Starting phenix.real_space_refine on Fri Jun 5 10:15:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iam_35310/06_2026/8iam_35310.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iam_35310/06_2026/8iam_35310.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iam_35310/06_2026/8iam_35310.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iam_35310/06_2026/8iam_35310.map" model { file = "/net/cci-nas-00/data/ceres_data/8iam_35310/06_2026/8iam_35310.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iam_35310/06_2026/8iam_35310.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/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: {'HIS:plan': 1, 'PHE:plan': 2} 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: 2 Planarities with less than four sites: {'PLP:plan-2': 1} Unresolved non-hydrogen planarities: 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: E, F, H, G Time building chain proxies: 6.61, per 1000 atoms: 0.33 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: 1.69 Conformation dependent library (CDL) restraints added in 934.7 milliseconds 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: 0.76 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: 3.51 Time building geometry restraints manager: 2.28 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=" O4P PLP F 601 " pdb=" P PLP F 601 " ideal model delta sigma weight residual 1.687 1.606 0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" O4P PLP B 601 " pdb=" P PLP B 601 " ideal model delta sigma weight residual 1.687 1.606 0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" C2 PLP B 601 " pdb=" N1 PLP B 601 " ideal model delta sigma weight residual 1.325 1.377 -0.052 2.00e-02 2.50e+03 6.86e+00 ... (remaining 20633 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 27654 2.83 - 5.65: 288 5.65 - 8.48: 23 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: 11530 21.03 - 42.06: 778 42.06 - 63.10: 96 63.10 - 84.13: 16 84.13 - 105.16: 6 Dihedral angle restraints: 12426 sinusoidal: 5026 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 12423 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=" C2 PLP B 601 " 0.017 2.00e-02 2.50e+03 1.12e-01 3.16e+02 pdb=" C2A PLP B 601 " 0.052 2.00e-02 2.50e+03 pdb=" C3 PLP B 601 " -0.074 2.00e-02 2.50e+03 pdb=" C4 PLP B 601 " -0.105 2.00e-02 2.50e+03 pdb=" C4A PLP B 601 " 0.267 2.00e-02 2.50e+03 pdb=" C5 PLP B 601 " -0.050 2.00e-02 2.50e+03 pdb=" C5A PLP B 601 " -0.092 2.00e-02 2.50e+03 pdb=" C6 PLP B 601 " 0.041 2.00e-02 2.50e+03 pdb=" N1 PLP B 601 " 0.075 2.00e-02 2.50e+03 pdb=" O3 PLP B 601 " -0.131 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 PLP F 601 " 0.017 2.00e-02 2.50e+03 1.12e-01 3.15e+02 pdb=" C2A PLP F 601 " 0.052 2.00e-02 2.50e+03 pdb=" C3 PLP F 601 " -0.074 2.00e-02 2.50e+03 pdb=" C4 PLP F 601 " -0.105 2.00e-02 2.50e+03 pdb=" C4A PLP F 601 " 0.267 2.00e-02 2.50e+03 pdb=" C5 PLP F 601 " -0.050 2.00e-02 2.50e+03 pdb=" C5A PLP F 601 " -0.092 2.00e-02 2.50e+03 pdb=" C6 PLP F 601 " 0.041 2.00e-02 2.50e+03 pdb=" N1 PLP F 601 " 0.074 2.00e-02 2.50e+03 pdb=" O3 PLP F 601 " -0.130 2.00e-02 2.50e+03 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 ... (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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'G' } 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: 1.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 20.750 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.110 ------------------------------------------------------------------------------- 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= 0.208 Angle : 0.730 14.137 27970 Z= 0.416 Chirality : 0.047 0.516 3170 Planarity : 0.006 0.112 3548 Dihedral : 13.918 105.161 7662 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.003 0.000 ARG D 92 TYR 0.015 0.001 TYR F 510 PHE 0.019 0.001 PHE G 62 TRP 0.009 0.001 TRP B 294 HIS 0.008 0.001 HIS F 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.21 (20638) covalent geometry : angle 0.73005 / 0.42 (27970) hydrogen bonds : bond 0.16968 / 11.24 ( 973) hydrogen bonds : angle 5.53071 / 3.83 ( 2847) Misc. bond : bond 0.00056 / 0.03 ( 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 : 0.802 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: 0.1345 time to fit residues: 55.1744 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 : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 0.4980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 247 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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 = 0.3505 r_free = 0.3505 target = 0.131880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.105302 restraints weight = 27557.660| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 1.66 r_work: 0.2997 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20640 Z= 0.130 Angle : 0.581 10.014 27970 Z= 0.301 Chirality : 0.042 0.174 3170 Planarity : 0.005 0.058 3548 Dihedral : 7.356 100.984 2852 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.45 % Favored : 94.40 % Rotamer: Outliers : 0.67 % Allowed : 6.41 % Favored : 92.