8686 (mtt) REVERT: F 530 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8720 (ttmp) REVERT: G 5 LYS cc_start: 0.8208 (ttpt) cc_final: 0.7914 (ptmt) outliers start: 41 outliers final: 28 residues processed: 239 average time/residue: 0.3051 time to fit residues: 114.7234 Evaluate side-chains 237 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 203 time to evaluate : 2.388 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 46 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 120 optimal weight: 7.9990 chunk 103 optimal weight: 0.0570 chunk 180 optimal weight: 3.9990 chunk 236 optimal weight: 0.0770 chunk 12 optimal weight: 5.9990 chunk 192 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 chunk 105 optimal weight: 0.0980 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 60 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.141270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.113094 restraints weight = 28387.631| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.80 r_work: 0.3153 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20614 Z= 0.097 Angle : 0.508 7.742 27958 Z= 0.265 Chirality : 0.040 0.186 3166 Planarity : 0.004 0.042 3552 Dihedral : 4.464 66.538 2758 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.57 % Favored : 95.27 % Rotamer: Outliers : 1.07 % Allowed : 10.48 % Favored : 88.45 % 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: 1.08 (0.17), residues: 2514 helix: 2.27 (0.15), residues: 1216 sheet: 0.23 (0.31), residues: 266 loop : -1.11 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 294 HIS 0.003 0.000 HIS A 61 PHE 0.037 0.001 PHE C 62 TYR 0.014 0.001 TYR H 173 ARG 0.006 0.000 ARG H 174 Details of bonding type rmsd hydrogen bonds : bond 0.03393 ( 1007) hydrogen bonds : angle 4.13462 ( 2877) covalent geometry : bond 0.00201 (20612) covalent geometry : angle 0.50783 (27958) Misc. bond : bond 0.00021 ( 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 246 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 222 time to evaluate : 2.327 Fit side-chains REVERT: A 348 ASP cc_start: 0.7653 (m-30) cc_final: 0.7328 (m-30) REVERT: A 469 MET cc_start: 0.8250 (tpp) cc_final: 0.8043 (tpt) REVERT: B 18 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7875 (pp) REVERT: B 83 MET cc_start: 0.4402 (mmm) cc_final: 0.2900 (ptm) REVERT: B 107 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7362 (pt0) REVERT: B 119 ASP cc_start: 0.8101 (t0) cc_final: 0.7639 (t0) REVERT: B 366 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.7714 (mttt) REVERT: B 452 ASP cc_start: 0.8065 (m-30) cc_final: 0.7555 (t0) REVERT: B 472 MET cc_start: 0.8859 (mtp) cc_final: 0.8656 (mtt) REVERT: F 18 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7852 (pp) REVERT: F 83 MET cc_start: 0.4413 (mmm) cc_final: 0.2976 (ptm) REVERT: F 107 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7357 (pt0) REVERT: F 119 ASP cc_start: 0.8085 (t0) cc_final: 0.7615 (t0) REVERT: F 366 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.7748 (mttt) REVERT: F 452 ASP cc_start: 0.8053 (m-30) cc_final: 0.7538 (t0) REVERT: F 472 MET cc_start: 0.8864 (mtp) cc_final: 0.8660 (mtt) REVERT: F 530 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8619 (ttmp) REVERT: H 118 TYR cc_start: 0.8739 (t80) cc_final: 0.8468 (t80) outliers start: 24 outliers final: 13 residues processed: 240 average time/residue: 0.2869 time to fit residues: 110.7361 Evaluate side-chains 226 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 208 time to evaluate : 2.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 187 SER 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 125 LYS Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain C residue 56 SER 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 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 125 LYS Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain G residue 56 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 141 optimal weight: 0.9990 chunk 84 optimal weight: 7.9990 chunk 224 optimal weight: 2.9990 chunk 188 optimal weight: 4.9990 chunk 172 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 244 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 145 optimal weight: 0.1980 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 60 HIS E 464 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.137507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.109050 restraints weight = 28487.105| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.84 r_work: 0.3092 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20614 Z= 0.144 Angle : 0.554 8.282 27958 Z= 0.290 Chirality : 0.042 0.169 3166 Planarity : 0.004 0.043 3552 Dihedral : 4.614 71.701 2758 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.21 % Favored : 94.63 % Rotamer: Outliers : 1.74 % Allowed : 10.93 % Favored : 87.33 % 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: 1.03 (0.17), residues: 2514 helix: 2.23 (0.15), residues: 1216 sheet: 0.45 (0.34), residues: 230 loop : -1.16 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 294 HIS 0.003 0.001 HIS A 374 PHE 0.038 0.001 PHE C 62 TYR 0.016 0.001 TYR B 510 ARG 0.005 0.000 ARG D 174 Details of bonding type rmsd hydrogen bonds : bond 0.04458 ( 1007) hydrogen bonds : angle 4.19375 ( 2877) covalent geometry : bond 0.00346 (20612) covalent geometry : angle 0.55369 (27958) Misc. bond : bond 0.00007 ( 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 240 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 201 time to evaluate : 2.617 Fit side-chains REVERT: B 18 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7934 (pp) REVERT: B 107 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7424 (pt0) REVERT: B 119 ASP cc_start: 0.8101 (t0) cc_final: 0.7655 (t0) REVERT: B 366 LYS cc_start: 0.9121 (OUTLIER) cc_final: 0.7995 (mttt) REVERT: B 452 ASP cc_start: 0.8152 (m-30) cc_final: 0.7642 (t0) REVERT: B 530 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8656 (ttmp) REVERT: F 18 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7867 (pp) REVERT: F 107 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7426 (pt0) REVERT: F 119 ASP cc_start: 0.8166 (t0) cc_final: 0.7687 (t0) REVERT: F 366 LYS cc_start: 0.9130 (OUTLIER) cc_final: 0.8010 (mttt) REVERT: F 452 ASP cc_start: 0.8144 (m-30) cc_final: 0.7610 (t0) REVERT: F 472 MET cc_start: 0.8916 (mtp) cc_final: 0.8713 (mtt) REVERT: F 530 LYS cc_start: 0.8960 (OUTLIER) cc_final: 0.8735 (ttmp) outliers start: 39 outliers final: 28 residues processed: 226 average time/residue: 0.3474 time to fit residues: 126.4607 Evaluate side-chains 231 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 197 time to evaluate : 2.760 ------------------------------------------------------------------------------- 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 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 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 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 172 optimal weight: 10.0000 chunk 3 optimal weight: 0.9990 chunk 219 optimal weight: 1.9990 chunk 79 optimal weight: 0.0470 chunk 139 optimal weight: 0.9980 chunk 221 optimal weight: 3.9990 chunk 223 optimal weight: 0.9990 chunk 182 optimal weight: 3.9990 chunk 143 optimal weight: 8.9990 chunk 33 optimal weight: 0.8980 chunk 208 optimal weight: 6.9990 overall best weight: 0.7882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 60 HIS E 464 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.139959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.111483 restraints weight = 28505.133| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.81 r_work: 0.3130 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2079 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= 0.102 Angle : 0.514 7.730 27958 Z= 0.269 Chirality : 0.040 0.179 3166 Planarity : 0.004 0.040 3552 Dihedral : 4.490 68.853 2758 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.53 % Favored : 95.31 % Rotamer: Outliers : 1.20 % Allowed : 11.33 % Favored : 87.47 % 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: 1.15 (0.17), residues: 2514 helix: 2.30 (0.15), residues: 1216 sheet: 0.47 (0.34), residues: 232 loop : -1.05 (0.19), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 294 HIS 0.003 0.000 HIS C 45 PHE 0.042 0.001 PHE C 62 TYR 0.012 0.001 TYR F 510 ARG 0.006 0.000 ARG H 174 Details of bonding type rmsd hydrogen bonds : bond 0.03605 ( 1007) hydrogen bonds : angle 4.11906 ( 2877) covalent geometry : bond 0.00224 (20612) covalent geometry : angle 0.51427 (27958) Misc. bond : bond 0.00008 ( 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 236 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 209 time to evaluate : 2.768 Fit side-chains REVERT: A 79 LYS cc_start: 0.7458 (tptm) cc_final: 0.7242 (tppt) REVERT: B 18 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7863 (pp) REVERT: B 83 MET cc_start: 0.4550 (mmm) cc_final: 0.3028 (ptm) REVERT: B 107 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7401 (pt0) REVERT: B 119 ASP cc_start: 0.8069 (t0) cc_final: 0.7625 (t0) REVERT: B 366 LYS cc_start: 0.9067 (OUTLIER) cc_final: 0.7845 (mttt) REVERT: B 452 ASP cc_start: 0.8026 (m-30) cc_final: 0.7634 (t0) REVERT: B 530 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8710 (ttmp) REVERT: F 18 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7848 (pp) REVERT: F 83 MET cc_start: 0.4515 (mmm) cc_final: 0.3010 (ptm) REVERT: F 107 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7397 (pt0) REVERT: F 119 ASP cc_start: 0.8100 (t0) cc_final: 0.7650 (t0) REVERT: F 366 LYS cc_start: 0.9069 (OUTLIER) cc_final: 0.7843 (mttt) REVERT: F 452 ASP cc_start: 0.8038 (m-30) cc_final: 0.7629 (t0) REVERT: F 530 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8712 (ttmp) outliers start: 27 outliers final: 20 residues processed: 230 average time/residue: 0.3713 time to fit residues: 139.0743 Evaluate side-chains 231 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 205 time to evaluate : 2.731 ------------------------------------------------------------------------------- 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 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 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 C residue 59 LEU 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 187 SER 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 125 LYS Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain G residue 11 ILE 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: 0.9990 chunk 109 optimal weight: 1.9990 chunk 181 optimal weight: 0.9980 chunk 221 optimal weight: 0.6980 chunk 60 optimal weight: 0.0070 chunk 24 optimal weight: 5.9990 chunk 142 optimal weight: 0.7980 chunk 247 optimal weight: 5.9990 chunk 204 optimal weight: 2.9990 chunk 193 optimal weight: 0.5980 overall best weight: 0.6198 ------------------------------------------------------------------------------- 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 = 0.3669 r_free = 0.3669 target = 0.141070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.112602 restraints weight = 28320.823| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.81 r_work: 0.3150 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 20614 Z= 0.099 Angle : 0.511 7.515 27958 Z= 0.267 Chirality : 0.040 0.178 3166 Planarity : 0.004 0.040 3552 Dihedral : 4.394 68.497 2758 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.89 % Favored : 94.95 % Rotamer: Outliers : 1.38 % Allowed : 11.02 % Favored : 87.60 % 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: 1.24 (0.17), residues: 2514 helix: 2.34 (0.15), residues: 1220 sheet: 0.55 (0.34), residues: 232 loop : -0.98 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 294 HIS 0.003 0.000 HIS A 61 PHE 0.049 0.001 PHE C 62 TYR 0.013 0.001 TYR B 510 ARG 0.006 0.000 ARG H 174 Details of bonding type rmsd hydrogen bonds : bond 0.03472 ( 1007) hydrogen bonds : angle 4.06742 ( 2877) covalent geometry : bond 0.00218 (20612) covalent geometry : angle 0.51115 (27958) Misc. bond : bond 0.00007 ( 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 251 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 220 time to evaluate : 2.725 Fit side-chains REVERT: B 18 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7875 (pp) REVERT: B 83 MET cc_start: 0.4436 (mmm) cc_final: 0.2970 (ptm) REVERT: B 107 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7376 (pt0) REVERT: B 119 ASP cc_start: 0.8065 (t0) cc_final: 0.7610 (t0) REVERT: B 366 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.7815 (mttt) REVERT: B 452 ASP cc_start: 0.8080 (m-30) cc_final: 0.7669 (t0) REVERT: B 530 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8663 (ttmp) REVERT: D 111 MET cc_start: 0.8175 (mmm) cc_final: 0.7312 (tmm) REVERT: F 18 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7845 (pp) REVERT: F 83 MET cc_start: 0.4431 (mmm) cc_final: 0.2992 (ptm) REVERT: F 107 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7403 (pt0) REVERT: F 119 ASP cc_start: 0.8070 (t0) cc_final: 0.7620 (t0) REVERT: F 366 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.7818 (mttt) REVERT: F 452 ASP cc_start: 0.8102 (m-30) cc_final: 0.7684 (t0) REVERT: F 530 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8687 (ttmp) outliers start: 31 outliers final: 20 residues processed: 243 average time/residue: 0.4105 time to fit residues: 162.6859 Evaluate side-chains 239 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 213 time to evaluate : 5.160 ------------------------------------------------------------------------------- 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 187 SER 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 398 MET Chi-restraints excluded: chain B residue 530 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 59 LEU 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 187 SER 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 F residue 530 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 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: 4.9990 chunk 162 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 240 optimal weight: 9.9990 chunk 219 optimal weight: 0.9990 chunk 78 optimal weight: 7.9990 chunk 132 optimal weight: 6.9990 chunk 161 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 60 