Starting phenix.real_space_refine on Tue May 20 14:05:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iam_35310/05_2025/8iam_35310.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iam_35310/05_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_35310/05_2025/8iam_35310.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iam_35310/05_2025/8iam_35310.map" model { file = "/net/cci-nas-00/data/ceres_data/8iam_35310/05_2025/8iam_35310.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iam_35310/05_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-5687/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: 15.66, per 1000 atoms: 0.78 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: 5.33 Conformation dependent library (CDL) restraints added in 2.6 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: 2.25 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: 6.23 Time building geometry restraints manager: 6.45 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: 0.10 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 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: 0.130 Set scattering table: 0.180 Process input model: 49.360 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.660 ------------------------------------------------------------------------------- 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 : 2.422 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: 0.2901 time to fit residues: 118.2236 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 : 2.156 ------------------------------------------------------------------------------- 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 = 0.130321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.103826 restraints weight = 27714.018| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 1.64 r_work: 0.2999 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- 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 : 2.203 Fit side-chains REVERT: B 119 ASP cc_start: 0.8535 (t70) cc_final: 0.7800 (t0) REVERT: B 158 MET cc_start: 0.9158 (ttp) cc_final: 0.8794 (ttm) REVERT: D 111 MET cc_start: 0.7969 (mmt) cc_final: 0.7759 (mmt) REVERT: D 137 ASP cc_start: 0.8769 (m-30) cc_final: 0.8552 (m-30) REVERT: C 51 MET cc_start: 0.9041 (mtt) cc_final: 0.8783 (mtt) REVERT: F 119 ASP cc_start: 0.8516 (t70) cc_final: 0.7777 (t0) REVERT: F 158 MET cc_start: 0.9163 (ttp) cc_final: 0.8812 (ttm) REVERT: G 51 MET cc_start: 0.9031 (mtt) cc_final: 0.8762 (mtt) outliers start: 19 outliers final: 12 residues processed: 233 average time/residue: 0.2979 time to fit residues: 110.4649 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 : 2.294 ------------------------------------------------------------------------------- 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: 4.9990 chunk 131 optimal weight: 0.0060 overall best weight: 1.9202 ------------------------------------------------------------------------------- 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 = 0.130073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.103121 restraints weight = 27580.952| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 1.65 r_work: 0.2974 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1185 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 11.433 27970 Z= 0.302 Chirality : 0.043 0.168 3170 Planarity : 0.005 0.054 3548 Dihedral : 7.621 98.325 2846 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.21 % Favored : 94.63 % Rotamer: Outliers : 1.61 % Allowed : 8.56 % 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: 0.25 (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 0.003 0.001 HIS B 142 PHE 0.019 0.001 PHE E 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 0.05178 ( 973) hydrogen bonds : angle 4.29016 ( 2847) covalent geometry : bond 0.00359 (20638) covalent geometry : angle 0.58616 (27970) Misc. bond : bond 0.00012 ( 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 261 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 225 time to evaluate : 2.161 Fit side-chains REVERT: A 477 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.8068 (tm-30) REVERT: B 119 ASP cc_start: 0.8575 (t70) cc_final: 0.7846 (t0) REVERT: B 158 MET cc_start: 0.9186 (ttp) cc_final: 0.8849 (ttm) REVERT: D 111 MET cc_start: 0.8112 (mmt) cc_final: 0.7910 (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: 0.8073 (tm-30) REVERT: F 119 ASP cc_start: 0.8572 (t70) cc_final: 0.7838 (t0) REVERT: F 158 MET cc_start: 0.9170 (ttp) cc_final: 0.8834 (ttm) REVERT: G 51 MET cc_start: 0.9027 (mtt) cc_final: 0.8782 (mtt) outliers start: 36 outliers final: 18 residues processed: 242 average time/residue: 0.2843 time to fit residues: 109.4761 Evaluate side-chains 234 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 214 time to evaluate : 2.