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.17), residues: 2516 helix: 1.70 (0.15), residues: 1214 sheet: -0.11 (0.33), residues: 264 loop : -1.85 (0.18), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 20 TYR 0.015 0.001 TYR F 510 PHE 0.013 0.001 PHE E 256 TRP 0.006 0.001 TRP B 380 HIS 0.003 0.001 HIS B 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (20638) covalent geometry : angle 0.58108 / 0.30 (27970) hydrogen bonds : bond 0.04812 / 3.22 ( 973) hydrogen bonds : angle 4.40008 / 3.03 ( 2847) Misc. bond : bond 0.00040 / 0.02 ( 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 246 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 231 time to evaluate : 0.872 Fit side-chains REVERT: B 119 ASP cc_start: 0.8507 (t70) cc_final: 0.7772 (t0) REVERT: B 158 MET cc_start: 0.9161 (ttp) cc_final: 0.8791 (ttm) REVERT: D 111 MET cc_start: 0.7981 (mmt) cc_final: 0.7780 (mmt) REVERT: D 137 ASP cc_start: 0.8755 (m-30) cc_final: 0.8528 (m-30) REVERT: C 51 MET cc_start: 0.9054 (mtt) cc_final: 0.8798 (mtt) REVERT: F 119 ASP cc_start: 0.8511 (t70) cc_final: 0.7763 (t0) REVERT: F 158 MET cc_start: 0.9161 (ttp) cc_final: 0.8780 (ttm) REVERT: G 51 MET cc_start: 0.9059 (mtt) cc_final: 0.8795 (mtt) outliers start: 15 outliers final: 9 residues processed: 238 average time/residue: 0.1393 time to fit residues: 52.7745 Evaluate side-chains 217 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 208 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 D residue 189 LEU Chi-restraints excluded: chain C residue 36 GLU 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 183 optimal weight: 7.9990 chunk 186 optimal weight: 10.0000 chunk 218 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 211 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 126 optimal weight: 7.9990 chunk 167 optimal weight: 10.0000 chunk 206 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 HIS D 62 ASN F 96 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 = 0.3474 r_free = 0.3474 target = 0.129448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.102368 restraints weight = 27915.140| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.67 r_work: 0.2959 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 20640 Z= 0.198 Angle : 0.628 11.724 27970 Z= 0.324 Chirality : 0.045 0.172 3170 Planarity : 0.005 0.056 3548 Dihedral : 7.482 98.337 2852 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.68 % Favored : 94.16 % Rotamer: Outliers : 1.52 % Allowed : 8.78 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.17), residues: 2516 helix: 1.71 (0.15), residues: 1212 sheet: -0.24 (0.32), residues: 284 loop : -1.85 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 20 TYR 0.019 0.002 TYR B 510 PHE 0.021 0.002 PHE A 256 TRP 0.010 0.002 TRP H 142 HIS 0.005 0.001 HIS E 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.20 (20638) covalent geometry : angle 0.62828 / 0.32 (27970) hydrogen bonds : bond 0.05802 / 3.88 ( 973) hydrogen bonds : angle 4.37496 / 3.02 ( 2847) Misc. bond : bond 0.00107 / 0.06 ( 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 254 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 220 time to evaluate : 0.775 Fit side-chains REVERT: A 477 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.8073 (tm-30) REVERT: B 119 ASP cc_start: 0.8619 (t70) cc_final: 0.7876 (t0) REVERT: C 51 MET cc_start: 0.9034 (mtt) cc_final: 0.8767 (mtt) REVERT: E 477 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8071 (tm-30) REVERT: E 533 MET cc_start: 0.7596 (mtm) cc_final: 0.7386 (mtm) REVERT: F 119 ASP cc_start: 0.8595 (t70) cc_final: 0.7843 (t0) outliers start: 34 outliers final: 19 residues processed: 236 average time/residue: 0.1371 time to fit residues: 51.7848 Evaluate side-chains 232 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 211 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 477 GLN 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 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 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 F residue 356 ASP Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain G residue 13 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 103 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 