Starting phenix.real_space_refine on Tue Nov 19 20:29:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iam_35310/11_2024/8iam_35310.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iam_35310/11_2024/8iam_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iam_35310/11_2024/8iam_35310.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iam_35310/11_2024/8iam_35310.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iam_35310/11_2024/8iam_35310.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iam_35310/11_2024/8iam_35310.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 114 5.16 5 C 12980 2.51 5 N 3358 2.21 5 O 3738 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 200 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 20192 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 3844 Classifications: {'peptide': 495} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 24, 'TRANS': 470} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'PHE:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 4394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 555, 4394 Classifications: {'peptide': 555} Link IDs: {'PTRANS': 29, 'TRANS': 525} Chain: "D" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1225 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 142} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 572 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'Z1T': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: G, H, E, F Time building chain proxies: 15.85, per 1000 atoms: 0.78 Number of scatterers: 20192 At special positions: 0 Unit cell: (171.72, 109.08, 124.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 114 16.00 P 2 15.00 O 3738 8.00 N 3358 7.00 C 12980 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.53 Conformation dependent library (CDL) restraints added in 2.7 seconds 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4764 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 12 sheets defined 53.4% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.10 Creating SS restraints... Processing helix chain 'A' and resid 60 through 77 Processing helix chain 'A' and resid 89 through 100 Processing helix chain 'A' and resid 115 through 120 Processing helix chain 'A' and resid 161 through 175 Processing helix chain 'A' and resid 189 through 204 removed outlier: 3.787A pdb=" N TYR A 193 " --> pdb=" O GLN A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'A' and resid 217 through 225 Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 239 through 250 removed outlier: 4.189A pdb=" N ARG A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 279 Processing helix chain 'A' and resid 302 through 314 removed outlier: 3.672A pdb=" N LEU A 306 " --> pdb=" O PRO A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 339 Processing helix chain 'A' and resid 342 through 347 Processing helix chain 'A' and resid 368 through 379 Processing helix chain 'A' and resid 379 through 384 Processing helix chain 'A' and resid 389 through 405 removed outlier: 3.869A pdb=" N VAL A 393 " --> pdb=" O PRO A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 427 removed outlier: 4.012A pdb=" N ASP A 427 " --> pdb=" O SER A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 458 removed outlier: 3.562A pdb=" N ARG A 454 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 476 removed outlier: 3.524A pdb=" N LEU A 465 " --> pdb=" O THR A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 504 Processing helix chain 'A' and resid 534 through 554 Processing helix chain 'B' and resid 20 through 28 Processing helix chain 'B' and resid 57 through 85 removed outlier: 3.953A pdb=" N SER B 61 " --> pdb=" O PRO B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 114 removed outlier: 3.560A pdb=" N ARG B 112 " --> pdb=" O SER B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 122 removed outlier: 3.569A pdb=" N ASP B 119 " --> pdb=" O MET B 116 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N ASP B 120 " --> pdb=" O ARG B 117 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE B 122 " --> pdb=" O ASP B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 186 removed outlier: 3.726A pdb=" N ASP B 177 " --> pdb=" O GLY B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 215 removed outlier: 3.672A pdb=" N ILE B 204 " --> pdb=" O THR B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 237 removed outlier: 4.728A pdb=" N PHE B 233 " --> pdb=" O ASN B 229 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ASN B 234 " --> pdb=" O ALA B 230 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA B 235 " --> pdb=" O ASN