Starting phenix.real_space_refine on Thu Mar 5 06:45:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iam_35310/03_2026/8iam_35310.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iam_35310/03_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_35310/03_2026/8iam_35310.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iam_35310/03_2026/8iam_35310.map" model { file = "/net/cci-nas-00/data/ceres_data/8iam_35310/03_2026/8iam_35310.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iam_35310/03_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/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: 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: 5.76, per 1000 atoms: 0.29 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: 1.76 Conformation dependent library (CDL) restraints added in 851.1 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: 0.62 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: 4.11 Time building geometry restraints manager: 2.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6422 1.34 - 1.46: 3882 1.46 - 1.58: 10158 1.58 - 1.69: 2 1.69 - 1.81: 174 Bond restraints: 20638 Sorted by residual: bond pdb=" C14 Z1T D 301 " pdb=" C15 Z1T D 301 " ideal model delta sigma weight residual 1.329 1.528 -0.199 2.00e-02 2.50e+03 9.92e+01 bond pdb=" C14 Z1T H 301 " pdb=" C15 Z1T H 301 " ideal model delta sigma weight residual 1.329 1.528 -0.199 2.00e-02 2.50e+03 9.87e+01 bond pdb=" C13 Z1T H 301 " pdb=" C14 Z1T H 301 " ideal model delta sigma weight residual 1.494 1.529 -0.035 2.00e-02 2.50e+03 3.10e+00 bond pdb=" C13 Z1T D 301 " pdb=" C14 Z1T D 301 " ideal model delta sigma weight residual 1.494 1.529 -0.035 2.00e-02 2.50e+03 3.10e+00 bond pdb=" N ASN E 257 " pdb=" CA ASN E 257 " ideal model delta sigma weight residual 1.457 1.476 -0.019 1.10e-02 8.26e+03 2.95e+00 ... (remaining 20633 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 27666 2.83 - 5.65: 278 5.65 - 8.48: 21 8.48 - 11.31: 3 11.31 - 14.14: 2 Bond angle restraints: 27970 Sorted by residual: angle pdb=" N ASN E 257 " pdb=" CA ASN E 257 " pdb=" C ASN E 257 " ideal model delta sigma weight residual 112.57 126.71 -14.14 1.13e+00 7.83e-01 1.57e+02 angle pdb=" N ASN A 257 " pdb=" CA ASN A 257 " pdb=" C ASN A 257 " ideal model delta sigma weight residual 112.57 126.68 -14.11 1.13e+00 7.83e-01 1.56e+02 angle pdb=" N GLY H 133 " pdb=" CA GLY H 133 " pdb=" C GLY H 133 " ideal model delta sigma weight residual 112.50 106.19 6.31 1.16e+00 7.43e-01 2.96e+01 angle pdb=" N GLY D 133 " pdb=" CA GLY D 133 " pdb=" C GLY D 133 " ideal model delta sigma weight residual 112.50 106.23 6.27 1.16e+00 7.43e-01 2.92e+01 angle pdb=" N LYS A 79 " pdb=" CA LYS A 79 " pdb=" C LYS A 79 " ideal model delta sigma weight residual 113.38 119.93 -6.55 1.23e+00 6.61e-01 2.83e+01 ... (remaining 27965 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.03: 11524 21.03 - 42.06: 776 42.06 - 63.10: 96 63.10 - 84.13: 18 84.13 - 105.16: 6 Dihedral angle restraints: 12420 sinusoidal: 5020 harmonic: 7400 Sorted by residual: dihedral pdb=" CA SER F 306 " pdb=" C SER F 306 " pdb=" N MET F 307 " pdb=" CA MET F 307 " ideal model delta harmonic sigma weight residual 180.00 159.77 20.23 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA SER B 306 " pdb=" C SER B 306 " pdb=" N MET B 307 " pdb=" CA MET B 307 " ideal model delta harmonic sigma weight residual 180.00 159.77 20.23 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA PRO F 19 " pdb=" C PRO F 19 " pdb=" N ASP F 20 " pdb=" CA ASP F 20 " ideal model delta harmonic sigma weight residual 180.00 160.94 19.06 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 12417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 3074 0.103 - 0.206: 90 0.206 - 0.309: 4 0.309 - 0.412: 0 0.412 - 0.516: 2 Chirality restraints: 3170 Sorted by residual: chirality pdb=" CA ASN E 257 " pdb=" N ASN E 257 " pdb=" C ASN E 257 " pdb=" CB ASN E 257 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.65e+00 chirality pdb=" CA ASN A 257 " pdb=" N ASN A 257 " pdb=" C ASN A 257 " pdb=" CB ASN A 257 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.61e+00 chirality pdb=" CA LYS A 79 " pdb=" N LYS A 79 " pdb=" C LYS A 79 " pdb=" CB LYS A 79 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.28e+00 ... (remaining 3167 not shown) Planarity restraints: 