184 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 153 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 E 375 GLN 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 = 0.3479 r_free = 0.3479 target = 0.129841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.102520 restraints weight = 27726.778| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.68 r_work: 0.2955 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 20640 Z= 0.174 Angle : 0.608 12.289 27970 Z= 0.312 Chirality : 0.044 0.249 3170 Planarity : 0.005 0.052 3548 Dihedral : 7.483 96.444 2852 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.60 % Favored : 94.24 % Rotamer: Outliers : 1.79 % Allowed : 10.26 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.17), residues: 2516 helix: 1.77 (0.15), residues: 1210 sheet: -0.05 (0.33), residues: 270 loop : -1.82 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 437 TYR 0.018 0.001 TYR B 510 PHE 0.019 0.002 PHE E 256 TRP 0.010 0.001 TRP D 142 HIS 0.004 0.001 HIS F 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.17 (20638) covalent geometry : angle 0.60790 / 0.31 (27970) hydrogen bonds : bond 0.05412 / 3.61 ( 973) hydrogen bonds : angle 4.29398 / 2.96 ( 2847) Misc. bond : bond 0.00089 / 0.05 ( 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 269 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 229 time to evaluate : 0.752 Fit side-chains REVERT: B 119 ASP cc_start: 0.8650 (t70) cc_final: 0.7869 (t0) REVERT: B 158 MET cc_start: 0.9166 (ttp) cc_final: 0.8848 (ttm) REVERT: C 51 MET cc_start: 0.9036 (mtt) cc_final: 0.8755 (mtt) REVERT: F 119 ASP cc_start: 0.8633 (t70) cc_final: 0.7851 (t0) REVERT: F 158 MET cc_start: 0.9166 (ttp) cc_final: 0.8850 (ttm) outliers start: 40 outliers final: 22 residues processed: 248 average time/residue: 0.1386 time to fit residues: 55.0292 Evaluate side-chains 244 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 222 time to evaluate : 0.815 ------------------------------------------------------------------------------- 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 183 VAL Chi-restraints excluded: chain B residue 342 THR 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 C residue 13 THR Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain E residue 124 THR 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 149 THR 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 G residue 13 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 91 optimal weight: 5.9990 chunk 228 optimal weight: 5.9990 chunk 157 optimal weight: 0.9980 chunk 237 optimal weight: 4.9990 chunk 96 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 2 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 HIS B 96 HIS D 62 ASN F 90 HIS F 96 HIS H 62 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.130216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.102901 restraints weight = 27508.986| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 1.69 r_work: 0.2977 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 20640 Z= 0.151 Angle : 0.579 12.056 27970 Z= 0.298 Chirality : 0.043 0.181 3170 Planarity : 0.005 0.050 3548 Dihedral : 7.406 95.272 2852 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.56 % Favored : 94.32 % Rotamer: Outliers : 1.97 % Allowed : 10.80 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.17), residues: 2516 helix: 1.87 (0.15), residues: 1216 sheet: -0.13 (0.33), residues: 284 loop : -1.76 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 20 TYR 0.016 0.001 TYR B 510 PHE 0.018 0.001 PHE A 256 TRP 0.009 0.001 TRP D 142 HIS 0.004 0.001 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 (20638) covalent geometry : angle 0.57863 / 0.30 (27970) hydrogen bonds : bond 0.04962 / 3.31 ( 973) hydrogen bonds : angle 4.21382 / 2.91 ( 2847) Misc. bond : bond 0.00073 / 0.04 ( 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 277 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 233 time to evaluate : 0.692 Fit side-chains REVERT: A 426 SER cc_start: 0.7671 (t) cc_final: 0.7424 (p) REVERT: A 477 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8195 (tt0) REVERT: A 533 MET cc_start: 0.7554 (mtm) cc_final: 0.7247 (mtm) REVERT: B 119 ASP cc_start: 0.8674 (t70) cc_final: 0.7876 (t0) REVERT: B 158 MET cc_start: 0.9180 (ttp) cc_final: 0.8828 (ttm) REVERT: C 51 MET cc_start: 0.9028 (mtt) cc_final: 0.8759 (mtt) REVERT: E 426 SER cc_start: 0.7662 (t) cc_final: 0.7413 (p) REVERT: E 477 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8193 (tt0) REVERT: F 119 ASP cc_start: 0.8663 (t70) cc_final: 0.7859 (t0) REVERT: F 158 MET cc_start: 0.9152 (ttp) cc_final: 