Starting phenix.real_space_refine on Tue Jun 17 14:34:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iam_35310/06_2025/8iam_35310.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iam_35310/06_2025/8iam_35310.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/8iam_35310/06_2025/8iam_35310.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iam_35310/06_2025/8iam_35310.map" model { file = "/net/cci-nas-00/data/ceres_data/8iam_35310/06_2025/8iam_35310.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iam_35310/06_2025/8iam_35310.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 12980 2.51 5 N 3358 2.21 5 O 3738 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 200 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 20192 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 3844 Classifications: {'peptide': 495} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 24, 'TRANS': 470} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'PHE:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 17 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: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1225 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 142} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 572 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 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 Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'Z1T': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: G, H, E, F Time building chain proxies: 14.97, per 1000 atoms: 0.74 Number of scatterers: 20192 At special positions: 0 Unit cell: (171.72, 109.08, 124.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 114 16.00 P 2 15.00 O 3738 8.00 N 3358 7.00 C 12980 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: 4.56 Conformation dependent library (CDL) restraints added in 2.3 seconds 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4764 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 12 sheets defined 53.4% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.91 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 161 through 175 Processing helix chain 'A' and resid 189 through 204 removed outlier: 3.787A 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: 4.189A 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: 3.672A 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 405 removed outlier: 3.869A pdb=" N VAL A 393 " --> pdb=" O PRO A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 427 removed outlier: 4.012A pdb=" N ASP A 427 " --> pdb=" O SER A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 458 removed outlier: 3.562A pdb=" N ARG A 454 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 476 removed outlier: 3.524A pdb=" N LEU A 465 " --> pdb=" O THR A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 504 Processing helix chain 'A' and resid 534 through 554 Processing helix chain 'B' and resid 20 through 28 Processing helix chain 'B' and resid 57 through 85 removed outlier: 3.953A pdb=" N SER B 61 " --> pdb=" O PRO B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 114 removed outlier: 3.560A pdb=" N ARG B 112 " --> pdb=" O SER B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 122 removed outlier: 3.569A pdb=" N ASP B 119 " --> pdb=" O MET B 116 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N ASP B 120 " --> pdb=" O ARG B 117 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE B 122 " --> pdb=" O ASP B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 186 removed outlier: 3.726A pdb=" N ASP B 177 " --> pdb=" O GLY B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 215 removed outlier: 3.672A pdb=" N ILE B 204 " --> pdb=" O THR B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 237 removed outlier: 4.728A pdb=" N PHE B 233 " --> pdb=" O ASN B 229 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ASN B 234 " --> pdb=" O ALA B 230 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA B 235 " --> pdb=" O ASN B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 261 removed outlier: 3.519A pdb=" N ARG B 254 " --> pdb=" O HIS B 250 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER B 260 " --> pdb=" O GLY B 256 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY B 261 " --> pdb=" O VAL B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 286 Processing helix chain 'B' and resid 313 through 325 Processing helix chain 'B' and resid 345 through 351 removed outlier: 3.605A 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 removed outlier: 3.550A pdb=" N SER B 395 " --> pdb=" O THR B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 415 removed outlier: 3.537A pdb=" N LEU B 403 " --> pdb=" O PRO B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 444 removed outlier: 3.717A pdb=" N GLU B 424 " --> pdb=" O GLY B 420 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA B 430 " --> pdb=" O LEU B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 476 removed outlier: 3.988A pdb=" N ALA B 468 " --> pdb=" O SER B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 522 Processing helix chain 'B' and resid 528 through 532 removed outlier: 4.023A pdb=" N SER B 531 " --> pdb=" O SER B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 553 Proline residue: B 550 - end of helix Processing helix chain 'B' and resid 554 through 559 removed outlier: 6.675A pdb=" N LYS B 557 " --> pdb=" O LYS B 554 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR B 558 " --> pdb=" O ASP B 555 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE B 559 " --> pdb=" O ASP B 556 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 554 through 559' Processing helix chain 'D' and resid 58 through 67 removed outlier: 4.134A pdb=" N LEU D 67 " --> pdb=" O ASP D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 77 removed outlier: 3.586A pdb=" N ASP D 76 " --> pdb=" O THR D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 99 removed outlier: 3.810A pdb=" N ILE D 85 " --> pdb=" O TRP D 81 " (cutoff:3.500A) removed outlier: 3.671A 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 140 through 145 Processing helix chain 'D' and resid 146 through 148 No H-bonds generated for 'chain 'D' and resid 146 through 148' Processing helix chain 'D' and resid 152 through 171 Proline residue: D 162 - end of helix removed outlier: 4.385A pdb=" N