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.140666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.112215 restraints weight = 28453.819| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.80 r_work: 0.3150 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 20614 Z= 0.104 Angle : 0.519 7.490 27958 Z= 0.271 Chirality : 0.040 0.177 3166 Planarity : 0.004 0.039 3552 Dihedral : 4.398 69.149 2758 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.81 % Favored : 95.03 % Rotamer: Outliers : 1.20 % Allowed : 11.37 % Favored : 87.42 % 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: 1.26 (0.17), residues: 2514 helix: 2.35 (0.15), residues: 1218 sheet: 0.58 (0.34), residues: 232 loop : -0.97 (0.19), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 294 HIS 0.003 0.000 HIS C 45 PHE 0.055 0.001 PHE C 62 TYR 0.013 0.001 TYR H 173 ARG 0.007 0.000 ARG H 174 Details of bonding type rmsd hydrogen bonds : bond 0.03531 ( 1007) hydrogen bonds : angle 4.06315 ( 2877) covalent geometry : bond 0.00233 (20612) covalent geometry : angle 0.51916 (27958) Misc. bond : bond 0.00004 ( 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 242 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 215 time to evaluate : 3.335 Fit side-chains REVERT: A 79 LYS cc_start: 0.7364 (tppt) cc_final: 0.6934 (tptm) REVERT: B 18 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7864 (pp) REVERT: B 83 MET cc_start: 0.4517 (mmm) cc_final: 0.3074 (ptm) REVERT: B 107 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7378 (pt0) REVERT: B 119 ASP cc_start: 0.8082 (t0) cc_final: 0.7626 (t0) REVERT: B 366 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.7836 (mttt) REVERT: B 452 ASP cc_start: 0.8171 (m-30) cc_final: 0.7747 (t0) REVERT: B 530 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8614 (ttmp) REVERT: D 111 MET cc_start: 0.8129 (mmm) cc_final: 0.7284 (tmm) REVERT: F 18 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7841 (pp) REVERT: F 83 MET cc_start: 0.4497 (mmm) cc_final: 0.3100 (ptm) REVERT: F 107 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7393 (pt0) REVERT: F 119 ASP cc_start: 0.8080 (t0) cc_final: 0.7626 (t0) REVERT: F 366 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.7839 (mttt) REVERT: F 452 ASP cc_start: 0.8163 (m-30) cc_final: 0.7741 (t0) REVERT: F 472 MET cc_start: 0.8901 (mtp) cc_final: 0.8636 (mtt) REVERT: F 530 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8683 (ttmp) outliers start: 27 outliers final: 20 residues processed: 233 average time/residue: 0.5340 time to fit residues: 201.6972 Evaluate side-chains 237 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 211 time to evaluate : 4.820 ------------------------------------------------------------------------------- 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 187 SER 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 398 MET Chi-restraints excluded: chain B residue 530 LYS Chi-restraints excluded: chain D residue 125 LYS Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain C residue 59 LEU 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 187 SER 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 F residue 530 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 11 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 6 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 140 optimal weight: 0.0040 chunk 133 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 237 optimal weight: 0.6980 chunk 200 optimal weight: 2.9990 overall best weight: 1.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 60 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.139134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.110504 restraints weight = 28592.960| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.82 r_work: 0.3118 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20614 Z= 0.121 Angle : 0.539 7.790 27958 Z= 0.282 Chirality : 0.041 0.171 3166 Planarity : 0.004 0.041 3552 Dihedral : 4.454 71.593 2756 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.01 % Favored : 94.83 % Rotamer: Outliers : 1.38 % Allowed : 11.11 % Favored : 87.51 % 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: 1.22 (0.17), residues: 2514 helix: 2.34 (0.15), residues: 1216 sheet: 0.58 (0.34), residues: 232 loop : -1.01 (0.19), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 294 HIS 0.003 0.001 HIS G 45 PHE 0.053 0.001 PHE C 62 TYR 0.014 0.001 TYR F 510 ARG 0.007 0.000 ARG D 174 Details of bonding type rmsd hydrogen bonds : bond 0.04018 ( 1007) hydrogen bonds : angle 4.11109 ( 2877) covalent geometry : bond 0.00282 (20612) covalent geometry : angle 0.53897 (27958) Misc. bond : bond 0.00002 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13002.27 seconds wall clock time: 234 minutes 52.83 seconds (14092.83 seconds total)