B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 261 removed outlier: 3.519A pdb=" N ARG B 254 " --> pdb=" O HIS B 250 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER B 260 " --> pdb=" O GLY B 256 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY B 261 " --> pdb=" O VAL B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 286 Processing helix chain 'B' and resid 313 through 325 Processing helix chain 'B' and resid 345 through 351 removed outlier: 3.605A pdb=" N ILE B 349 " --> pdb=" O GLY B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 389 Processing helix chain 'B' and resid 390 through 395 removed outlier: 3.550A pdb=" N SER B 395 " --> pdb=" O THR B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 415 removed outlier: 3.537A pdb=" N LEU B 403 " --> pdb=" O PRO B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 444 removed outlier: 3.717A pdb=" N GLU B 424 " --> pdb=" O GLY B 420 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA B 430 " --> pdb=" O LEU B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 476 removed outlier: 3.988A pdb=" N ALA B 468 " --> pdb=" O SER B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 522 Processing helix chain 'B' and resid 528 through 532 removed outlier: 4.023A pdb=" N SER B 531 " --> pdb=" O SER B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 553 Proline residue: B 550 - end of helix Processing helix chain 'B' and resid 554 through 559 removed outlier: 6.675A pdb=" N LYS B 557 " --> pdb=" O LYS B 554 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR B 558 " --> pdb=" O ASP B 555 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE B 559 " --> pdb=" O ASP B 556 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 554 through 559' Processing helix chain 'D' and resid 58 through 67 removed outlier: 4.134A pdb=" N LEU D 67 " --> pdb=" O ASP D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 77 removed outlier: 3.586A pdb=" N ASP D 76 " --> pdb=" O THR D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 99 removed outlier: 3.810A pdb=" N ILE D 85 " --> pdb=" O TRP D 81 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY D 99 " --> pdb=" O TYR D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 122 Processing helix chain 'D' and resid 140 through 145 Processing helix chain 'D' and resid 146 through 148 No H-bonds generated for 'chain 'D' and resid 146 through 148' Processing helix chain 'D' and resid 152 through 171 Proline residue: D 162 - end of helix removed outlier: 4.385A pdb=" N GLN D 171 " --> pdb=" O LEU D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 191 Processing helix chain 'C' and resid 13 through 22 Processing helix chain 'C' and resid 27 through 45 removed outlier: 4.143A pdb=" N HIS C 45 " --> pdb=" O THR C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 75 Processing helix chain 'E' and resid 61 through 77 Processing helix chain 'E' and resid 89 through 100 Processing helix chain 'E' and resid 115 through 120 Processing helix chain 'E' and resid 161 through 175 Processing helix chain 'E' and resid 189 through 204 removed outlier: 3.787A pdb=" N TYR E 193 " --> pdb=" O GLN E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 216 Processing helix chain 'E' and resid 217 through 225 Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 239 through 250 removed outlier: 4.189A pdb=" N ARG E 250 " --> pdb=" O LEU E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 279 Processing helix chain 'E' and resid 302 through 314 removed outlier: 3.672A pdb=" N LEU E 306 " --> pdb=" O PRO E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 339 Processing helix chain 'E' and resid 342 through 347 Processing helix chain 'E' and resid 368 through 379 Processing helix chain 'E' and resid 379 through 384 Processing helix chain 'E' and resid 389 through 405 removed outlier: 3.869A pdb=" N VAL E 393 " --> pdb=" O PRO E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 427 removed outlier: 4.012A pdb=" N ASP E 427 " --> pdb=" O SER E 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 450 through 458 removed outlier: 3.562A pdb=" N ARG E 454 " --> pdb=" O THR E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 461 through 476 removed outlier: 3.524A pdb=" N LEU E 465 " --> pdb=" O THR E 461 " (cutoff:3.500A) Processing helix chain 'E' and resid 482 through 504 Processing helix chain 'E' and resid 534 through 554 Processing helix chain 'F' and resid 20 through 28 Processing helix chain 'F' and resid 57 through 85 removed outlier: 3.953A pdb=" N SER F 61 " --> pdb=" O PRO F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 114 removed outlier: 3.560A pdb=" N ARG F 112 " --> pdb=" O