GLN D 171 " --> pdb=" O LEU D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 191 Processing helix chain 'C' and resid 13 through 22 Processing helix chain 'C' and resid 27 through 45 removed outlier: 4.143A pdb=" N HIS C 45 " --> pdb=" O THR C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 75 Processing helix chain 'E' and resid 61 through 77 Processing helix chain 'E' and resid 89 through 100 Processing helix chain 'E' and resid 115 through 120 Processing helix chain 'E' and resid 161 through 175 Processing helix chain 'E' and resid 189 through 204 removed outlier: 3.787A 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: 4.189A 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: 3.672A 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 405 removed outlier: 3.869A pdb=" N VAL E 393 " --> pdb=" O PRO E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 427 removed outlier: 4.012A pdb=" N ASP E 427 " --> pdb=" O SER E 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 450 through 458 removed outlier: 3.562A pdb=" N ARG E 454 " --> pdb=" O THR E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 461 through 476 removed outlier: 3.524A pdb=" N LEU E 465 " --> pdb=" O THR E 461 " (cutoff:3.500A) Processing helix chain 'E' and resid 482 through 504 Processing helix chain 'E' and resid 534 through 554 Processing helix chain 'F' and resid 20 through 28 Processing helix chain 'F' and resid 57 through 85 removed outlier: 3.953A pdb=" N SER F 61 " --> pdb=" O PRO F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 114 removed outlier: 3.560A pdb=" N ARG F 112 " --> pdb=" O SER F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 122 removed outlier: 3.569A pdb=" N ASP F 119 " --> pdb=" O MET F 116 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ASP F 120 " --> pdb=" O ARG F 117 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE F 122 " --> pdb=" O ASP F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 186 removed outlier: 3.726A pdb=" N ASP F 177 " --> pdb=" O GLY F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 215 removed outlier: 3.672A pdb=" N ILE F 204 " --> pdb=" O THR F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 237 removed outlier: 4.728A pdb=" N PHE F 233 " --> pdb=" O ASN F 229 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ASN F 234 " --> pdb=" O ALA F 230 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA F 235 " --> pdb=" O ASN F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 261 removed outlier: 3.519A pdb=" N ARG F 254 " --> pdb=" O HIS F 250 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER F 260 " --> pdb=" O GLY F 256 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY F 261 " --> pdb=" O VAL F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 286 Processing helix chain 'F' and resid 313 through 325 Processing helix chain 'F' and resid 345 through 351 removed outlier: 3.605A 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 removed outlier: 3.550A pdb=" N SER F 395 " --> pdb=" O THR F 391 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 415 removed outlier: 3.538A pdb=" N LEU F 403 " --> pdb=" O PRO F 399 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 444 removed outlier: 3.717A pdb=" N GLU F 424 " --> pdb=" O GLY F 420 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA F 430 " --> pdb=" O LEU F 426 " (cutoff:3.500A) Processing helix chain 'F' and resid 464 through 476 removed outlier: 3.987A pdb=" N ALA F 468 " --> pdb=" O SER F 464 " (cutoff:3.500A) Processing helix chain 'F' and resid 504 through 522 Processing helix chain 'F' and resid 528 through 532 removed outlier: 4.022A pdb=" N SER F 531 " --> pdb=" O SER F 528 " (cutoff:3.500A) Processing helix chain 'F' and resid 541 through 553 Proline residue: F 550 - end of helix Processing helix chain 'F' and resid 554 through 559 removed outlier: 6.675A pdb=" N LYS F 557 " --> pdb=" O LYS F 554 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR F 558 " --> pdb=" O ASP F 555 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE F 559 " --> pdb=" O ASP F 556 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 554 through 559' Processing helix chain 'H' and resid 58 through 67 removed outlier: 4.133A pdb=" N LEU H 67 " --> pdb=" O ASP H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 77 removed outlier: 3.586A pdb=" N ASP H 76 " --> pdb=" O THR H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 99 removed outlier: 3.810A pdb=" N ILE H 85 " --> pdb=" O TRP H 81 " (cutoff:3.500A) removed outlier: 3.671A 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 140 through 145 Processing helix chain 'H' and resid 146 through 148 No H-bonds generated for 'chain 'H' and resid 146 through 148' Processing helix chain 'H' and resid 152 through 171 Proline residue: H 162 - end of helix removed outlier: 4.385A pdb=" N GLN H 171 " --> pdb=" O LEU H 167 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 191 Processing helix chain 'G' and resid 13 through 22 Processing helix chain 'G' and resid 27 through 45 removed outlier: 4.142A pdb=" N HIS G 45 " --> pdb=" O THR G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 52 through 75 Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 137 removed outlier: 7.183A pdb=" N ILE A 135 " --> pdb=" O THR A 145 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N THR A 145 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ARG A 137 " --> pdb=" O LYS A 143 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N LYS A 143 " --> pdb=" O ARG A 137 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N LEU A 506 " --> pdb=" O ASN A 146 " (cutoff:3.500A) removed outlier: 6.781A 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: 6.803A pdb=" N LYS A 286 " --> pdb=" O ARG A 316 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N PHE A 318 " --> pdb=" O LYS A 286 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ILE A 288 " --> pdb=" O PHE A 318 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N ASP A 320 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N THR A 290 " --> pdb=" O ASP A 320 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 444 through 447 removed outlier: 4.099A pdb=" N LEU A 447 " --> pdb=" O LEU A 525 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 126 through 127 removed outlier: 4.031A pdb=" N ARG B 