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 477 GLN Chi-restraints excluded: chain A residue 522 VAL 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 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 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 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: 0.8980 chunk 127 optimal weight: 3.9990 chunk 237 optimal weight: 10.0000 chunk 176 optimal weight: 1.9990 chunk 182 optimal weight: 9.9990 chunk 226 optimal weight: 2.9990 chunk 208 optimal weight: 0.6980 chunk 141 optimal weight: 8.9990 chunk 96 optimal weight: 3.9990 chunk 218 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 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 90 HIS D 62 ASN F 90 HIS H 62 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.130453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.103215 restraints weight = 27587.214| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.68 r_work: 0.2947 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 20640 Z= 0.160 Angle : 0.592 12.218 27970 Z= 0.304 Chirality : 0.044 0.244 3170 Planarity : 0.005 0.052 3548 Dihedral : 7.661 96.305 2846 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.48 % Favored : 94.36 % Rotamer: Outliers : 1.66 % Allowed : 10.44 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.17), residues: 2516 helix: 1.85 (0.15), residues: 1214 sheet: -0.04 (0.33), residues: 274 loop : -1.77 (0.18), residues: 1028 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 E 256 TYR 0.017 0.001 TYR B 510 ARG 0.003 0.000 ARG G 20 Details of bonding type rmsd hydrogen bonds : bond 0.05153 ( 973) hydrogen bonds : angle 4.24372 ( 2847) covalent geometry : bond 0.00384 (20638) covalent geometry : angle 0.59227 (27970) Misc. bond : bond 0.00016 ( 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 268 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 231 time to evaluate : 2.117 Fit side-chains REVERT: A 426 SER cc_start: 0.7679 (t) cc_final: 0.7437 (p) REVERT: A 533 MET cc_start: 0.7469 (mtm) cc_final: 0.7255 (mtm) REVERT: B 119 ASP cc_start: 0.8640 (t70) cc_final: 0.7888 (t0) REVERT: B 158 MET cc_start: 0.9175 (ttp) cc_final: 0.8837 (ttm) REVERT: C 51 MET cc_start: 0.9056 (mtt) cc_final: 0.8794 (mtt) REVERT: E 426 SER cc_start: 0.7640 (t) cc_final: 0.7392 (p) REVERT: E 533 MET cc_start: 0.7458 (mtm) cc_final: 0.7245 (mtm) REVERT: F 119 ASP cc_start: 0.8644 (t70) cc_final: 0.7894 (t0) REVERT: F 158 MET cc_start: 0.9169 (ttp) cc_final: 0.8821 (ttm) REVERT: G 51 MET cc_start: 0.9052 (mtt) cc_final: 0.8788 (mtt) outliers start: 37 outliers final: 20 residues processed: 249 average time/residue: 0.2811 time to fit residues: 111.3804 Evaluate side-chains 240 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 220 time to evaluate : 2.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 356 ASP 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 36 GLU Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 524 SER Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 187 SER 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 120 MET Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 189 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 112 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 161 optimal weight: 9.9990 chunk 14 optimal weight: 0.9980 chunk 94 optimal weight: 0.0970 chunk 10 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 HIS D 62 ASN F 90 HIS H 62 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.131711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.104400 restraints weight = 27551.660| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.70 r_work: 0.3002 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 20640 Z= 0.125 Angle : 0.551 11.185 27970 Z= 0.283 Chirality : 0.042 0.175 3170 Planarity : 0.005 0.049 3548 Dihedral : 7.524 95.326 2846 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.25 % Favored : 94.67 % Rotamer: Outliers : 1.39 % Allowed : 11.20 % Favored : 87.41 % 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: 0.50 (0.17), residues: 2516 helix: 1.98 (0.15), residues: 1216 sheet: -0.11 (0.33), residues: 288 loop : -1.68 (0.18), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 294 HIS 0.003 0.001 HIS B 90 PHE 0.016 0.001 PHE E 256 TYR 0.014 0.001 TYR F 510 ARG 0.004 0.000 ARG G 20 Details of bonding type rmsd hydrogen bonds : bond 0.04436 ( 973) hydrogen bonds : angle 4.13919 ( 2847) covalent geometry : bond 0.00287 (20638) covalent geometry : angle 0.55108 (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 265 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 234 time to evaluate : 2.460 Fit side-chains REVERT: A 309 LEU cc_start: 0.8079 (pp) cc_final: 0.7733 (mt) REVERT: A 477 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.8219 (tt0) REVERT: B 16 GLU cc_start: 0.6417 (OUTLIER) cc_final: 0.6182 (pt0) REVERT: B 119 ASP cc_start: 0.8594 (t70) cc_final: 0.7844 (t0) REVERT: B 158 MET cc_start: 0.9178 (ttp) cc_final: 0.8803 (ttm) REVERT: C 51 MET cc_start: 0.9032 (mtt) cc_final: 0.8769 (mtt) REVERT: E 309 LEU cc_start: 0.8084 (pp) cc_final: 0.7738 (mt) REVERT: E 477 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.8221 (tt0) REVERT: F 16 GLU cc_start: 0.6403 (OUTLIER) cc_final: 0.6191 (pt0) REVERT: F 119 ASP cc_start: 0.8608 (t70) cc_final: 0.7852 (t0) REVERT: F 158 MET cc_start: 0.9165 (ttp) cc_final: 0.8785 (ttm) REVERT: G 51 MET cc_start: 0.9032 (mtt) cc_final: 0.8765 (mtt) outliers start: 31 outliers final: 19 residues processed: 255 average time/residue: 0.3078 time to fit residues: 125.0011 Evaluate side-chains 243 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 220 time to evaluate : 2.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 199 THR Chi-restraints excluded: chain B residue 356 ASP Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 189 LEU 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 187 SER Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 356 ASP 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 66 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 35 optimal weight: 5.9990 chunk 167 optimal weight: 8.9990 chunk 79 optimal weight: 7.9990 chunk 203 optimal weight: 7.9990 chunk 173 optimal weight: 4.9990 chunk 211 optimal weight: 0.0670 chunk 14 optimal weight: 6.9990 chunk 43 optimal weight: 8.9990 chunk 176 optimal weight: 0.8980 chunk 108 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 overall best weight: 2.9924 ------------------------------------------------------------------------------- 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 D 110 ASN F 90 HIS F 96 HIS H 62 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.127700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.100631 restraints weight = 27624.488| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.68 r_work: 0.2945 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 20640 Z= 0.210 Angle : 0.644 13.017 27970 Z= 0.328 Chirality : 0.045 0.176 3170 Planarity : 0.005 0.049 3548 Dihedral : 7.881 94.154 2846 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.44 % Favored : 93.48 % Rotamer: Outliers : 2.24 % Allowed : 11.47 % 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: 0.35 (0.17), residues: 2516 helix: 1.91 (0.15), residues: 1204 sheet: -0.23 (0.32), residues: 288 loop : -1.77 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 142 HIS 0.005 0.001 HIS E 258 PHE 0.022 0.002 PHE A 256 TYR 0.020 0.002 TYR B 510 ARG 0.004 0.000 ARG G 20 Details of bonding type rmsd hydrogen bonds : bond 0.05890 ( 973) hydrogen bonds : angle 4.27380 ( 2847) covalent geometry : bond 0.00515 (20638) covalent geometry : angle 0.64368 (27970) Misc. bond : bond 0.00019 ( 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 269 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 219 time to evaluate : 2.321 Fit side-chains REVERT: A 477 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.8194 (tt0) REVERT: B 119 ASP cc_start: 0.8707 (t70) cc_final: 0.7960 (t0) REVERT: B 158 MET cc_start: 0.9166 (ttp) cc_final: 0.8822 (ttm) REVERT: D 189 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7957 (mp) REVERT: E 477 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.8190 (tt0) REVERT: F 119 ASP cc_start: 0.8695 (t70) cc_final: 0.7951 (t0) REVERT: F 158 MET cc_start: 0.9151 (ttp) cc_final: 0.8807 (ttm) outliers start: 50 outliers final: 39 residues processed: 249 average time/residue: 0.2894 time to fit residues: 115.1732 Evaluate side-chains 261 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 219 time to evaluate : 2.035 ------------------------------------------------------------------------------- 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 A residue 524 SER Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 53 VAL 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 356 ASP Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 504 THR 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 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 E residue 524 SER 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 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 