0.8810 (ttm) REVERT: G 51 MET cc_start: 0.9037 (mtt) cc_final: 0.8767 (mtt) outliers start: 44 outliers final: 28 residues processed: 260 average time/residue: 0.1370 time to fit residues: 57.3276 Evaluate side-chains 251 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 221 time to evaluate : 0.897 ------------------------------------------------------------------------------- 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 A residue 524 SER Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 53 VAL 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 D residue 82 LEU Chi-restraints excluded: chain D residue 152 THR 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 136 THR Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 477 GLN Chi-restraints excluded: chain E residue 524 SER Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 120 MET Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 66 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 95 optimal weight: 0.9990 chunk 27 optimal weight: 8.9990 chunk 151 optimal weight: 8.9990 chunk 181 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 189 optimal weight: 6.9990 chunk 153 optimal weight: 5.9990 chunk 193 optimal weight: 0.9990 chunk 167 optimal weight: 1.9990 chunk 210 optimal weight: 3.9990 chunk 213 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 HIS D 62 ASN F 96 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 = 0.3482 r_free = 0.3482 target = 0.130018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.103100 restraints weight = 27497.825| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 1.67 r_work: 0.2993 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20640 Z= 0.143 Angle : 0.575 11.814 27970 Z= 0.293 Chirality : 0.043 0.165 3170 Planarity : 0.005 0.048 3548 Dihedral : 7.366 94.509 2852 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.76 % Favored : 94.16 % Rotamer: Outliers : 2.24 % Allowed : 11.11 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.17), residues: 2516 helix: 1.93 (0.15), residues: 1216 sheet: 0.04 (0.34), residues: 274 loop : -1.69 (0.18), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 20 TYR 0.016 0.001 TYR F 510 PHE 0.018 0.001 PHE A 256 TRP 0.009 0.001 TRP D 142 HIS 0.004 0.001 HIS F 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 (20638) covalent geometry : angle 0.57460 / 0.29 (27970) hydrogen bonds : bond 0.04795 / 3.20 ( 973) hydrogen bonds : angle 4.17566 / 2.89 ( 2847) Misc. bond : bond 0.00067 / 0.04 ( 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 279 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 229 time to evaluate : 0.825 Fit side-chains REVERT: A 426 SER cc_start: 0.7657 (t) cc_final: 0.7413 (p) REVERT: A 477 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.8223 (tt0) REVERT: A 533 MET cc_start: 0.7304 (mtm) cc_final: 0.6969 (mtm) REVERT: B 119 ASP cc_start: 0.8672 (t70) cc_final: 0.7873 (t0) REVERT: B 158 MET cc_start: 0.9170 (ttp) cc_final: 0.8829 (ttm) REVERT: D 189 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.8037 (mp) REVERT: C 51 MET cc_start: 0.9025 (mtt) cc_final: 0.8755 (mtt) REVERT: E 426 SER cc_start: 0.7647 (t) cc_final: 0.7399 (p) REVERT: E 477 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.8220 (tt0) REVERT: F 119 ASP cc_start: 0.8665 (t70) cc_final: 0.7861 (t0) REVERT: F 158 MET cc_start: 0.9163 (ttp) cc_final: 0.8803 (ttm) REVERT: H 189 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.8035 (mp) REVERT: G 51 MET cc_start: 0.9032 (mtt) cc_final: 0.8764 (mtt) outliers start: 50 outliers final: 38 residues processed: 261 average time/residue: 0.1359 time to fit residues: 57.0156 Evaluate side-chains 264 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 222 time to evaluate : 0.783 ------------------------------------------------------------------------------- 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 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 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 149 THR Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 504 THR 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 H residue 198 ILE Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 66 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 160 optimal weight: 8.9990 chunk 69 optimal weight: 0.5980 chunk 111 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 chunk 235 optimal weight: 7.9990 chunk 214 optimal weight: 0.2980 chunk 135 optimal weight: 5.9990 chunk 147 optimal weight: 5.9990 chunk 169 optimal weight: 20.0000 chunk 209 optimal weight: 3.9990 chunk 198 optimal weight: 7.