135 " --> pdb=" O THR B 127 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASP B 138 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ALA B 153 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N ILE B 140 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N SER B 151 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N HIS B 142 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N THR B 149 " --> pdb=" O HIS B 142 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N ALA B 479 " --> pdb=" O PRO B 156 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N MET B 158 " --> pdb=" O ALA B 479 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 218 through 222 removed outlier: 3.638A pdb=" N GLY B 373 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ILE B 297 " --> pdb=" O TYR B 327 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N PHE B 329 " --> pdb=" O ILE B 297 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE B 299 " --> pdb=" O PHE B 329 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ASP B 331 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ALA B 301 " --> pdb=" O ASP B 331 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N GLU B 302 " --> pdb=" O ASP B 246 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE B 267 " --> pdb=" O SER B 245 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 455 through 459 removed outlier: 4.102A pdb=" N VAL B 481 " --> pdb=" O ARG B 496 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 132 through 137 removed outlier: 7.183A pdb=" N ILE E 135 " --> pdb=" O THR E 145 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N THR E 145 " --> pdb=" O ILE E 135 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ARG E 137 " --> pdb=" O LYS E 143 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N LYS E 143 " --> pdb=" O ARG E 137 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N LEU E 506 " --> pdb=" O ASN E 146 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE E 148 " --> pdb=" O LEU E 506 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 207 through 211 removed outlier: 6.802A pdb=" N LYS E 286 " --> pdb=" O ARG E 316 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N PHE E 318 " --> pdb=" O LYS E 286 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ILE E 288 " --> pdb=" O PHE E 318 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ASP E 320 " --> pdb=" O ILE E 288 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N THR E 290 " --> pdb=" O ASP E 320 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 444 through 447 removed outlier: 4.099A pdb=" N LEU E 447 " --> pdb=" O LEU E 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 126 through 127 removed outlier: 4.031A pdb=" N ARG F 135 " --> pdb=" O THR F 127 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP F 138 " --> pdb=" O ALA F 153 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ALA F 153 " --> pdb=" O ASP F 138 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N ILE F 140 " --> pdb=" O SER F 151 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N SER F 151 " --> pdb=" O ILE F 140 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N HIS F 142 " --> pdb=" O THR F 149 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N THR F 149 " --> pdb=" O HIS F 142 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N ALA F 479 " --> pdb=" O PRO F 156 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N MET F 158 " --> pdb=" O ALA F 479 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 218 through 222 removed outlier: 3.638A pdb=" N GLY F 373 " --> pdb=" O PHE F 222 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ILE F 297 " --> pdb=" O TYR F 327 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N PHE F 329 " --> pdb=" O ILE F 297 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE F 299 " --> pdb=" O PHE F 329 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ASP F 331 " --> pdb=" O ILE F 299 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ALA F 301 " --> pdb=" O ASP F 331 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N GLU F 302 " --> pdb=" O ASP F 246 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE F 267 " --> pdb=" O SER F 245 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 455 through 459 removed outlier: 4.102A pdb=" N VAL F 481 " --> pdb=" O ARG F 496 " (cutoff:3.500A) 973 hydrogen bonds defined for protein. 2847 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: 5.74 Time building geometry restraints manager: 5.41 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: 6422 1.34 - 1.46: 3882 1.46 - 1.58: 10158 1.58 - 1.69: 2 1.69 - 1.81: 174 Bond restraints: 20638 Sorted by residual: bond pdb=" C14 Z1T D 301 " pdb=" C15 Z1T D 301 " ideal model delta sigma weight residual 1.329 1.528 -0.199 2.00e-02 2.50e+03 9.92e+01 bond pdb=" C14 Z1T H 301 " pdb=" C15 Z1T H 301 " ideal model delta sigma weight residual 1.329 1.528 -0.199 2.00e-02 2.50e+03 9.87e+01 bond pdb=" C13 Z1T H 301 " pdb=" C14 Z1T H 301 " ideal model delta sigma weight residual 1.494 1.529 -0.035 2.00e-02 2.50e+03 3.10e+00 bond pdb=" C13 Z1T D 301 " pdb=" C14 Z1T D 301 " ideal model delta sigma weight residual 1.494 1.529 -0.035 2.00e-02 2.50e+03 3.10e+00 bond pdb=" N ASN E 257 " pdb=" CA ASN E 257 " ideal model delta sigma weight residual 1.457 1.476 -0.019 1.10e-02 8.26e+03 2.95e+00 ... (remaining 20633 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 27666 2.83 - 5.65: 278 5.65 - 8.48: 21 8.48 - 11.31: 3 11.31 - 14.14: 2 Bond angle restraints: 27970 Sorted by residual: angle pdb=" N ASN E 257 " pdb=" CA ASN E 257 " pdb=" C ASN E 257 " ideal model delta sigma weight residual 112.57 126.71 -14.14 1.13e+00 7.83e-01 1.57e+02 angle pdb=" N ASN A 257 " pdb=" CA ASN A 257 " pdb=" C ASN A 257 " ideal model delta sigma weight residual 112.57 126.68 -14.11 1.13e+00 7.83e-01 1.56e+02 angle pdb=" N GLY H 133 " pdb=" CA GLY H 133 " pdb=" C GLY H 133 " ideal model delta sigma weight residual 112.50 106.19 6.31 1.16e+00 7.43e-01 2.96e+01 angle pdb=" N GLY D 133 " pdb=" CA GLY D 133 " pdb=" C GLY D 133 " ideal model delta sigma weight residual 112.50 106.23 6.27 1.16e+00 7.43e-01 2.92e+01 angle pdb=" N LYS A 79 " pdb=" CA LYS A 79 " pdb=" C LYS A 79 " ideal model delta sigma weight residual 113.38 119.93 -6.55 1.23e+00 6.61e-01 2.83e+01 ... (remaining 27965 