3548 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 256 " 0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C PHE A 256 " -0.057 2.00e-02 2.50e+03 pdb=" O PHE A 256 " 0.021 2.00e-02 2.50e+03 pdb=" N ASN A 257 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE E 256 " -0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C PHE E 256 " 0.057 2.00e-02 2.50e+03 pdb=" O PHE E 256 " -0.021 2.00e-02 2.50e+03 pdb=" N ASN E 257 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS E 82 " -0.045 5.00e-02 4.00e+02 6.85e-02 7.50e+00 pdb=" N PRO E 83 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO E 83 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO E 83 " -0.037 5.00e-02 4.00e+02 ... (remaining 3545 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 260 2.66 - 3.22: 18338 3.22 - 3.78: 28804 3.78 - 4.34: 40412 4.34 - 4.90: 70115 Nonbonded interactions: 157929 Sorted by model distance: nonbonded pdb=" O LYS E 79 " pdb=" OG SER E 80 " model vdw 2.098 3.040 nonbonded pdb=" O LYS A 79 " pdb=" OG SER A 80 " model vdw 2.098 3.040 nonbonded pdb=" OH TYR E 460 " pdb=" OE1 GLU E 488 " model vdw 2.114 3.040 nonbonded pdb=" OH TYR A 460 " pdb=" OE1 GLU A 488 " model vdw 2.114 3.040 nonbonded pdb=" OG SER A 417 " pdb=" O SER A 442 " model vdw 2.158 3.040 ... (remaining 157924 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 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: 1.570 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: 0.030 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 19.870 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.199 20640 Z= 0.199 Angle : 0.720 14.137 27970 Z= 0.414 Chirality : 0.047 0.516 3170 Planarity : 0.005 0.068 3548 Dihedral : 13.959 105.161 7656 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.56 % Favored : 94.12 % Rotamer: Outliers : 0.27 % Allowed : 0.94 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 covalent geometry : bond 0.00410 (20638) covalent geometry : angle 0.71997 (27970) hydrogen bonds : bond 0.16968 ( 973) hydrogen bonds : angle 5.53071 ( 2847) Misc. bond : bond 0.00056 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 253 time to evaluate : 0.711 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: 0.1246 time to fit residues: 51.2667 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 : 0.753 ------------------------------------------------------------------------------- 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: 4.9990 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: 1.6184 ------------------------------------------------------------------------------- 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 = 0.3490 r_free = 0.3490 target = 0.130723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.104564 restraints weight = 27592.404| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.72 r_work: 0.2973 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.0941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20640 Z= 0.147 Angle : 0.601 10.476 27970 Z= 0.311 Chirality : 0.043 0.172 3170 Planarity : 0.005 0.058 3548 Dihedral : 7.650 101.232 2846 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.48 % Favored : 94.36 % Rotamer: Outliers : 0.67 % Allowed : 6.99 % Favored : 92.34 % 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: 0.13 (0.17), residues: 2516 helix: 1.64 (0.15), residues: 1224 sheet: -0.13 (0.33), residues: 264 loop : -1.86 (0.18), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 20 TYR 0.016 0.001 TYR F 510 PHE 0.017 0.001 PHE E 256 TRP 0.010 0.001 TRP B 294 HIS 0.003 0.001 HIS B 90 Details of bonding type rmsd covalent geometry : bond 0.00335 (20638) covalent geometry : angle 0.60129 (27970) hydrogen bonds : bond 0.05235 ( 973) hydrogen bonds : angle 4.43457 ( 2847) Misc. bond : bond 0.00009 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 225 time to evaluate : 0.726 Fit side-chains REVERT: B 119 ASP cc_start: 0.8554 (t70) cc_final: 0.7818 (t0) REVERT: B 158 MET cc_start: 0.9175 (ttp) cc_final: 0.8814 (ttm) REVERT: C 51 MET cc_start: 0.9047 (mtt) cc_final: 0.8783 (mtt) REVERT: F 119 ASP cc_start: 0.8534 (t70) cc_final: 0.7794 (t0) REVERT: F 158 MET cc_start: 0.9179 (ttp) cc_final: 0.8832 (ttm) REVERT: G 51 MET cc_start: 0.9033 (mtt) cc_final: 0.8763 (mtt) outliers start: 15 