356 ASP 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 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: 5.9990 chunk 44 optimal weight: 1.9990 chunk 187 optimal weight: 3.9990 chunk 129 optimal weight: 6.9990 chunk 229 optimal weight: 6.9990 chunk 203 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 239 optimal weight: 10.0000 chunk 173 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.127409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.100487 restraints weight = 27618.888| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 1.67 r_work: 0.2948 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 20640 Z= 0.217 Angle : 0.640 12.958 27970 Z= 0.329 Chirality : 0.046 0.177 3170 Planarity : 0.005 0.049 3548 Dihedral : 8.002 93.175 2846 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.32 % Favored : 93.60 % Rotamer: Outliers : 2.42 % Allowed : 12.28 % Favored : 85.30 % 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: 0.25 (0.17), residues: 2516 helix: 1.81 (0.15), residues: 1206 sheet: -0.18 (0.34), residues: 274 loop : -1.81 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 142 HIS 0.005 0.001 HIS B 142 PHE 0.022 0.002 PHE A 256 TYR 0.020 0.002 TYR B 510 ARG 0.003 0.000 ARG G 20 Details of bonding type rmsd hydrogen bonds : bond 0.05863 ( 973) hydrogen bonds : angle 4.30619 ( 2847) covalent geometry : bond 0.00535 (20638) covalent geometry : angle 0.63954 (27970) Misc. bond : bond 0.00021 ( 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 271 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 217 time to evaluate : 2.487 Fit side-chains REVERT: A 136 THR cc_start: 0.8729 (OUTLIER) cc_final: 0.8445 (m) REVERT: A 477 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.8209 (tt0) REVERT: A 533 MET cc_start: 0.7452 (mtm) cc_final: 0.7090 (mtm) REVERT: B 158 MET cc_start: 0.9167 (ttp) cc_final: 0.8854 (ttm) REVERT: D 189 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7954 (mp) REVERT: E 136 THR cc_start: 0.8726 (OUTLIER) cc_final: 0.8438 (m) REVERT: E 477 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.8212 (tt0) REVERT: E 533 MET cc_start: 0.7499 (mtm) cc_final: 0.7153 (mtm) REVERT: F 158 MET cc_start: 0.9153 (ttp) cc_final: 0.8836 (ttm) outliers start: 54 outliers final: 38 residues processed: 249 average time/residue: 0.2986 time to fit residues: 118.5499 Evaluate side-chains 260 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 217 time to evaluate : 2.253 ------------------------------------------------------------------------------- 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 A residue 524 SER Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 53 VAL 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 356 ASP Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 388 ASP 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 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 E residue 524 SER 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 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 356 ASP 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 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: 4.9990 chunk 233 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 242 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 202 optimal weight: 0.8980 chunk 211 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 overall best weight: 2.3784 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.129178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.102177 restraints weight = 27802.856| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.69 r_work: 0.2966 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20640 Z= 0.173 Angle : 0.608 12.347 27970 Z= 0.310 Chirality : 0.044 0.169 3170 Planarity : 0.005 0.050 3548 Dihedral : 7.868 93.020 2846 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.92 % Favored : 94.00 % Rotamer: Outliers : 2.20 % Allowed : 12.86 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.17), residues: 2516 helix: 1.83 (0.15), residues: 1216 sheet: -0.37 (0.32), residues: 292 loop : -1.75 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 294 HIS 0.003 0.001 HIS B 142 PHE 0.020 0.002 PHE E 256 TYR 0.018 0.001 TYR F 510 ARG 0.002 0.000 ARG G 20 Details of bonding type rmsd hydrogen bonds : bond 0.05274 ( 973) hydrogen bonds : angle 4.24726 ( 2847) covalent geometry : bond 0.00418 (20638) covalent geometry : angle 0.60780 (27970) Misc. bond : bond 0.00020 ( 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 269 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 220 time to evaluate : 2.361 Fit side-chains REVERT: A 136 THR cc_start: 