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.03: 11524 21.03 - 42.06: 776 42.06 - 63.10: 96 63.10 - 84.13: 18 84.13 - 105.16: 6 Dihedral angle restraints: 12420 sinusoidal: 5020 harmonic: 7400 Sorted by residual: dihedral pdb=" CA SER F 306 " pdb=" C SER F 306 " pdb=" N MET F 307 " pdb=" CA MET F 307 " ideal model delta harmonic sigma weight residual 180.00 159.77 20.23 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA SER B 306 " pdb=" C SER B 306 " pdb=" N MET B 307 " pdb=" CA MET B 307 " ideal model delta harmonic sigma weight residual 180.00 159.77 20.23 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA PRO F 19 " pdb=" C PRO F 19 " pdb=" N ASP F 20 " pdb=" CA ASP F 20 " ideal model delta harmonic sigma weight residual 180.00 160.94 19.06 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 12417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 3074 0.103 - 0.206: 90 0.206 - 0.309: 4 0.309 - 0.412: 0 0.412 - 0.516: 2 Chirality restraints: 3170 Sorted by residual: chirality pdb=" CA ASN E 257 " pdb=" N ASN E 257 " pdb=" C ASN E 257 " pdb=" CB ASN E 257 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.65e+00 chirality pdb=" CA ASN A 257 " pdb=" N ASN A 257 " pdb=" C ASN A 257 " pdb=" CB ASN A 257 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.61e+00 chirality pdb=" CA LYS A 79 " pdb=" N LYS A 79 " pdb=" C LYS A 79 " pdb=" CB LYS A 79 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.28e+00 ... (remaining 3167 not shown) Planarity restraints: 3548 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 256 " 0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C PHE A 256 " -0.057 2.00e-02 2.50e+03 pdb=" O PHE A 256 " 0.021 2.00e-02 2.50e+03 pdb=" N ASN A 257 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE E 256 " -0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C PHE E 256 " 0.057 2.00e-02 2.50e+03 pdb=" O PHE E 256 " -0.021 2.00e-02 2.50e+03 pdb=" N ASN E 257 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS E 82 " -0.045 5.00e-02 4.00e+02 6.85e-02 7.50e+00 pdb=" N PRO E 83 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO E 83 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO E 83 " -0.037 5.00e-02 4.00e+02 ... (remaining 3545 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 260 2.66 - 3.22: 18338 3.22 - 3.78: 28804 3.78 - 4.34: 40412 4.34 - 4.90: 70115 Nonbonded interactions: 157929 Sorted by model distance: nonbonded pdb=" O LYS E 79 " pdb=" OG SER E 80 " model vdw 2.098 3.040 nonbonded pdb=" O LYS A 79 " pdb=" OG SER A 80 " model vdw 2.098 3.040 nonbonded pdb=" OH TYR E 460 " pdb=" OE1 GLU E 488 " model vdw 2.114 3.040 nonbonded pdb=" OH TYR A 460 " pdb=" OE1 GLU A 488 " model vdw 2.114 3.040 nonbonded pdb=" OG SER A 417 " pdb=" O SER A 442 " model vdw 2.158 3.040 ... (remaining 157924 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: 0.09 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 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: 0.680 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 45.000 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 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 : 0.004 0.199 20640 Z= 0.199 Angle : 0.720 14.137 27970 Z= 0.414 Chirality : 0.047 0.516 3170 Planarity : 0.005 0.068 3548 Dihedral : 13.959 105.161 7656 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.56 % Favored : 94.12 % Rotamer: Outliers : 0.27 % Allowed : 0.94 % Favored : 98.79 % 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: -0.12 (0.17), residues: 2516 helix: 1.50 (0.15), residues: 1212 sheet: -0.41 (0.35), residues: 224 loop : -1.94 (0.17), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 294 HIS 0.008 0.001 HIS F 78 PHE 0.019 0.001 PHE G 62 TYR 0.015 0.001 TYR F 510 ARG 0.003 0.000 ARG D 92 Details of bonding type rmsd hydrogen bonds : bond 0.16968 ( 973) hydrogen bonds : angle 5.53071 ( 2847) covalent geometry : bond 0.00410 (20638) covalent geometry : angle 0.71997 (27970) Misc. bond : bond 0.00056 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 253 time to evaluate : 2.083 Fit side-chains REVERT: B 119 ASP cc_start: 0.7841 (t70) cc_final: 0.7267 (t0) REVERT: B 158 MET cc_start: 0.8765 (ttp) cc_final: 0.8457 (ttm) REVERT: D 143 GLU cc_start: 0.8562 (mt-10) cc_final: 0.8322 (mt-10) REVERT: F 119 ASP cc_start: 0.7807 (t70) cc_final: 0.7232 (t0) REVERT: F 158 MET cc_start: 0.8750 (ttp) cc_final: 0.8443 (ttm) REVERT: H 143 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8312 (mt-10) outliers start: 6 outliers final: 0 residues processed: 257 average time/residue: 0.2923 time to fit residues: 119.1764 Evaluate side-chains 206 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 2.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 104 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 chunk 126 optimal weight: 7.9990 chunk 100 optimal weight: 4.9990 chunk 194 optimal weight: 0.0970 chunk 75 optimal weight: 1.9990 chunk 118 optimal weight: 8.9990 chunk 144 optimal weight: 5.9990 chunk 225 optimal weight: 0.9980 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 HIS B 90 HIS B 96 HIS B 145 ASN D 62 ASN D 110 ASN E 421 HIS F 90 HIS F 96 HIS F 145 ASN H 62 ASN H 110 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.130318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.103861 restraints weight = 27716.202| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.64 r_work: 0.3005 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.0938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20640 Z= 0.146 Angle : 0.601 10.557 27970 Z= 0.311 Chirality : 0.043 0.172 3170 Planarity : 0.005 0.058 3548 Dihedral : 7.656 101.543 2846 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.48 % Favored : 94.36 % Rotamer: Outliers : 0.85 % Allowed : 6.68 % Favored : 92.47 % 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: 0.13 (0.17), residues: 2516 helix: 1.64 (0.15), residues: 1224 sheet: -0.13 (0.33), residues: 264 loop : -1.86 (0.18), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 142 HIS 0.003 0.001 HIS B 90 PHE 0.017 0.001 PHE E 256 TYR 0.016 0.001 TYR F 510 ARG 0.008 0.000 ARG G 20 Details of bonding type rmsd hydrogen bonds : bond 0.05231 ( 973) hydrogen bonds : angle 4.43713 ( 2847) covalent geometry : bond 0.00335 (20638) covalent geometry : angle 0.60112 (27970) Misc. bond : bond 0.00009 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 225 time to evaluate : 2.412 Fit side-chains REVERT: B 119 ASP cc_start: 0.8526 (t70) cc_final: 0.7791 (t0) REVERT: B 158 MET cc_start: 0.9156 (ttp) cc_final: 0.8791 (ttm) REVERT: D 111 MET cc_start: 0.7974 (mmt) cc_final: 0.7765 (mmt) REVERT: D 137 ASP cc_start: 0.8766 (m-30) cc_final: 0.8549 (m-30) REVERT: C 51 MET cc_start: 0.9042 (mtt) cc_final: 0.8784 (mtt) REVERT: F 119 ASP cc_start: 0.8504 (t70) cc_final: 0.7766 (t0) REVERT: F 158 MET cc_start: 0.9161 (ttp) cc_final: 0.8808 (ttm) REVERT: G 51 MET cc_start: 0.9031 (mtt) cc_final: 0.8763 (mtt) outliers start: 19 outliers final: 12 residues processed: 233 average time/residue: 0.3273 time to fit residues: 120.7525 Evaluate side-chains 220 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 208 time to evaluate : 2.