SER F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 122 removed outlier: 3.569A pdb=" N ASP F 119 " --> pdb=" O MET F 116 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ASP F 120 " --> pdb=" O ARG F 117 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE F 122 " --> pdb=" O ASP F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 186 removed outlier: 3.726A pdb=" N ASP F 177 " --> pdb=" O GLY F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 215 removed outlier: 3.672A pdb=" N ILE F 204 " --> pdb=" O THR F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 237 removed outlier: 4.728A pdb=" N PHE F 233 " --> pdb=" O ASN F 229 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ASN F 234 " --> pdb=" O ALA F 230 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA F 235 " --> pdb=" O ASN F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 261 removed outlier: 3.519A pdb=" N ARG F 254 " --> pdb=" O HIS F 250 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER F 260 " --> pdb=" O GLY F 256 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY F 261 " --> pdb=" O VAL F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 286 Processing helix chain 'F' and resid 313 through 325 Processing helix chain 'F' and resid 345 through 351 removed outlier: 3.605A pdb=" N ILE F 349 " --> pdb=" O GLY F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 378 through 389 Processing helix chain 'F' and resid 390 through 395 removed outlier: 3.550A pdb=" N SER F 395 " --> pdb=" O THR F 391 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 415 removed outlier: 3.538A pdb=" N LEU F 403 " --> pdb=" O PRO F 399 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 444 removed outlier: 3.717A pdb=" N GLU F 424 " --> pdb=" O GLY F 420 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA F 430 " --> pdb=" O LEU F 426 " (cutoff:3.500A) Processing helix chain 'F' and resid 464 through 476 removed outlier: 3.987A pdb=" N ALA F 468 " --> pdb=" O SER F 464 " (cutoff:3.500A) Processing helix chain 'F' and resid 504 through 522 Processing helix chain 'F' and resid 528 through 532 removed outlier: 4.022A pdb=" N SER F 531 " --> pdb=" O SER F 528 " (cutoff:3.500A) Processing helix chain 'F' and resid 541 through 553 Proline residue: F 550 - end of helix Processing helix chain 'F' and resid 554 through 559 removed outlier: 6.675A pdb=" N LYS F 557 " --> pdb=" O LYS F 554 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR F 558 " --> pdb=" O ASP F 555 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE F 559 " --> pdb=" O ASP F 556 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 554 through 559' Processing helix chain 'H' and resid 58 through 67 removed outlier: 4.133A pdb=" N LEU H 67 " --> pdb=" O ASP H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 77 removed outlier: 3.586A pdb=" N ASP H 76 " --> pdb=" O THR H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 99 removed outlier: 3.810A pdb=" N ILE H 85 " --> pdb=" O TRP H 81 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY H 99 " --> pdb=" O TYR H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 122 Processing helix chain 'H' and resid 140 through 145 Processing helix chain 'H' and resid 146 through 148 No H-bonds generated for 'chain 'H' and resid 146 through 148' Processing helix chain 'H' and resid 152 through 171 Proline residue: H 162 - end of helix removed outlier: 4.385A pdb=" N GLN H 171 " --> pdb=" O LEU H 167 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 191 Processing helix chain 'G' and resid 13 through 22 Processing helix chain 'G' and resid 27 through 45 removed outlier: 4.142A pdb=" N HIS G 45 " --> pdb=" O THR G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 52 through 75 Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 137 removed outlier: 7.183A pdb=" N ILE A 135 " --> pdb=" O THR A 145 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N THR A 145 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ARG A 137 " --> pdb=" O LYS A 143 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N LYS A 143 " --> pdb=" O ARG A 137 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N LEU A 506 " --> pdb=" O ASN A 146 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE A 148 " --> pdb=" O LEU A 506 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 207 through 211 removed outlier: 6.803A pdb=" N LYS A 286 " --> pdb=" O ARG A 316 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N PHE A 318 " --> pdb=" O LYS A 286 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ILE A 288 " --> pdb=" O PHE A 318 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N