outliers final: 9 residues processed: 231 average time/residue: 0.1246 time to fit residues: 45.8882 Evaluate side-chains 218 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 209 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 189 LEU 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: 9.9990 chunk 218 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 115 optimal weight: 3.9990 chunk 211 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 77 optimal weight: 0.0070 chunk 126 optimal weight: 7.9990 chunk 167 optimal weight: 10.0000 chunk 206 optimal weight: 0.0060 overall best weight: 1.1618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 GLN D 62 ASN H 62 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.132332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.105480 restraints weight = 27816.240| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.67 r_work: 0.3001 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 20640 Z= 0.117 Angle : 0.544 10.360 27970 Z= 0.281 Chirality : 0.042 0.168 3170 Planarity : 0.005 0.054 3548 Dihedral : 7.462 98.210 2846 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.17 % Favored : 94.67 % Rotamer: Outliers : 1.30 % Allowed : 8.74 % Favored : 89.96 % 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: 0.41 (0.17), residues: 2516 helix: 1.90 (0.15), residues: 1214 sheet: -0.14 (0.32), residues: 288 loop : -1.72 (0.18), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 20 TYR 0.014 0.001 TYR F 510 PHE 0.017 0.001 PHE E 256 TRP 0.007 0.001 TRP D 142 HIS 0.002 0.001 HIS C 60 Details of bonding type rmsd covalent geometry : bond 0.00260 (20638) covalent geometry : angle 0.54425 (27970) hydrogen bonds : bond 0.04393 ( 973) hydrogen bonds : angle 4.19883 ( 2847) Misc. bond : bond 0.00013 ( 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 263 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 234 time to evaluate : 0.812 Fit side-chains REVERT: A 309 LEU cc_start: 0.7966 (pp) cc_final: 0.7762 (mt) REVERT: A 426 SER cc_start: 0.7582 (t) cc_final: 0.7328 (p) REVERT: A 477 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.8074 (tm-30) REVERT: B 119 ASP cc_start: 0.8532 (t70) cc_final: 0.7796 (t0) REVERT: B 158 MET cc_start: 0.9169 (ttp) cc_final: 0.8783 (ttm) REVERT: C 51 MET cc_start: 0.9038 (mtt) cc_final: 0.8799 (mtt) REVERT: E 309 LEU cc_start: 0.7978 (pp) cc_final: 0.7778 (mt) REVERT: E 426 SER cc_start: 0.7567 (t) cc_final: 0.7311 (p) REVERT: E 477 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.8050 (tm-30) REVERT: F 119 ASP cc_start: 0.8522 (t70) cc_final: 0.7787 (t0) REVERT: F 158 MET cc_start: 0.9156 (ttp) cc_final: 0.8749 (ttm) REVERT: G 51 MET cc_start: 0.9038 (mtt) cc_final: 0.8789 (mtt) outliers start: 29 outliers final: 13 residues processed: 250 average time/residue: 0.1220 time to fit residues: 48.9656 Evaluate side-chains 232 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 217 time to evaluate : 0.835 ------------------------------------------------------------------------------- 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 183 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain E residue 477 GLN Chi-restraints excluded: chain E residue 524 SER Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 189 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 103 optimal weight: 8.9990 chunk 7 optimal weight: 0.7980 chunk 55 optimal weight: 6.9990 chunk 184 optimal weight: 4.9990 chunk 24 optimal weight: 0.4980 chunk 105 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 121 optimal weight: 5.9990 chunk 153 optimal weight: 0.0040 chunk 40 optimal weight: 0.8980 overall best weight: 1.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 HIS D 62 ASN F 90 HIS H 62 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.131732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.104781 restraints weight = 27669.935| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.67 r_work: 0.3025 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 20640 Z= 0.128 Angle : 0.550 11.054 27970 Z= 0.283 Chirality : 0.042 0.236 3170 Planarity : 0.005 0.052 3548 Dihedral : 7.454 96.623 2846 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.29 % Favored : 94.55 % Rotamer: Outliers : 1.43 % Allowed : 10.13 % Favored : 88.44 % 