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain E residue 524 SER Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 152 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 98 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 240 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 149 optimal weight: 5.9990 chunk 128 optimal weight: 8.9990 chunk 131 optimal weight: 0.0050 overall best weight: 1.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 GLN D 62 ASN H 62 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.130066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.103096 restraints weight = 27557.613| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.65 r_work: 0.2969 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 20640 Z= 0.152 Angle : 0.586 11.456 27970 Z= 0.302 Chirality : 0.043 0.167 3170 Planarity : 0.005 0.054 3548 Dihedral : 7.622 98.015 2846 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.29 % Favored : 94.55 % Rotamer: Outliers : 1.52 % Allowed : 8.65 % Favored : 89.83 % 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: 0.26 (0.17), residues: 2516 helix: 1.78 (0.15), residues: 1212 sheet: -0.23 (0.32), residues: 288 loop : -1.78 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 142 HIS 0.004 0.001 HIS B 142 PHE 0.019 0.001 PHE A 256 TYR 0.017 0.001 TYR B 510 ARG 0.002 0.000 ARG G 20 Details of bonding type rmsd hydrogen bonds : bond 0.05176 ( 973) hydrogen bonds : angle 4.28685 ( 2847) covalent geometry : bond 0.00358 (20638) covalent geometry : angle 0.58608 (27970) Misc. bond : bond 0.00010 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 225 time to evaluate : 3.254 Fit side-chains REVERT: A 477 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8066 (tm-30) REVERT: B 119 ASP cc_start: 0.8583 (t70) cc_final: 0.7856 (t0) REVERT: B 158 MET cc_start: 0.9178 (ttp) cc_final: 0.8840 (ttm) REVERT: D 111 MET cc_start: 0.8098 (mmt) cc_final: 0.7896 (mmt) REVERT: C 51 MET cc_start: 0.9037 (mtt) cc_final: 0.8777 (mtt) REVERT: E 477 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8071 (tm-30) REVERT: F 119 ASP cc_start: 0.8573 (t70) cc_final: 0.7838 (t0) REVERT: F 158 MET cc_start: 0.9171 (ttp) cc_final: 0.8839 (ttm) REVERT: G 51 MET cc_start: 0.9028 (mtt) cc_final: 0.8782 (mtt) outliers start: 34 outliers final: 16 residues processed: 241 average time/residue: 0.3792 time to fit residues: 146.3797 Evaluate side-chains 231 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 213 time to evaluate : 2.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 477 GLN Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain E residue 477 GLN Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 356 ASP Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain G residue 13 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 21 optimal weight: 1.9990 chunk 127 optimal weight: 0.0870 chunk 237 optimal weight: 8.9990 chunk 176 optimal weight: 0.9990 chunk 182 optimal weight: 9.9990 chunk 226 optimal weight: 0.9990 chunk 208 optimal weight: 0.6980 chunk 141 optimal weight: 8.9990 chunk 96 optimal weight: 5.9990 chunk 218 optimal weight: 6.9990 chunk 93 optimal weight: 0.0060 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 GLN B 90 HIS D 62 ASN F 90 HIS H 62 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.134923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.108002 restraints weight = 27516.967| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.76 r_work: 0.3053 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 20640 Z= 0.098 Angle : 0.518 9.865 27970 Z= 0.265 Chirality : 0.041 0.227 3170 Planarity : 0.004 0.051 3548 Dihedral : 7.312 96.433 2846 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.41 % Favored : 95.43 % Rotamer: Outliers : 1.21 % Allowed : 10.17 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.17), residues: 2516 helix: 2.05 (0.15), residues: 1218 sheet: 0.02 (0.33), residues: 276 loop : -1.57 (0.19), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 294 HIS 0.003 0.001 HIS F 90 PHE 0.013 0.001 PHE F 236 TYR 0.011 0.001 TYR B 510 ARG 0.002 0.000 ARG C 20 Details of bonding type rmsd hydrogen bonds : bond 0.03512 ( 973) hydrogen bonds : angle 4.09415 ( 2847) covalent geometry : bond 0.00201 (20638) covalent geometry : angle 0.51801 (27970) Misc. bond : bond 0.00012 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 255 time to evaluate : 2.171 Fit side-chains REVERT: A 477 GLN cc_start: 0.8508 (tm-30) cc_final: 0.8137 (tt0) REVERT: B 119 ASP cc_start: 0.8537 (t70) cc_final: 0.7790 (t0) REVERT: B 158 MET cc_start: 0.9156 (ttp) cc_final: 0.8714 (ttm) REVERT: D 111 MET cc_start: 0.7930 (mmt) cc_final: 0.7713 (mmt) REVERT: C 51 MET cc_start: 0.9053 (mtt) cc_final: 0.8788 (mtt) REVERT: E 477 GLN cc_start: 0.8503 (tm-30) cc_final: 0.8130 (tt0) REVERT: F 119 ASP cc_start: 0.8525 (t70) cc_final: 0.7771 (t0) REVERT: F 158 MET cc_start: 0.9126 (ttp) cc_final: 0.8680 (ttm) REVERT: G 51 MET cc_start: 0.9059 (mtt) cc_final: 0.8812 (mtt) outliers start: 27 outliers final: 17 residues processed: 269 average time/residue: 0.2881 time to fit residues: 123.7520 Evaluate side-chains 243 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 226 time to evaluate : 2.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 86 GLN Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 120 MET Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 66 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 112 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 161 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 94 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 100 optimal weight: 0.0060 overall best weight: 1.