ASP A 320 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N THR A 290 " --> pdb=" O ASP A 320 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 444 through 447 removed outlier: 4.099A pdb=" N LEU A 447 " --> pdb=" O LEU A 525 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 126 through 127 removed outlier: 4.031A pdb=" N ARG B 135 " --> pdb=" O THR B 127 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASP B 138 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ALA B 153 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N ILE B 140 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N SER B 151 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N HIS B 142 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N THR B 149 " --> pdb=" O HIS B 142 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N ALA B 479 " --> pdb=" O PRO B 156 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N MET B 158 " --> pdb=" O ALA B 479 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 218 through 222 removed outlier: 3.638A pdb=" N GLY B 373 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ILE B 297 " --> pdb=" O TYR B 327 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N PHE B 329 " --> pdb=" O ILE B 297 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE B 299 " --> pdb=" O PHE B 329 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ASP B 331 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ALA B 301 " --> pdb=" O ASP B 331 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N GLU B 302 " --> pdb=" O ASP B 246 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE B 267 " --> pdb=" O SER B 245 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 455 through 459 removed outlier: 4.102A pdb=" N VAL B 481 " --> pdb=" O ARG B 496 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 132 through 137 removed outlier: 7.183A pdb=" N ILE E 135 " --> pdb=" O THR E 145 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N THR E 145 " --> pdb=" O ILE E 135 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ARG E 137 " --> pdb=" O LYS E 143 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N LYS E 143 " --> pdb=" O ARG E 137 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N LEU E 506 " --> pdb=" O ASN E 146 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE E 148 " --> pdb=" O LEU E 506 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 207 through 211 removed outlier: 6.802A pdb=" N LYS E 286 " --> pdb=" O ARG E 316 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N PHE E 318 " --> pdb=" O LYS E 286 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ILE E 288 " --> pdb=" O PHE E 318 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ASP E 320 " --> pdb=" O ILE E 288 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N THR E 290 " --> pdb=" O ASP E 320 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 444 through 447 removed outlier: 4.099A pdb=" N LEU E 447 " --> pdb=" O LEU E 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 126 through 127 removed outlier: 4.031A pdb=" N ARG F 135 " --> pdb=" O THR F 127 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP F 138 " --> pdb=" O ALA F 153 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ALA F 153 " --> pdb=" O ASP F 138 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N ILE F 140 " --> pdb=" O SER F 151 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N SER F 151 " --> pdb=" O ILE F 140 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N HIS F 142 " --> pdb=" O THR F 149 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N THR F 149 " --> pdb=" O HIS F 142 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N ALA F 479 " --> pdb=" O PRO F 156 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N MET F 158 " --> pdb=" O ALA F 479 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 218 through 222 removed outlier: 3.638A pdb=" N GLY F 373 " --> pdb=" O PHE F 222 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ILE F 297 " --> pdb=" O TYR F 327 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N PHE F 329 " --> pdb=" O ILE F 297 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE F 299 " --> pdb=" O PHE F 329 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ASP F 331 " --> pdb=" O ILE F 299 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ALA F 301 " --> pdb=" O ASP F 331 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N GLU F 302 " --> pdb=" O ASP F 246 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE F 267 " --> pdb=" O SER F 245 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 455 through 459 removed outlier: 4.102A pdb=" N VAL F 481 " --> pdb=" O ARG F 496 " (cutoff:3.500A) 973 hydrogen bonds defined for protein. 