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: 0.55 (0.17), residues: 2516 helix: 2.03 (0.15), residues: 1214 sheet: 0.00 (0.33), residues: 274 loop : -1.66 (0.18), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 20 TYR 0.015 0.001 TYR F 510 PHE 0.017 0.001 PHE E 256 TRP 0.007 0.001 TRP D 142 HIS 0.003 0.001 HIS B 90 Details of bonding type rmsd covalent geometry : bond 0.00294 (20638) covalent geometry : angle 0.55044 (27970) hydrogen bonds : bond 0.04493 ( 973) hydrogen bonds : angle 4.14076 ( 2847) Misc. bond : bond 0.00012 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 230 time to evaluate : 0.780 Fit side-chains REVERT: A 426 SER cc_start: 0.7583 (t) cc_final: 0.7331 (p) REVERT: A 533 MET cc_start: 0.7354 (mtm) cc_final: 0.7120 (mtm) REVERT: B 119 ASP cc_start: 0.8572 (t70) cc_final: 0.7815 (t0) REVERT: B 158 MET cc_start: 0.9163 (ttp) cc_final: 0.8780 (ttm) REVERT: C 51 MET cc_start: 0.9070 (mtt) cc_final: 0.8817 (mtt) REVERT: E 533 MET cc_start: 0.7335 (mtm) cc_final: 0.7096 (mtm) REVERT: F 119 ASP cc_start: 0.8560 (t70) cc_final: 0.7800 (t0) REVERT: F 158 MET cc_start: 0.9148 (ttp) cc_final: 0.8765 (ttm) REVERT: G 51 MET cc_start: 0.9056 (mtt) cc_final: 0.8804 (mtt) outliers start: 32 outliers final: 16 residues processed: 249 average time/residue: 0.1239 time to fit residues: 49.8980 Evaluate side-chains 233 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 217 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 524 SER Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 120 MET Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 189 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 91 optimal weight: 3.9990 chunk 228 optimal weight: 10.0000 chunk 157 optimal weight: 2.9990 chunk 237 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 150 optimal weight: 0.5980 chunk 154 optimal weight: 3.9990 chunk 27 optimal weight: 0.4980 chunk 2 optimal weight: 0.0050 chunk 136 optimal weight: 4.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 GLN B 90 HIS D 62 ASN F 90 HIS H 62 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.134463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.107638 restraints weight = 27365.456| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.68 r_work: 0.3058 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 20640 Z= 0.099 Angle : 0.512 9.702 27970 Z= 0.263 Chirality : 0.041 0.167 3170 Planarity : 0.004 0.049 3548 Dihedral : 7.259 95.563 2846 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.97 % Favored : 94.95 % Rotamer: Outliers : 1.48 % Allowed : 10.48 % Favored : 88.04 % 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: 0.77 (0.17), residues: 2516 helix: 2.19 (0.15), residues: 1216 sheet: 0.22 (0.33), residues: 278 loop : -1.57 (0.19), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 20 TYR 0.012 0.001 TYR F 510 PHE 0.013 0.001 PHE F 236 TRP 0.006 0.001 TRP F 294 HIS 0.002 0.001 HIS F 90 Details of bonding type rmsd covalent geometry : bond 0.00204 (20638) covalent geometry : angle 0.51232 (27970) hydrogen bonds : bond 0.03540 ( 973) hydrogen bonds : angle 4.02366 ( 2847) Misc. bond : bond 0.00018 ( 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 271 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 238 time to evaluate : 0.728 Fit side-chains REVERT: A 477 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.8205 (tt0) REVERT: B 16 GLU cc_start: 0.6312 (OUTLIER) cc_final: 0.6009 (pt0) REVERT: B 119 ASP cc_start: 0.8584 (t70) cc_final: 0.7838 (t0) REVERT: B 158 MET cc_start: 0.9133 (ttp) cc_final: 0.8705 (ttm) REVERT: D 189 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7852 (mp) REVERT: C 51 MET cc_start: 0.9041 (mtt) cc_final: 0.8789 (mtt) REVERT: E 477 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8199 (tt0) REVERT: F 16 GLU cc_start: 0.6320 (OUTLIER) cc_final: 0.6031 (pt0) REVERT: F 119 ASP cc_start: 0.8563 (t70) cc_final: 0.7820 (t0) REVERT: F 158 MET cc_start: 0.9118 (ttp) cc_final: 0.8658 (ttm) REVERT: H 189 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7852 (mp) REVERT: G 51 MET cc_start: 0.9050 (mtt) cc_final: 0.8808 (mtt) outliers start: 33 outliers final: 17 residues processed: 258 average time/residue: 0.1275 time to fit residues: 52.5475 Evaluate side-chains 241 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 