0.8696 (OUTLIER) cc_final: 0.8429 (m) REVERT: A 477 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.8255 (tt0) REVERT: B 158 MET cc_start: 0.9165 (ttp) cc_final: 0.8828 (ttm) REVERT: E 136 THR cc_start: 0.8699 (OUTLIER) cc_final: 0.8420 (m) REVERT: E 477 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.8262 (tt0) REVERT: F 16 GLU cc_start: 0.6408 (OUTLIER) cc_final: 0.6187 (pt0) REVERT: F 158 MET cc_start: 0.9145 (ttp) cc_final: 0.8812 (ttm) REVERT: H 137 ASP cc_start: 0.8632 (OUTLIER) cc_final: 0.8251 (m-30) outliers start: 49 outliers final: 38 residues processed: 252 average time/residue: 0.3004 time to fit residues: 120.8780 Evaluate side-chains 257 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 213 time to evaluate : 2.281 ------------------------------------------------------------------------------- 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 A residue 524 SER Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 53 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 388 ASP 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 E residue 524 SER 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 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 356 ASP 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 137 ASP Chi-restraints excluded: chain H residue 152 THR 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: 10.0000 chunk 97 optimal weight: 2.9990 chunk 225 optimal weight: 0.8980 chunk 165 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 76 optimal weight: 0.0670 chunk 10 optimal weight: 3.9990 chunk 237 optimal weight: 7.9990 chunk 212 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 233 optimal weight: 5.9990 overall best weight: 1.3924 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.130138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.103199 restraints weight = 27658.559| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.66 r_work: 0.3008 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 20640 Z= 0.126 Angle : 0.557 11.305 27970 Z= 0.286 Chirality : 0.042 0.165 3170 Planarity : 0.005 0.049 3548 Dihedral : 7.629 92.835 2846 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.37 % Favored : 94.55 % Rotamer: Outliers : 1.66 % Allowed : 13.35 % Favored : 84.99 % 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: 0.54 (0.17), residues: 2516 helix: 1.99 (0.15), residues: 1216 sheet: 0.18 (0.34), residues: 264 loop : -1.68 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 294 HIS 0.002 0.001 HIS F 78 PHE 0.016 0.001 PHE E 256 TYR 0.014 0.001 TYR B 510 ARG 0.002 0.000 ARG G 20 Details of bonding type rmsd hydrogen bonds : bond 0.04384 ( 973) hydrogen bonds : angle 4.14053 ( 2847) covalent geometry : bond 0.00289 (20638) covalent geometry : angle 0.55705 (27970) Misc. bond : bond 0.00015 ( 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 264 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 227 time to evaluate : 2.247 Fit side-chains REVERT: A 136 THR cc_start: 0.8675 (OUTLIER) cc_final: 0.8418 (m) REVERT: A 309 LEU cc_start: 0.8008 (pp) cc_final: 0.7689 (mt) REVERT: A 477 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.8255 (tt0) REVERT: B 119 ASP cc_start: 0.8652 (t70) cc_final: 0.7840 (t0) REVERT: B 158 MET cc_start: 0.9162 (ttp) cc_final: 0.8808 (ttm) REVERT: C 51 MET cc_start: 0.9032 (mtt) cc_final: 0.8767 (mtt) REVERT: E 136 THR cc_start: 0.8679 (OUTLIER) cc_final: 0.8423 (m) REVERT: E 309 LEU cc_start: 0.8019 (pp) cc_final: 0.7699 (mt) REVERT: E 477 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.8261 (tt0) REVERT: F 16 GLU cc_start: 0.6358 (OUTLIER) cc_final: 0.6123 (pt0) REVERT: F 158 MET cc_start: 0.9149 (ttp) cc_final: 0.8792 (ttm) REVERT: H 137 ASP cc_start: 0.8609 (OUTLIER) cc_final: 0.8190 (m-30) REVERT: G 51 MET cc_start: 0.9041 (mtt) cc_final: 0.8777 (mtt) outliers start: 37 outliers final: 28 residues processed: 249 average time/residue: 0.2851 time to fit residues: 113.0525 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 : 2.