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 HIS B 96 HIS D 62 ASN F 90 HIS F 96 HIS H 62 ASN H 110 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.132476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.105327 restraints weight = 27732.236| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.71 r_work: 0.3021 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 20640 Z= 0.115 Angle : 0.531 10.232 27970 Z= 0.272 Chirality : 0.042 0.175 3170 Planarity : 0.005 0.049 3548 Dihedral : 7.322 95.738 2846 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.25 % Favored : 94.67 % Rotamer: Outliers : 1.48 % Allowed : 10.35 % Favored : 88.17 % 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: 0.71 (0.17), residues: 2516 helix: 2.15 (0.15), residues: 1216 sheet: 0.04 (0.33), residues: 288 loop : -1.59 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 142 HIS 0.002 0.001 HIS F 90 PHE 0.016 0.001 PHE A 256 TYR 0.014 0.001 TYR A 453 ARG 0.004 0.000 ARG C 20 Details of bonding type rmsd hydrogen bonds : bond 0.04026 ( 973) hydrogen bonds : angle 4.03812 ( 2847) covalent geometry : bond 0.00261 (20638) covalent geometry : angle 0.53105 (27970) Misc. bond : bond 0.00016 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 229 time to evaluate : 2.502 Fit side-chains REVERT: A 477 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.8206 (tt0) REVERT: B 119 ASP cc_start: 0.8588 (t70) cc_final: 0.7842 (t0) REVERT: B 158 MET cc_start: 0.9170 (ttp) cc_final: 0.8732 (ttm) REVERT: D 66 MET cc_start: 0.7439 (tpp) cc_final: 0.7126 (ttm) REVERT: D 111 MET cc_start: 0.8051 (mmt) cc_final: 0.7843 (mmt) REVERT: C 51 MET cc_start: 0.9059 (mtt) cc_final: 0.8817 (mtt) REVERT: E 477 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.8189 (tt0) REVERT: F 16 GLU cc_start: 0.6372 (OUTLIER) cc_final: 0.6089 (pt0) REVERT: F 119 ASP cc_start: 0.8582 (t70) cc_final: 0.7832 (t0) REVERT: F 158 MET cc_start: 0.9142 (ttp) cc_final: 0.8706 (ttm) REVERT: H 66 MET cc_start: 0.7471 (tpp) cc_final: 0.7173 (ttm) REVERT: G 51 MET cc_start: 0.9071 (mtt) cc_final: 0.8840 (mtt) outliers start: 33 outliers final: 17 residues processed: 249 average time/residue: 0.3203 time to fit residues: 128.1455 Evaluate side-chains 242 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 222 time to evaluate : 2.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 477 GLN Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 477 GLN Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 120 MET Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 66 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 35 optimal weight: 4.9990 chunk 167 optimal weight: 0.9980 chunk 79 optimal weight: 9.9990 chunk 203 optimal weight: 5.9990 chunk 173 optimal weight: 3.9990 chunk 211 optimal weight: 0.4980 chunk 14 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 176 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 GLN B 90 HIS D 62 ASN F 90 HIS H 62 ASN H 110 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.132209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.105246 restraints weight = 27647.415| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.67 r_work: 0.2991 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 20640 Z= 0.127 Angle : 0.538 10.756 27970 Z= 0.278 Chirality : 0.042 0.171 3170 Planarity : 0.005 0.048 3548 Dihedral : 7.390 94.555 2846 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.29 % Favored : 94.63 % Rotamer: Outliers : 1.48 % Allowed : 11.42 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.17), residues: 2516 helix: 2.20 (0.15), residues: 1216 sheet: 0.22 (0.34), residues: 280 loop : -1.62 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 294 HIS 0.002 0.001 HIS F 90 PHE 0.018 0.001 PHE E 256 TYR 0.016 0.001 TYR B 510 ARG 0.003 0.000 ARG C 20 Details of bonding type rmsd hydrogen bonds : bond 0.04330 ( 973) hydrogen bonds : angle 4.03248 ( 2847) covalent geometry : bond 0.00294 (20638) covalent geometry : angle 0.53823 (27970) Misc. bond : bond 0.00013 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 227 time to evaluate : 2.296 Fit side-chains REVERT: A 477 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.8218 (tt0) REVERT: A 533 MET cc_start: 0.7305 (mtm) cc_final: 0.7051 (mtm) REVERT: B 119 ASP cc_start: 0.8568 (t70) cc_final: 0.7835 (t0) REVERT: B 158 MET cc_start: 0.9170 (ttp) cc_final: 0.8770 (ttm) REVERT: D 66 MET cc_start: 0.7488 (tpp) cc_final: 0.7074 (ttm) REVERT: C 51 MET cc_start: 0.9075 (mtt) cc_final: 0.8823 (mtt) REVERT: E 477 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.8221 (tt0) REVERT: E 533 MET cc_start: 0.7298 (mtm) cc_final: 0.7038 (mtm) REVERT: F 16 GLU cc_start: 0.6278 (OUTLIER) cc_final: 0.6020 (pt0) REVERT: F 119 ASP cc_start: 0.8567 (t70) cc_final: 0.7836 (t0) REVERT: F 158 MET cc_start: 0.9142 (ttp) cc_final: 0.8742 (ttm) REVERT: H 66 MET cc_start: 0.7485 (tpp) cc_final: 0.7093 (ttm) REVERT: G 51 MET cc_start: 0.9071 (mtt) cc_final: 0.8832 (mtt) outliers start: 33 outliers final: 25 residues processed: 247 average time/residue: 0.2908 time to fit residues: 114.3897 Evaluate side-chains 249 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 221 time to evaluate : 2.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 477 GLN Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 477 GLN Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 504 THR Chi-restraints excluded: chain H residue 120 MET Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 66 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 38 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 chunk 187 optimal weight: 8.9990 chunk 129 optimal weight: 5.9990 chunk 229 optimal weight: 8.9990 chunk 203 optimal weight: 7.9990 chunk 110 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 239 optimal weight: 6.9990 chunk 173 optimal weight: 0.0970 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 GLN B 90 HIS B 96 HIS D 62 ASN F 90 HIS F 96 HIS H 62 ASN H 110 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.130601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.103522 restraints weight = 27634.281| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 1.70 r_work: 