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 HIS D 62 ASN F 96 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 = 0.3441 r_free = 0.3441 target = 0.126843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.099722 restraints weight = 27816.186| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.68 r_work: 0.2916 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 20640 Z= 0.229 Angle : 0.653 13.241 27970 Z= 0.334 Chirality : 0.046 0.180 3170 Planarity : 0.005 0.050 3548 Dihedral : 7.693 93.473 2852 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.52 % Favored : 93.40 % Rotamer: Outliers : 2.42 % Allowed : 11.69 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.17), residues: 2516 helix: 1.77 (0.15), residues: 1218 sheet: -0.33 (0.33), residues: 288 loop : -1.77 (0.18), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 20 TYR 0.020 0.002 TYR B 510 PHE 0.022 0.002 PHE A 256 TRP 0.012 0.002 TRP D 142 HIS 0.004 0.001 HIS E 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.23 (20638) covalent geometry : angle 0.65251 / 0.33 (27970) hydrogen bonds : bond 0.06028 / 4.02 ( 973) hydrogen bonds : angle 4.30924 / 2.98 ( 2847) Misc. bond : bond 0.00091 / 0.05 ( 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 273 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 219 time to evaluate : 0.856 Fit side-chains REVERT: A 477 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.8204 (tt0) REVERT: A 533 MET cc_start: 0.7413 (mtm) cc_final: 0.7146 (mtm) REVERT: D 189 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.8052 (mp) REVERT: E 477 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.8197 (tt0) REVERT: F 158 MET cc_start: 0.9163 (ttp) cc_final: 0.8862 (ttm) REVERT: H 137 ASP cc_start: 0.8712 (OUTLIER) cc_final: 0.8356 (m-30) REVERT: H 189 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.8018 (mp) outliers start: 54 outliers final: 45 residues processed: 253 average time/residue: 0.1337 time to fit residues: 54.3748 Evaluate side-chains 267 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 217 time to evaluate : 0.800 ------------------------------------------------------------------------------- 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 522 VAL Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain B residue 12 LEU 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 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 D residue 198 ILE 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 12 LEU 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 149 THR Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 342 THR 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 H residue 189 LEU Chi-restraints excluded: chain H residue 198 ILE Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 66 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 58 optimal weight: 7.9990 chunk 173 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 179 optimal weight: 5.9990 chunk 209 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 174 optimal weight: 0.9990 chunk 218 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 HIS D 62 ASN F 96 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 = 0.3473 r_free = 0.3473 target = 0.129313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.102349 restraints weight = 27678.187| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.69 r_work: 0.2963 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 20640 Z= 0.154 Angle : 0.591 12.162 27970 Z= 0.302 Chirality : 0.043 0.166 3170 Planarity : 0.005 0.047 3548 Dihedral : 7.478 93.232 2852 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.56 % Favored : 94.36 % Rotamer: Outliers : 2.42 % Allowed : 12.50 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.17), residues: 2516 helix: 1.88 (0.15), residues: 1216 sheet: -0.11 (0.34), residues: 274 loop : -1.73 (0.18), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 20 TYR 0.017 0.001 TYR F 510 PHE 0.019 0.001 PHE A 256 TRP 0.010 0.001 TRP F 294 HIS 0.004 0.001 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.15 (20638) covalent geometry : angle 0.59090 / 0.30 (27970) hydrogen bonds : bond 0.05015 / 3.35 ( 973) hydrogen bonds : angle 4.21311 / 2.91 ( 2847) Misc. bond : bond 0.00076 / 0.04 ( 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 279 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 225 time to evaluate : 0.542 Fit side-chains REVERT: A 136 THR cc_start: 0.8715 (OUTLIER) cc_final: 0.8441 (m) REVERT: A 426 SER cc_start: 0.7685 (t) cc_final: 0.7429 (p) REVERT: A 477 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.8232 (tt0) REVERT: A 533 MET cc_start: 0.7264 (mtm) cc_final: 0.7000 (mtm) REVERT: D 189 