2847 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.98 Time building geometry restraints manager: 6.34 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.800 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 48.540 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.180 ------------------------------------------------------------------------------- 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 20638 Z= 0.268 Angle : 0.720 14.137 27970 Z= 0.414 Chirality : 0.047 0.516 3170 Planarity : 0.005 0.068 3548 Dihedral : 13.959 105.161 7656 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.56 % Favored : 94.12 % Rotamer: Outliers : 0.27 % Allowed : 0.94 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.17), residues: 2516 helix: 1.50 (0.15), residues: 1212 sheet: -0.41 (0.35), residues: 224 loop : -1.94 (0.17), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 294 HIS 0.008 0.001 HIS F 78 PHE 0.019 0.001 PHE G 62 TYR 0.015 0.001 TYR F 510 ARG 0.003 0.000 ARG D 92 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 253 time to evaluate : 2.488 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: 0.3228 time to fit residues: 132.1062 Evaluate side-chains 206 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 2.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 3.9990 chunk 187 optimal weight: 0.9980 chunk 104 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 chunk 126 optimal weight: 7.9990 chunk 100 optimal weight: 4.9990 chunk 194 optimal weight: 0.0970 chunk 75 optimal weight: 1.9990 chunk 118 optimal weight: 8.9990 chunk 144 optimal weight: 5.9990 chunk 225 optimal weight: 0.9980 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 HIS B 90 HIS B 96 HIS B 145 ASN D 62 ASN D 110 ASN E 421 HIS F 90 HIS F 96 HIS F 145 ASN H 62 ASN H 110 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.0938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20638 Z= 0.216 Angle : 0.601 10.557 27970 Z= 0.311 Chirality : 0.043 0.172 3170 Planarity : 0.005 0.058 3548 Dihedral : 7.656 101.543 2846 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.48 % Favored : 94.36 % Rotamer: Outliers : 0.85 % Allowed : 6.68 % Favored : 92.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.17), residues: 2516 helix: 1.64 (0.15), residues: 1224 sheet: -0.13 (0.33), residues: 264 loop : -1.86 (0.18), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 142 HIS 0.003 0.001 HIS B 90 PHE 0.017 0.001 PHE E 256 TYR 0.016 0.001 TYR F 510 ARG 0.008 0.000 ARG G 20 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 225 time to evaluate : 2.621 Fit side-chains REVERT: B 119 ASP cc_start: 0.7780 (t70) cc_final: 0.7235 (t0) REVERT: B 158 MET cc_start: 0.8779 (ttp) cc_final: 0.8349 (ttm) REVERT: D 111 MET cc_start: 0.7412 (mmt) cc_final: 0.7040 (mmt) REVERT: D 137 ASP cc_start: 0.8437 (m-30) cc_final: 0.8213 (m-30) REVERT: C 51 MET cc_start: 0.8886 (mtt) cc_final: 0.8664 (mtt) REVERT: F 119 ASP cc_start: 0.7735 (t70) cc_final: 0.7239 (t0) REVERT: F 158 MET cc_start: 0.8788 (ttp) cc_final: 0.8368 (ttm) REVERT: H 111 MET cc_start: 0.7400 (mmt) cc_final: 0.7043 (mmt) REVERT: G 51 MET cc_start: 0.8884 (mtt) cc_final: 0.8651 (mtt) outliers start: 19 outliers final: 12 residues processed: 233 average time/residue: 0.3344 time to fit residues: 123.5697 Evaluate side-chains 220 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 208 time to evaluate : 2.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain E residue 524 SER Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 152 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 125 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 chunk 187 optimal weight: 5.9990 chunk 153 optimal weight: 8.9990 chunk 62 optimal weight: 10.0000 chunk 225 optimal weight: 10.0000 chunk 243 optimal weight: 5.9990 chunk 200 optimal weight: 2.9990 chunk 223 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 180 optimal weight: 10.0000 overall best weight: 3.1786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 20638 Z= 0.356 Angle : 0.658 12.746 27970 Z= 0.339 Chirality : 0.046 0.174 3170 Planarity : 0.005 0.055 3548 Dihedral : 7.876 97.802 2846 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.12 % Favored : 93.72 % Rotamer: Outliers : 1.93 % Allowed : 9.14 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.17), residues: 2516 helix: 1.57 (0.15), residues: 1224 sheet: -0.27 (0.32), residues: 284 loop : -1.86 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 142 HIS 0.005 0.001 HIS B 142 PHE 0.022 0.002 PHE A 256 TYR 0.020 0.002 