0.2980 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 20640 Z= 0.154 Angle : 0.579 11.663 27970 Z= 0.296 Chirality : 0.043 0.171 3170 Planarity : 0.005 0.048 3548 Dihedral : 7.546 93.368 2846 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.96 % Favored : 93.96 % Rotamer: Outliers : 1.88 % Allowed : 11.83 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.17), residues: 2516 helix: 2.15 (0.15), residues: 1216 sheet: 0.19 (0.34), residues: 280 loop : -1.64 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 142 HIS 0.003 0.001 HIS E 258 PHE 0.019 0.001 PHE A 256 TYR 0.018 0.001 TYR F 510 ARG 0.005 0.000 ARG G 20 Details of bonding type rmsd hydrogen bonds : bond 0.04868 ( 973) hydrogen bonds : angle 4.08938 ( 2847) covalent geometry : bond 0.00369 (20638) covalent geometry : angle 0.57865 (27970) Misc. bond : bond 0.00016 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 230 time to evaluate : 2.252 Fit side-chains REVERT: A 477 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.8226 (tt0) REVERT: B 16 GLU cc_start: 0.6376 (OUTLIER) cc_final: 0.6163 (pt0) REVERT: B 119 ASP cc_start: 0.8661 (t70) cc_final: 0.7897 (t0) REVERT: B 158 MET cc_start: 0.9178 (ttp) cc_final: 0.8808 (ttm) REVERT: D 66 MET cc_start: 0.7583 (tpp) cc_final: 0.7178 (ttm) REVERT: C 51 MET cc_start: 0.9054 (mtt) cc_final: 0.8785 (mtt) REVERT: E 477 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.8218 (tt0) REVERT: F 16 GLU cc_start: 0.6457 (OUTLIER) cc_final: 0.6183 (pt0) REVERT: F 119 ASP cc_start: 0.8667 (t70) cc_final: 0.7900 (t0) REVERT: F 158 MET cc_start: 0.9140 (ttp) cc_final: 0.8773 (ttm) REVERT: H 66 MET cc_start: 0.7583 (tpp) cc_final: 0.7173 (ttm) REVERT: G 51 MET cc_start: 0.9048 (mtt) cc_final: 0.8791 (mtt) outliers start: 42 outliers final: 31 residues processed: 258 average time/residue: 0.3399 time to fit residues: 138.5778 Evaluate side-chains 257 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 222 time to evaluate : 4.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 477 GLN Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 437 THR Chi-restraints excluded: chain E residue 477 GLN Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 504 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 120 MET Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 66 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 197 optimal weight: 6.9990 chunk 233 optimal weight: 6.9990 chunk 60 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 242 optimal weight: 0.9990 chunk 165 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 202 optimal weight: 3.9990 chunk 211 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 GLN D 62 ASN D 110 ASN H 62 ASN H 110 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.130229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.103123 restraints weight = 27879.755| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 1.69 r_work: 0.2982 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 20640 Z= 0.158 Angle : 0.579 11.685 27970 Z= 0.298 Chirality : 0.043 0.168 3170 Planarity : 0.005 0.048 3548 Dihedral : 7.622 92.637 2846 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.80 % Favored : 94.12 % Rotamer: Outliers : 1.75 % Allowed : 12.32 % Favored : 85.93 % 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: 0.67 (0.17), residues: 2516 helix: 2.10 (0.15), residues: 1216 sheet: 0.28 (0.34), residues: 266 loop : -1.62 (0.18), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 294 HIS 0.003 0.001 HIS E 258 PHE 0.020 0.001 PHE A 256 TYR 0.017 0.001 TYR B 510 ARG 0.004 0.000 ARG C 20 Details of bonding type rmsd hydrogen bonds : bond 0.04898 ( 973) hydrogen bonds : angle 4.11008 ( 2847) covalent geometry : bond 0.00379 (20638) covalent geometry : angle 0.57943 (27970) Misc. bond : bond 0.00018 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 221 time to evaluate : 3.851 Fit side-chains REVERT: A 477 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.8262 (tt0) REVERT: A 533 MET cc_start: 0.7374 (mtm) cc_final: 0.6849 (mtm) REVERT: B 119 ASP cc_start: 0.8678 (t70) cc_final: 0.7883 (t0) REVERT: B 158 MET cc_start: 0.9159 (ttp) cc_final: 0.8772 (ttm) REVERT: D 66 MET cc_start: 0.7607 (tpp) cc_final: 0.7171 (ttm) REVERT: C 51 MET cc_start: 0.9053 (mtt) cc_final: 0.8799 (mtt) REVERT: E 477 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.8243 (tt0) REVERT: E 533 MET cc_start: 0.7372 (mtm) cc_final: 0.6849 (mtm) REVERT: F 16 GLU cc_start: 0.6381 (OUTLIER) cc_final: 0.6137 (pt0) REVERT: F 119 ASP cc_start: 0.8685 (t70) cc_final: 0.7894 (t0) REVERT: F 158 MET cc_start: 0.9141 (ttp) cc_final: 0.8783 (ttm) REVERT: H 66 MET cc_start: 0.7566 (tpp) cc_final: 0.7135 (ttm) REVERT: G 51 MET cc_start: 0.9039 (mtt) cc_final: 0.8784 (mtt) outliers start: 39 outliers final: 36 residues processed: 244 average time/residue: 0.4359 time to fit residues: 168.4112 Evaluate side-chains 260 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 221 time to evaluate : 3.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 477 GLN Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 437 THR Chi-restraints excluded: chain E residue 477 GLN Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 504 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 120 MET Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 66 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 151 optimal weight: 0.0870 chunk 97 optimal weight: 3.9990 chunk 225 optimal weight: 0.9980 chunk 165 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 237 optimal weight: 10.0000 chunk 212 optimal weight: 2.9990 chunk 134 optimal weight: 0.6980 chunk 233 optimal weight: 5.