218 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 477 GLN Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 86 GLN Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain C residue 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 F residue 16 GLU Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 120 MET Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain G residue 5 LYS 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: 3.9990 chunk 27 optimal weight: 6.9990 chunk 151 optimal weight: 6.9990 chunk 181 optimal weight: 0.0970 chunk 39 optimal weight: 3.9990 chunk 189 optimal weight: 6.9990 chunk 153 optimal weight: 9.9990 chunk 193 optimal weight: 0.5980 chunk 167 optimal weight: 0.9990 chunk 210 optimal weight: 3.9990 chunk 213 optimal weight: 0.8980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 HIS B 96 HIS D 62 ASN D 110 ASN F 90 HIS H 62 ASN H 110 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.133281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.106006 restraints weight = 27520.040| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.71 r_work: 0.3015 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 20640 Z= 0.119 Angle : 0.534 10.377 27970 Z= 0.273 Chirality : 0.042 0.166 3170 Planarity : 0.005 0.048 3548 Dihedral : 7.297 94.928 2846 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.37 % Favored : 94.55 % Rotamer: Outliers : 1.61 % Allowed : 11.47 % Favored : 86.92 % 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: 0.80 (0.17), residues: 2516 helix: 2.21 (0.15), residues: 1216 sheet: 0.24 (0.34), residues: 280 loop : -1.57 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 20 TYR 0.014 0.001 TYR F 510 PHE 0.016 0.001 PHE E 256 TRP 0.007 0.001 TRP F 294 HIS 0.003 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00273 (20638) covalent geometry : angle 0.53411 (27970) hydrogen bonds : bond 0.04043 ( 973) hydrogen bonds : angle 4.00450 ( 2847) Misc. bond : bond 0.00017 ( 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 259 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 223 time to evaluate : 0.677 Fit side-chains REVERT: A 477 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.8236 (tt0) REVERT: B 16 GLU cc_start: 0.6321 (OUTLIER) cc_final: 0.6017 (pt0) REVERT: B 119 ASP cc_start: 0.8589 (t70) cc_final: 0.7843 (t0) REVERT: B 158 MET cc_start: 0.9146 (ttp) cc_final: 0.8720 (ttm) REVERT: D 66 MET cc_start: 0.7485 (tpp) cc_final: 0.7189 (ttm) REVERT: D 189 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7860 (mp) REVERT: C 51 MET cc_start: 0.9077 (mtt) cc_final: 0.8849 (mtt) REVERT: E 477 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.8212 (tt0) REVERT: F 16 GLU cc_start: 0.6318 (OUTLIER) cc_final: 0.6021 (pt0) REVERT: F 119 ASP cc_start: 0.8579 (t70) cc_final: 0.7833 (t0) REVERT: F 158 MET cc_start: 0.9140 (ttp) cc_final: 0.8720 (ttm) REVERT: H 66 MET cc_start: 0.7456 (tpp) cc_final: 0.7195 (ttm) REVERT: G 51 MET cc_start: 0.9073 (mtt) cc_final: 0.8838 (mtt) outliers start: 36 outliers final: 26 residues processed: 245 average time/residue: 0.1276 time to fit residues: 49.6953 Evaluate side-chains 248 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 217 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 477 GLN Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 477 GLN 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 187 SER 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 G residue 5 LYS 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: 6.9990 chunk 69 optimal weight: 0.6980 chunk 111 optimal weight: 4.9990 chunk 207 optimal weight: 6.9990 chunk 235 optimal weight: 5.9990 chunk 214 optimal weight: 3.9990 chunk 135 optimal weight: 6.9990 chunk 147 optimal weight: 7.9990 chunk 169 optimal weight: 0.9980 chunk 209 optimal weight: 2.9990 chunk 198 optimal weight: 3.