TYR B 510 ARG 0.002 0.000 ARG D 155 *********************** 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 267 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 224 time to evaluate : 2.567 Fit side-chains REVERT: A 477 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.7983 (tm-30) REVERT: B 119 ASP cc_start: 0.7895 (t70) cc_final: 0.7303 (t0) REVERT: D 111 MET cc_start: 0.7535 (mmt) cc_final: 0.7226 (mmt) REVERT: D 137 ASP cc_start: 0.8513 (m-30) cc_final: 0.8248 (m-30) REVERT: E 477 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.7987 (tm-30) REVERT: F 119 ASP cc_start: 0.7888 (t70) cc_final: 0.7299 (t0) REVERT: H 111 MET cc_start: 0.7529 (mmt) cc_final: 0.7224 (mmt) outliers start: 43 outliers final: 23 residues processed: 245 average time/residue: 0.3163 time to fit residues: 123.1170 Evaluate side-chains 240 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 215 time to evaluate : 2.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 477 GLN Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 356 ASP Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain E residue 477 GLN Chi-restraints excluded: chain E residue 524 SER Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 342 THR Chi-restraints excluded: chain F residue 356 ASP Chi-restraints excluded: chain F residue 388 ASP Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain G residue 13 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 222 optimal weight: 1.9990 chunk 169 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 151 optimal weight: 6.9990 chunk 226 optimal weight: 1.9990 chunk 239 optimal weight: 6.9990 chunk 118 optimal weight: 20.0000 chunk 214 optimal weight: 0.2980 chunk 64 optimal weight: 0.7980 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 20638 Z= 0.203 Angle : 0.573 11.833 27970 Z= 0.294 Chirality : 0.043 0.230 3170 Planarity : 0.005 0.051 3548 Dihedral : 7.669 96.430 2846 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.89 % Favored : 94.95 % Rotamer: Outliers : 1.08 % Allowed : 10.84 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.17), residues: 2516 helix: 1.83 (0.15), residues: 1210 sheet: -0.04 (0.34), residues: 270 loop : -1.78 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 294 HIS 0.004 0.001 HIS B 90 PHE 0.016 0.001 PHE A 256 TYR 0.016 0.001 TYR B 510 ARG 0.002 0.000 ARG G 20 *********************** 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 249 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 225 time to evaluate : 2.378 Fit side-chains REVERT: B 119 ASP cc_start: 0.7896 (t70) cc_final: 0.7261 (t0) REVERT: B 158 MET cc_start: 0.8751 (ttp) cc_final: 0.8339 (ttm) REVERT: D 111 MET cc_start: 0.7392 (mmt) cc_final: 0.7064 (mmt) REVERT: C 51 MET cc_start: 0.8884 (mtt) cc_final: 0.8661 (mtt) REVERT: F 119 ASP cc_start: 0.7885 (t70) cc_final: 0.7256 (t0) REVERT: F 158 MET cc_start: 0.8753 (ttp) cc_final: 0.8342 (ttm) REVERT: H 111 MET cc_start: 0.7379 (mmt) cc_final: 0.7048 (mmt) REVERT: G 51 MET cc_start: 0.8881 (mtt) cc_final: 0.8655 (mtt) outliers start: 24 outliers final: 15 residues processed: 243 average time/residue: 0.3132 time to fit residues: 121.6756 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 : 2.545 ------------------------------------------------------------------------------- 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 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 124 THR Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 120 MET Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 189 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 199 optimal weight: 0.9980 chunk 136 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 178 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 204 optimal weight: 1.9990 chunk 165 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 122 optimal weight: 0.9980 chunk 215 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 20638 Z= 0.165 Angle : 0.538 10.952 27970 Z= 0.276 Chirality : 0.042 0.169 3170 Planarity : 0.005 0.049 3548 Dihedral : 7.485 95.561 2846 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.41 % Favored : 94.52 % Rotamer: Outliers : 1.66 % Allowed : 10.84 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.17), residues: 2516 helix: 1.99 (0.15), residues: 1216 sheet: -0.11 (0.32), residues: 288 loop : -1.66 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 294 HIS 0.003 0.001 HIS F 90 PHE 0.016 0.001 PHE E 256 TYR 0.013 0.001 TYR F 510 ARG 0.005 0.000 ARG C 20 *********************** 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 275 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 238 time to evaluate : 2.573 Fit side-chains REVERT: A 269 ASN cc_start: 0.7246 (t0) cc_final: 0.7006 (t0) REVERT: A 477 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.8081 (tt0) REVERT: A 533 MET cc_start: 0.7358 (mtm) cc_final: 0.7046 (mtm) REVERT: B 119 ASP cc_start: 0.7844 (t70) cc_final: 0.7272 (t0) REVERT: B 158 MET cc_start: 0.8768 (ttp) cc_final: 0.8289 (ttm) REVERT: D 111 MET cc_start: 0.7315 (mmt) cc_final: 0.7028 (mmt) REVERT: C 51 MET cc_start: 0.8889 (mtt) cc_final: 0.8671 (mtt) REVERT: E 269 ASN cc_start: 0.7258 (t0) cc_final: 0.7016 (t0) REVERT: E 477 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.8082 (tt0) REVERT: E 533 MET cc_start: 0.7362 (mtm) cc_final: 0.7048 (mtm) REVERT: F 119 ASP cc_start: 0.7843 (t70) cc_final: 0.7269 (t0) REVERT: F 158 MET cc_start: 0.8771 (ttp) cc_final: 0.8289 (ttm) REVERT: H 111 MET cc_start: 0.7319 (mmt) cc_final: 0.7031 (mmt) REVERT: G 51 MET cc_start: 0.8904 (mtt) cc_final: 0.8698 (mtt) outliers start: 37 outliers final: 20 residues processed: 262 average time/residue: 0.3215 time to fit residues: 134.5723 Evaluate side-chains 247 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 225 time to evaluate : 2.432 ------------------------------------------------------------------------------- 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 53 VAL Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain 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 53 VAL Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain H residue 120 MET Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain G residue 66 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 80 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 140 optimal weight: 0.2980 chunk 59 optimal weight: 2.9990 chunk 239 optimal weight: 8.9990 chunk 199 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 79 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 20638 Z= 0.244 Angle : 0.580 11.638 27970 Z= 0.297 Chirality : 0.043 0.167 3170 Planarity : 0.005 0.048 3548 Dihedral : 7.619 94.662 2846 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.68 % Favored : 94.24 % Rotamer: Outliers : 1.84 % Allowed : 11.69 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.17), residues: 2516 helix: 1.99 (0.15), residues: 1216 sheet: -0.14 (0.33), residues: 288 loop : -1.67 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 142 HIS 0.003 0.001 HIS E 258 PHE 0.019 0.001 PHE E 256 TYR 0.017 0.001 TYR F 510 ARG 0.003 0.000 ARG C 20 *********************** 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 268 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 227 time to evaluate : 2.530 Fit side-chains REVERT: A 477 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.8089 (tt0) REVERT: A 533 MET cc_start: 0.7322 (mtm) cc_final: 0.7013 (mtm) REVERT: B 119 ASP cc_start: 0.7911 (t70) cc_final: 0.7290 (t0) REVERT: B 158 MET cc_start: 0.8757 (ttp) cc_final: 0.8341 (ttm) REVERT: D 111 MET cc_start: 0.7326 (mmt) cc_final: 0.7057 (mmt) REVERT: C 51 MET cc_start: 0.8888 (mtt) cc_final: 0.8667 (mtt) REVERT: E 477 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.8088 (tt0) REVERT: E 533 MET cc_start: 0.7326 (mtm) cc_final: 0.7013 (mtm) REVERT: F 119 ASP cc_start: 0.7909 (t70) cc_final: 0.7285 (t0) REVERT: F 158 MET cc_start: 0.8762 (ttp) cc_final: 0.8342 (ttm) REVERT: H 111 MET cc_start: 0.7338 (mmt) cc_final: 0.7063 (mmt) REVERT: G 51 MET cc_start: 0.8890 (mtt) cc_final: 0.8666 (mtt) outliers start: 41 outliers final: 30 residues processed: 251 average time/residue: 0.3042 time to fit residues: 121.7598 Evaluate side-chains 253 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 221 time to evaluate : 2.494 ------------------------------------------------------------------------------- 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 187 SER Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 437 THR Chi-restraints excluded: chain E residue 477 GLN Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 504 THR Chi-restraints excluded: chain H residue 120 MET Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain G residue 66 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 231 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 chunk 136 optimal weight: 0.9990 chunk 175 optimal weight: 6.9990 chunk 135 optimal weight: 5.9990 chunk 201 optimal weight: 1.9990 chunk 133 optimal weight: 0.0980 chunk 239 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 chunk 145 optimal weight: 10.0000 chunk 110 optimal weight: 4.