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.8046 (mp) REVERT: C 51 MET cc_start: 0.9045 (mtt) cc_final: 0.8768 (mtt) REVERT: E 136 THR cc_start: 0.8714 (OUTLIER) cc_final: 0.8441 (m) REVERT: E 477 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.8219 (tt0) REVERT: F 158 MET cc_start: 0.9161 (ttp) cc_final: 0.8802 (ttm) REVERT: H 189 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.8050 (mp) REVERT: G 51 MET cc_start: 0.9046 (mtt) cc_final: 0.8787 (mtt) outliers start: 54 outliers final: 40 residues processed: 258 average time/residue: 0.1351 time to fit residues: 55.9784 Evaluate side-chains 268 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 222 time to evaluate : 0.800 ------------------------------------------------------------------------------- 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 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 361 MET Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 437 THR Chi-restraints excluded: chain E residue 477 GLN Chi-restraints excluded: chain E residue 524 SER Chi-restraints excluded: chain F residue 12 LEU 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 149 THR Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 504 THR Chi-restraints excluded: chain H residue 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 H residue 198 ILE 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 183 optimal weight: 3.9990 chunk 104 optimal weight: 8.9990 chunk 247 optimal weight: 5.9990 chunk 163 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 chunk 241 optimal weight: 2.9990 chunk 190 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 151 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 HIS D 62 ASN F 96 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 = 0.3462 r_free = 0.3462 target = 0.128487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.101414 restraints weight = 27440.054| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 1.67 r_work: 0.2962 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20640 Z= 0.183 Angle : 0.614 12.692 27970 Z= 0.315 Chirality : 0.044 0.170 3170 Planarity : 0.005 0.049 3548 Dihedral : 7.524 92.760 2852 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.36 % Favored : 93.56 % Rotamer: Outliers : 2.55 % Allowed : 12.28 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.17), residues: 2516 helix: 1.85 (0.15), residues: 1216 sheet: -0.33 (0.33), residues: 288 loop : -1.77 (0.18), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 20 TYR 0.018 0.001 TYR F 510 PHE 0.020 0.002 PHE A 256 TRP 0.010 0.001 TRP F 294 HIS 0.004 0.001 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.18 (20638) covalent geometry : angle 0.61372 / 0.31 (27970) hydrogen bonds : bond 0.05430 / 3.63 ( 973) hydrogen bonds : angle 4.25009 / 2.94 ( 2847) Misc. bond : bond 0.00079 / 0.05 ( 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 274 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 217 time to evaluate : 0.835 Fit side-chains REVERT: A 136 THR cc_start: 0.8684 (OUTLIER) cc_final: 0.8436 (m) REVERT: A 477 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.8227 (tt0) REVERT: A 533 MET cc_start: 0.7404 (mtm) cc_final: 0.7139 (mtm) REVERT: D 189 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.8047 (mp) REVERT: E 136 THR cc_start: 0.8687 (OUTLIER) cc_final: 0.8430 (m) REVERT: E 477 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.8229 (tt0) REVERT: F 158 MET cc_start: 0.9149 (ttp) cc_final: 0.8814 (ttm) REVERT: H 137 ASP cc_start: 0.8658 (OUTLIER) cc_final: 0.8253 (m-30) REVERT: H 189 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7999 (mp) outliers start: 57 outliers final: 44 residues processed: 254 average time/residue: 0.1427 time to fit residues: 58.4490 Evaluate side-chains 266 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 215 time to evaluate : 0.675 ------------------------------------------------------------------------------- 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 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 361 MET Chi-restraints excluded: chain B residue 391 THR 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 D residue 198 ILE 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 12 LEU 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 149 THR Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain F residue 504 THR 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 H residue 189 LEU Chi-restraints excluded: chain H residue 198 ILE Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 66 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 83 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 238 optimal weight: 1.9990 chunk 191 optimal weight: 5.9990 chunk 189 optimal weight: 5.9990 chunk 201 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 160 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 215 optimal weight: 0.9980 chunk 229 optimal weight: 7.