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 GLN D 62 ASN D 110 ASN H 62 ASN H 110 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.134059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.107455 restraints weight = 27591.651| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.68 r_work: 0.3052 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 20640 Z= 0.100 Angle : 0.528 11.511 27970 Z= 0.268 Chirality : 0.041 0.168 3170 Planarity : 0.004 0.046 3548 Dihedral : 7.354 92.227 2846 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.97 % Favored : 94.95 % Rotamer: Outliers : 1.70 % Allowed : 12.59 % Favored : 85.71 % 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: 0.89 (0.17), residues: 2516 helix: 2.25 (0.15), residues: 1218 sheet: 0.27 (0.34), residues: 278 loop : -1.47 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 294 HIS 0.002 0.001 HIS E 374 PHE 0.015 0.001 PHE F 236 TYR 0.017 0.001 TYR E 453 ARG 0.005 0.000 ARG C 20 Details of bonding type rmsd hydrogen bonds : bond 0.03558 ( 973) hydrogen bonds : angle 3.98351 ( 2847) covalent geometry : bond 0.00213 (20638) covalent geometry : angle 0.52820 (27970) Misc. bond : bond 0.00012 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 231 time to evaluate : 3.195 Fit side-chains REVERT: A 136 THR cc_start: 0.8610 (OUTLIER) cc_final: 0.8321 (m) REVERT: B 16 GLU cc_start: 0.6350 (OUTLIER) cc_final: 0.6131 (pt0) REVERT: B 119 ASP cc_start: 0.8611 (t70) cc_final: 0.7863 (t0) REVERT: B 158 MET cc_start: 0.9173 (ttp) cc_final: 0.8738 (ttm) REVERT: D 66 MET cc_start: 0.7528 (tpp) cc_final: 0.7090 (ttm) REVERT: D 189 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7916 (mp) REVERT: C 51 MET cc_start: 0.9053 (mtt) cc_final: 0.8817 (mtt) REVERT: E 136 THR cc_start: 0.8624 (OUTLIER) cc_final: 0.8332 (m) REVERT: F 119 ASP cc_start: 0.8611 (t70) cc_final: 0.7863 (t0) REVERT: F 158 MET cc_start: 0.9143 (ttp) cc_final: 0.8706 (ttm) REVERT: H 66 MET cc_start: 0.7519 (tpp) cc_final: 0.7081 (ttm) REVERT: H 189 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7932 (mp) REVERT: G 51 MET cc_start: 0.9042 (mtt) cc_final: 0.8809 (mtt) outliers start: 38 outliers final: 29 residues processed: 254 average time/residue: 0.4050 time to fit residues: 167.6198 Evaluate side-chains 254 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 220 time to evaluate : 2.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 437 THR Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 504 THR Chi-restraints excluded: chain H residue 120 MET Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 66 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 147 optimal weight: 5.9990 chunk 206 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 195 optimal weight: 0.9990 chunk 167 optimal weight: 6.9990 chunk 201 optimal weight: 2.9990 chunk 140 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 105 optimal weight: 7.9990 chunk 238 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 GLN D 62 ASN D 110 ASN E 477 GLN H 62 ASN H 110 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.130675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.103875 restraints weight = 27785.152| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.67 r_work: 0.2998 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 20640 Z= 0.150 Angle : 0.577 11.315 27970 Z= 0.294 Chirality : 0.043 0.165 3170 Planarity : 0.005 0.049 3548 Dihedral : 7.554 92.193 2846 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.92 % Favored : 94.00 % Rotamer: Outliers : 1.70 % Allowed : 12.81 % Favored : 85.48 % 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: 0.81 (0.17), residues: 2516 helix: 2.20 (0.15), residues: 1218 sheet: 0.22 (0.34), residues: 280 loop : -1.54 (0.19), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 142 HIS 0.003 0.001 HIS E 258 PHE 0.019 0.001 PHE A 256 TYR 0.017 0.001 TYR F 510 ARG 0.006 0.000 ARG G 20 Details of bonding type rmsd hydrogen bonds : bond 0.04688 ( 973) hydrogen bonds : angle 4.05265 ( 2847) covalent geometry : bond 0.00360 (20638) covalent geometry : angle 0.57710 (27970) Misc. bond : bond 0.00018 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 217 time to evaluate : 4.990 Fit side-chains REVERT: A 136 THR cc_start: 0.8718 (OUTLIER) cc_final: 0.8424 (m) REVERT: B 119 ASP cc_start: 0.8699 (t70) cc_final: 0.7924 (t0) REVERT: B 158 MET cc_start: 0.9172 (ttp) cc_final: 0.8799 (ttm) REVERT: D 189 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7976 (mp) REVERT: C 51 MET cc_start: 0.9047 (mtt) cc_final: 0.8787 (mtt) REVERT: E 136 THR cc_start: 0.8717 (OUTLIER) cc_final: 0.8432 (m) REVERT: F 16 GLU cc_start: 0.6410 (OUTLIER) cc_final: 0.6085 (pt0) REVERT: F 119 ASP cc_start: 0.8658 (t70) cc_final: 0.7919 (t0) REVERT: F 158 MET cc_start: 0.9143 (ttp) cc_final: 0.8762 (ttm) REVERT: H 189 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7975 (mp) REVERT: G 51 MET cc_start: 0.9049 (mtt) cc_final: 0.8792 (mtt) outliers start: 38 outliers final: 32 residues processed: 243 average time/residue: 0.4799 time to fit residues: 194.4664 Evaluate side-chains 253 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 216 time to evaluate : 3.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 437 THR Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 504 THR Chi-restraints excluded: chain H residue 120 MET Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 66 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 79 optimal weight: 5.9990 chunk 178 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 157 optimal weight: 0.8980 chunk 108 optimal weight: 0.0980 chunk 20 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 228 optimal weight: 6.9990 chunk 155 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 62 ASN D 110 ASN H 62 ASN H 110 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.133832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.107156 restraints weight = 27724.455| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.76 r_work: 0.3027 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 20640 Z= 0.102 Angle : 0.527 10.270 27970 Z= 0.268 Chirality : 0.041 0.167 3170 Planarity : 0.004 0.048 3548 Dihedral : 7.308 91.571 2846 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.85 % Favored : 95.07 % Rotamer: Outliers : 1.57 % Allowed : 12.95 % Favored : 85.48 % 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: 0.95 (0.17), residues: 2516 helix: 2.29 (0.15), residues: 1220 sheet: 0.29 (0.34), residues: 276 loop : -1.44 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 294 HIS 0.002 0.001 HIS A 374 PHE 0.015 0.001 PHE B 236 TYR 0.016 0.001 TYR A 453 ARG 0.005 0.000 ARG C 20 Details of bonding type rmsd hydrogen bonds : bond 0.03627 ( 973) hydrogen bonds : angle 3.96779 ( 2847) covalent geometry : bond 0.00219 (20638) covalent geometry : angle 0.52658 (27970) Misc. bond : bond 0.00011 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12591.47 seconds wall clock time: 228 minutes 45.62 seconds (13725.62 seconds total)