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 48 LEU 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 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 149 THR 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 356 ASP 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 137 ASP Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 189 LEU 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: 3.9990 chunk 206 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 195 optimal weight: 0.9980 chunk 167 optimal weight: 8.9990 chunk 201 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 105 optimal weight: 7.9990 chunk 238 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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 = 0.3484 r_free = 0.3484 target = 0.130237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.103207 restraints weight = 27639.271| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.69 r_work: 0.2976 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1719 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= 0.155 Angle : 0.593 11.945 27970 Z= 0.301 Chirality : 0.043 0.167 3170 Planarity : 0.005 0.052 3548 Dihedral : 7.669 92.477 2846 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.96 % Favored : 93.96 % Rotamer: Outliers : 1.84 % Allowed : 13.22 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.17), residues: 2516 helix: 1.99 (0.15), residues: 1216 sheet: -0.03 (0.33), residues: 280 loop : -1.69 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 294 HIS 0.003 0.001 HIS E 258 PHE 0.019 0.001 PHE E 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 0.04906 ( 973) hydrogen bonds : angle 4.16804 ( 2847) covalent geometry : bond 0.00369 (20638) covalent geometry : angle 0.59286 (27970) Misc. bond : bond 0.00017 ( 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 262 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 221 time to evaluate : 2.161 Fit side-chains REVERT: A 136 THR cc_start: 0.8701 (OUTLIER) cc_final: 0.8438 (m) REVERT: A 477 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.8252 (tt0) REVERT: B 119 ASP cc_start: 0.8722 (t70) cc_final: 0.7979 (t0) REVERT: B 158 MET cc_start: 0.9154 (ttp) cc_final: 0.8814 (ttm) REVERT: C 51 MET cc_start: 0.9047 (mtt) cc_final: 0.8773 (mtt) REVERT: E 136 THR cc_start: 0.8695 (OUTLIER) cc_final: 0.8450 (m) REVERT: E 477 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.8263 (tt0) REVERT: F 158 MET cc_start: 0.9144 (ttp) cc_final: 0.8805 (ttm) REVERT: H 137 ASP cc_start: 0.8613 (OUTLIER) cc_final: 0.8204 (m-30) REVERT: G 51 MET cc_start: 0.9057 (mtt) cc_final: 0.8795 (mtt) outliers start: 41 outliers final: 36 residues processed: 243 average time/residue: 0.2918 time to fit residues: 113.6065 Evaluate side-chains 262 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 221 time to evaluate : 2.382 ------------------------------------------------------------------------------- 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 A residue 524 SER Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 48 LEU 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 209 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 388 ASP 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 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 E residue 522 VAL Chi-restraints excluded: chain E residue 524 SER Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 119 ASP Chi-restraints excluded: chain F residue 149 THR 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 137 ASP Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 189 LEU 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: 0.0770 chunk 178 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 157 optimal weight: 1.9990 chunk 108 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 228 optimal weight: 7.9990 chunk 155 optimal weight: 0.8980 overall best weight: 0.6738 ------------------------------------------------------------------------------- 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 = 0.3514 r_free = 0.3514 target = 0.132684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.106144 restraints weight = 27680.502| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.67 r_work: 0.3047 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1863 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= 0.103 Angle : 0.540 10.238 27970 Z= 0.273 Chirality : 0.041 0.168 3170 Planarity : 0.005 0.049 3548 Dihedral : 7.361 92.155 2846 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.77 % Favored : 95.15 % Rotamer: Outliers : 1.61 % Allowed : 13.62 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.17), residues: 2516 helix: 2.15 (0.15), residues: 1218 sheet: 0.26 (0.34), residues: 264 loop : -1.50 (0.19), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 294 HIS 0.003 0.001 HIS A 374 PHE 0.015 0.001 PHE F 236 TYR 0.011 0.001 TYR F 510 ARG 0.002 0.000 ARG G 20 Details of bonding type rmsd hydrogen bonds : bond 0.03679 ( 973) hydrogen bonds : angle 4.05605 ( 2847) covalent geometry : bond 0.00217 (20638) covalent geometry : angle 0.53955 (27970) Misc. bond : bond 0.00011 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10402.75 seconds wall clock time: 180 minutes 58.34 seconds (10858.34 seconds total)