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 GLN B 90 HIS D 62 ASN D 110 ASN F 90 HIS F 96 HIS H 62 ASN H 110 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.129201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.102042 restraints weight = 27797.022| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.70 r_work: 0.2976 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 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 0.040 20640 Z= 0.183 Angle : 0.602 12.015 27970 Z= 0.310 Chirality : 0.044 0.174 3170 Planarity : 0.005 0.048 3548 Dihedral : 7.621 93.707 2846 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.00 % Favored : 93.92 % Rotamer: Outliers : 1.97 % Allowed : 11.65 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.65 (0.17), residues: 2516 helix: 2.14 (0.15), residues: 1206 sheet: 0.15 (0.34), residues: 280 loop : -1.67 (0.18), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 20 TYR 0.019 0.002 TYR F 510 PHE 0.021 0.002 PHE A 256 TRP 0.010 0.002 TRP D 142 HIS 0.004 0.001 HIS A 258 Details of bonding type rmsd covalent geometry : bond 0.00445 (20638) covalent geometry : angle 0.60224 (27970) hydrogen bonds : bond 0.05317 ( 973) hydrogen bonds : angle 4.13494 ( 2847) Misc. bond : bond 0.00016 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 226 time to evaluate : 0.633 Fit side-chains REVERT: A 477 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.8241 (tt0) REVERT: A 533 MET cc_start: 0.7352 (mtm) cc_final: 0.7142 (mtm) REVERT: B 16 GLU cc_start: 0.6415 (OUTLIER) cc_final: 0.6146 (pt0) REVERT: B 119 ASP cc_start: 0.8663 (t70) cc_final: 0.7894 (t0) REVERT: B 158 MET cc_start: 0.9151 (ttp) cc_final: 0.8803 (ttm) REVERT: D 66 MET cc_start: 0.7518 (tpp) cc_final: 0.7215 (ttm) REVERT: C 51 MET cc_start: 0.9051 (mtt) cc_final: 0.8797 (mtt) REVERT: E 477 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.8229 (tt0) REVERT: F 16 GLU cc_start: 0.6422 (OUTLIER) cc_final: 0.6158 (pt0) REVERT: F 119 ASP cc_start: 0.8668 (t70) cc_final: 0.7891 (t0) REVERT: F 158 MET cc_start: 0.9134 (ttp) cc_final: 0.8781 (ttm) REVERT: H 66 MET cc_start: 0.7488 (tpp) cc_final: 0.7225 (ttm) REVERT: G 51 MET cc_start: 0.9051 (mtt) cc_final: 0.8797 (mtt) outliers start: 44 outliers final: 32 residues processed: 254 average time/residue: 0.1258 time to fit residues: 51.2913 Evaluate side-chains 258 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 222 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 477 GLN Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 437 THR Chi-restraints excluded: chain E residue 477 GLN Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 504 THR Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 120 MET Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain G residue 5 LYS 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: 9.9990 chunk 173 optimal weight: 0.7980 chunk 155 optimal weight: 0.6980 chunk 82 optimal weight: 4.9990 chunk 179 optimal weight: 5.9990 chunk 209 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 chunk 174 optimal weight: 5.9990 chunk 218 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 HIS D 62 ASN D 110 ASN H 62 ASN H 110 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.130484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.102999 restraints weight = 27765.076| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.71 r_work: 0.2984 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20640 Z= 0.134 Angle : 0.559 11.398 27970 Z= 0.287 Chirality : 0.042 0.165 3170 Planarity : 0.005 0.047 3548 Dihedral : 7.527 93.004 2846 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.72 % Favored : 94.20 % Rotamer: Outliers : 1.79 % Allowed : 12.23 % Favored : 85.98 % 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: 0.68 (0.17), residues: 2516 helix: 2.13 (0.15), residues: 1216 sheet: 0.01 (0.33), residues: 288 loop : -1.60 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 20 TYR 0.016 0.001 TYR B 510 PHE 0.018 0.001 PHE A 256 TRP 0.008 0.001 TRP B 294 HIS 0.003 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00314 (20638) covalent geometry : angle 0.55935 (27970) hydrogen bonds : bond 0.04549 ( 973) hydrogen bonds : angle 4.08762 ( 2847) Misc. bond : bond 0.00018 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 222 time to evaluate : 0.695 Fit side-chains REVERT: A 136 THR cc_start: 0.8716 (OUTLIER) cc_final: 0.8427 (m) REVERT: A 477 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.8257 (tt0) REVERT: A 533 MET cc_start: 0.7221 (mtm) cc_final: 0.7012 (mtm) REVERT: B 16 GLU cc_start: 0.6387 (OUTLIER) cc_final: 0.6085 (pt0) REVERT: B 119 ASP cc_start: 0.8665 (t70) cc_final: 0.7892 (t0) REVERT: B 158 MET cc_start: 0.9162 (ttp) cc_final: 0.8790 (ttm) REVERT: D 66 MET cc_start: 0.7575 (tpp) cc_final: 0.7150 (ttm) REVERT: C 51 MET cc_start: 0.9051 (mtt) cc_final: 0.8799 (mtt) REVERT: E 136 THR cc_start: 0.8718 (OUTLIER) cc_final: 0.8431 (m) REVERT: E 477 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.8245 (tt0) REVERT: F 16 GLU cc_start: 0.6396 (OUTLIER) cc_final: 0.6098 (pt0) REVERT: F 119 ASP cc_start: 0.8670 (t70) cc_final: 0.7896 (t0) REVERT: F 158 MET cc_start: 0.9143 (ttp) cc_final: 0.8765 (ttm) REVERT: H 66 MET cc_start: 0.7532 (tpp) cc_final: 0.7111 (ttm) REVERT: G 51 MET cc_start: 0.9049 (mtt) cc_final: 0.8798 (mtt) outliers start: 40 outliers final: 29 residues processed: 245 average time/residue: 0.1233 time to fit residues: 48.3144 Evaluate side-chains 250 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 215 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 477 GLN Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 437 THR Chi-restraints excluded: chain E residue 477 GLN Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 187 SER 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 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: 6.9990 chunk 104 optimal weight: 0.4980 chunk 247 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 155 optimal weight: 0.8980 chunk 241 optimal weight: 2.9990 chunk 190 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 151 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 62 ASN D 110 ASN H 62 ASN H 110 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.131370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.104009 restraints weight = 27488.122| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.71 r_work: 0.3010 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1767 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= 0.128 Angle : 0.548 11.265 27970 Z= 0.282 Chirality : 0.042 0.164 3170 Planarity : 0.005 0.049 3548 Dihedral : 7.484 92.579 2846 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.68 % Favored : 94.24 % Rotamer: Outliers : 1.48 % Allowed : 12.37 % Favored : 86.16 % 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: 0.75 (0.17), residues: 2516 helix: 2.18 (0.15), residues: 1216 sheet: 0.17 (0.33), residues: 280 loop : -1.60 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 20 TYR 0.015 0.001 TYR A 453 PHE 0.016 0.001 PHE A 256 TRP 0.008 0.001 TRP B 294 HIS 0.003 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00297 (20638) covalent geometry : angle 0.54790 (27970) hydrogen bonds : bond 0.04355 ( 973) hydrogen bonds : angle 4.04941 ( 2847) Misc. bond : bond 0.00015 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 222 time to evaluate : 0.600 Fit side-chains REVERT: A 136 THR cc_start: 0.8700 (OUTLIER) cc_final: 0.8411 (m) REVERT: A 477 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.8262 (tt0) REVERT: B 16 GLU cc_start: 0.6407 (OUTLIER) cc_final: 0.6117 (pt0) REVERT: B 119 ASP cc_start: 0.8662 (t70) cc_final: 0.7893 (t0) REVERT: B 158 MET cc_start: 0.9163 (ttp) cc_final: 0.8782 (ttm) REVERT: C 51 MET cc_start: 0.9043 (mtt) cc_final: 0.8792 (mtt) REVERT: E 136 THR cc_start: 0.8711 (OUTLIER) cc_final: 0.8423 (m) REVERT: E 477 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.8232 (tt0) REVERT: F 16 GLU cc_start: 0.6404 (OUTLIER) cc_final: 0.6107 (pt0) REVERT: F 119 ASP cc_start: 0.8663 (t70) cc_final: 0.7891 (t0) REVERT: F 158 MET cc_start: 0.9146 (ttp) cc_final: 0.8736 (ttm) REVERT: H 66 MET cc_start: 0.7551 (tpp) cc_final: 0.7109 (ttm) REVERT: G 51 MET cc_start: 0.9040 (mtt) cc_final: 0.8811 (mtt) outliers start: 33 outliers final: 26 residues processed: 239 average time/residue: 0.1255 time to fit residues: 47.7724 Evaluate side-chains 250 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 218 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 477 GLN Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 437 THR Chi-restraints excluded: chain E residue 477 GLN Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 504 THR Chi-restraints excluded: chain H residue 120 MET Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain 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: 0.9980 chunk 36 optimal weight: 5.9990 chunk 238 optimal weight: 0.9980 chunk 191 optimal weight: 7.9990 chunk 189 optimal weight: 5.9990 chunk 201 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 160 optimal weight: 8.9990 chunk 169 optimal weight: 20.0000 chunk 215 optimal weight: 2.9990 chunk 229 optimal weight: 8.