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 HIS D 62 ASN F 96 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 = 0.3464 r_free = 0.3464 target = 0.128674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.101802 restraints weight = 27749.268| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 1.68 r_work: 0.2972 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1679 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= 0.162 Angle : 0.597 12.086 27970 Z= 0.305 Chirality : 0.044 0.167 3170 Planarity : 0.005 0.050 3548 Dihedral : 7.458 92.587 2852 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.45 % Favored : 94.48 % Rotamer: Outliers : 2.33 % Allowed : 12.63 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.17), residues: 2516 helix: 1.89 (0.15), residues: 1216 sheet: -0.15 (0.34), residues: 274 loop : -1.73 (0.18), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 20 TYR 0.017 0.001 TYR F 510 PHE 0.019 0.001 PHE A 256 TRP 0.010 0.001 TRP F 294 HIS 0.004 0.001 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.16 (20638) covalent geometry : angle 0.59720 / 0.30 (27970) hydrogen bonds : bond 0.05067 / 3.38 ( 973) hydrogen bonds : angle 4.22035 / 2.92 ( 2847) Misc. bond : bond 0.00071 / 0.04 ( 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 271 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 219 time to evaluate : 0.840 Fit side-chains REVERT: A 136 THR cc_start: 0.8686 (OUTLIER) cc_final: 0.8448 (m) REVERT: A 477 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.8262 (tt0) REVERT: A 533 MET cc_start: 0.7337 (mtm) cc_final: 0.7065 (mtm) REVERT: D 189 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8074 (mp) REVERT: E 136 THR cc_start: 0.8691 (OUTLIER) cc_final: 0.8454 (m) REVERT: E 477 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.8259 (tt0) REVERT: F 158 MET cc_start: 0.9152 (ttp) cc_final: 0.8818 (ttm) REVERT: H 189 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.8048 (mp) outliers start: 52 outliers final: 43 residues processed: 251 average time/residue: 0.1373 time to fit residues: 55.2112 Evaluate side-chains 265 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 216 time to evaluate : 0.799 ------------------------------------------------------------------------------- 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 16 GLU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 198 ILE 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 12 LEU 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 149 THR Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain F residue 504 THR 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 H residue 198 ILE Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 66 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 28 optimal weight: 0.5980 chunk 170 optimal weight: 1.9990 chunk 2 optimal weight: 0.0770 chunk 111 optimal weight: 1.9990 chunk 176 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 194 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 108 optimal weight: 0.7980 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 96 HIS D 62 ASN F 96 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 = 0.3526 r_free = 0.3526 target = 0.133559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.106566 restraints weight = 27693.886| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.70 r_work: 0.3032 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 20640 Z= 0.102 Angle : 0.531 10.122 27970 Z= 0.270 Chirality : 0.041 0.168 3170 Planarity : 0.004 0.048 3548 Dihedral : 7.009 92.240 2852 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.73 % Favored : 95.19 % Rotamer: Outliers : 1.93 % Allowed : 12.99 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.17), residues: 2516 helix: 2.14 (0.15), residues: 1216 sheet: 0.06 (0.32), residues: 282 loop : -1.60 (0.19), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 20 TYR 0.010 0.001 TYR F 510 PHE 0.016 0.001 PHE B 236 TRP 0.011 0.001 TRP F 294 HIS 0.003 0.001 HIS F 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (20638) covalent geometry : angle 0.53059 / 0.27 (27970) hydrogen bonds : bond 0.03561 / 2.38 ( 973) hydrogen bonds : angle 4.05743 / 2.80 ( 2847) Misc. bond : bond 0.00024 / 0.01 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5561.65 seconds wall clock time: 95 minutes 54.52 seconds (5754.52 seconds total)