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 62 ASN D 110 ASN H 62 ASN H 110 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.130512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.103089 restraints weight = 27742.654| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.70 r_work: 0.2992 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 20640 Z= 0.153 Angle : 0.585 11.884 27970 Z= 0.298 Chirality : 0.043 0.165 3170 Planarity : 0.005 0.051 3548 Dihedral : 7.615 92.084 2846 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.12 % Favored : 93.80 % Rotamer: Outliers : 1.52 % Allowed : 12.50 % Favored : 85.98 % 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: 0.70 (0.17), residues: 2516 helix: 2.15 (0.15), residues: 1216 sheet: 0.23 (0.34), residues: 266 loop : -1.62 (0.18), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 20 TYR 0.017 0.001 TYR B 510 PHE 0.019 0.001 PHE A 256 TRP 0.008 0.001 TRP D 142 HIS 0.003 0.001 HIS E 258 Details of bonding type rmsd covalent geometry : bond 0.00367 (20638) covalent geometry : angle 0.58508 (27970) hydrogen bonds : bond 0.04822 ( 973) hydrogen bonds : angle 4.09055 ( 2847) Misc. bond : bond 0.00017 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 220 time to evaluate : 0.604 Fit side-chains REVERT: A 136 THR cc_start: 0.8699 (OUTLIER) cc_final: 0.8422 (m) REVERT: A 477 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.8254 (tt0) REVERT: B 16 GLU cc_start: 0.6412 (OUTLIER) cc_final: 0.6123 (pt0) REVERT: B 119 ASP cc_start: 0.8711 (t70) cc_final: 0.7922 (t0) REVERT: B 158 MET cc_start: 0.9158 (ttp) cc_final: 0.8785 (ttm) REVERT: C 51 MET cc_start: 0.9051 (mtt) cc_final: 0.8795 (mtt) REVERT: E 136 THR cc_start: 0.8697 (OUTLIER) cc_final: 0.8418 (m) REVERT: E 477 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.8235 (tt0) REVERT: F 16 GLU cc_start: 0.6390 (OUTLIER) cc_final: 0.6110 (pt0) REVERT: F 119 ASP cc_start: 0.8715 (t70) cc_final: 0.7921 (t0) REVERT: F 158 MET cc_start: 0.9147 (ttp) cc_final: 0.8770 (ttm) REVERT: G 51 MET cc_start: 0.9050 (mtt) cc_final: 0.8800 (mtt) outliers start: 34 outliers final: 27 residues processed: 238 average time/residue: 0.1257 time to fit residues: 47.7458 Evaluate side-chains 253 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 220 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 477 GLN Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 437 THR Chi-restraints excluded: chain E residue 477 GLN Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 504 THR Chi-restraints excluded: chain H residue 120 MET Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain 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: 6.9990 chunk 170 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 111 optimal weight: 0.0050 chunk 176 optimal weight: 0.4980 chunk 14 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 chunk 194 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 62 ASN D 110 ASN H 62 ASN H 110 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.134189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.106939 restraints weight = 27763.663| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.72 r_work: 0.3060 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 20640 Z= 0.098 Angle : 0.521 10.249 27970 Z= 0.265 Chirality : 0.041 0.169 3170 Planarity : 0.004 0.047 3548 Dihedral : 7.286 91.631 2846 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.49 % Favored : 95.43 % Rotamer: Outliers : 1.30 % Allowed : 12.63 % Favored : 86.07 % 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: 0.92 (0.17), residues: 2516 helix: 2.31 (0.15), residues: 1220 sheet: 0.26 (0.33), residues: 278 loop : -1.49 (0.19), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 20 TYR 0.017 0.001 TYR A 453 PHE 0.017 0.001 PHE F 236 TRP 0.010 0.001 TRP B 294 HIS 0.002 0.000 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00206 (20638) covalent geometry : angle 0.52136 (27970) hydrogen bonds : bond 0.03423 ( 973) hydrogen bonds : angle 3.96962 ( 2847) Misc. bond : bond 0.00008 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4979.23 seconds wall clock time: 85 minutes 53.49 seconds (5153.49 seconds total)