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 HIS D 62 ASN F 96 HIS H 62 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20638 Z= 0.219 Angle : 0.564 11.613 27970 Z= 0.290 Chirality : 0.043 0.167 3170 Planarity : 0.005 0.047 3548 Dihedral : 7.614 94.090 2846 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.56 % Favored : 94.36 % Rotamer: Outliers : 2.06 % Allowed : 12.01 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.17), residues: 2516 helix: 2.02 (0.15), residues: 1216 sheet: -0.11 (0.33), residues: 288 loop : -1.65 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 294 HIS 0.003 0.001 HIS F 78 PHE 0.018 0.001 PHE E 256 TYR 0.016 0.001 TYR F 510 ARG 0.004 0.000 ARG C 20 *********************** 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 277 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 231 time to evaluate : 2.422 Fit side-chains REVERT: A 136 THR cc_start: 0.8533 (OUTLIER) cc_final: 0.8248 (m) REVERT: A 533 MET cc_start: 0.7221 (mtm) cc_final: 0.6885 (mtm) REVERT: B 119 ASP cc_start: 0.7916 (t70) cc_final: 0.7292 (t0) REVERT: B 158 MET cc_start: 0.8751 (ttp) cc_final: 0.8327 (ttm) REVERT: D 111 MET cc_start: 0.7335 (mmt) cc_final: 0.7071 (mmt) REVERT: C 51 MET cc_start: 0.8871 (mtt) cc_final: 0.8657 (mtt) REVERT: E 136 THR cc_start: 0.8543 (OUTLIER) cc_final: 0.8258 (m) REVERT: E 533 MET cc_start: 0.7223 (mtm) cc_final: 0.6893 (mtm) REVERT: F 119 ASP cc_start: 0.7918 (t70) cc_final: 0.7288 (t0) REVERT: F 158 MET cc_start: 0.8756 (ttp) cc_final: 0.8336 (ttm) REVERT: H 111 MET cc_start: 0.7347 (mmt) cc_final: 0.7076 (mmt) REVERT: G 51 MET cc_start: 0.8872 (mtt) cc_final: 0.8651 (mtt) outliers start: 46 outliers final: 34 residues processed: 258 average time/residue: 0.3074 time to fit residues: 127.0363 Evaluate side-chains 257 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 221 time to evaluate : 2.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 437 THR Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 504 THR Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 120 MET Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain G residue 66 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 147 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 142 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 151 optimal weight: 0.0670 chunk 162 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 187 optimal weight: 4.9990 chunk 217 optimal weight: 5.9990 overall best weight: 1.1922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 62 ASN H 62 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 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 0.029 20638 Z= 0.169 Angle : 0.542 10.895 27970 Z= 0.277 Chirality : 0.042 0.165 3170 Planarity : 0.004 0.046 3548 Dihedral : 7.495 93.479 2846 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.21 % Favored : 94.71 % Rotamer: Outliers : 1.66 % Allowed : 12.68 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.17), residues: 2516 helix: 2.11 (0.15), residues: 1216 sheet: 0.11 (0.33), residues: 280 loop : -1.59 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 294 HIS 0.002 0.001 HIS B 78 PHE 0.016 0.001 PHE A 256 TYR 0.013 0.001 TYR F 510 ARG 0.005 0.000 ARG C 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 232 time to evaluate : 2.475 Fit side-chains REVERT: A 136 THR cc_start: 0.8552 (OUTLIER) cc_final: 0.8288 (m) REVERT: A 533 MET cc_start: 0.7120 (mtm) cc_final: 0.6742 (mtm) REVERT: B 119 ASP cc_start: 0.7977 (t70) cc_final: 0.7359 (t0) REVERT: B 158 MET cc_start: 0.8750 (ttp) cc_final: 0.8283 (ttm) REVERT: D 110 ASN cc_start: 0.7827 (t0) cc_final: 0.7608 (t0) REVERT: D 111 MET cc_start: 0.7350 (mmt) cc_final: 0.7102 (mmt) REVERT: C 51 MET cc_start: 0.8882 (mtt) cc_final: 0.8654 (mtt) REVERT: E 136 THR cc_start: 0.8555 (OUTLIER) cc_final: 0.8292 (m) REVERT: E 533 MET cc_start: 0.7126 (mtm) cc_final: 0.6749 (mtm) REVERT: F 119 ASP cc_start: 0.7971 (t70) cc_final: 0.7361 (t0) REVERT: F 158 MET cc_start: 0.8754 (ttp) cc_final: 0.8283 (ttm) REVERT: H 110 ASN cc_start: 0.7824 (t0) cc_final: 0.7603 (t0) REVERT: H 111 MET cc_start: 0.7362 (mmt) cc_final: 0.7107 (mmt) REVERT: G 51 MET cc_start: 0.8887 (mtt) cc_final: 0.8680 (mtt) outliers start: 37 outliers final: 32 residues processed: 255 average time/residue: 0.3310 time to fit residues: 136.3190 Evaluate side-chains 253 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 219 time to evaluate : 2.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 437 THR Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 504 THR Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 120 MET Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain G residue 66 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 228 optimal weight: 9.9990 chunk 208 optimal weight: 4.9990 chunk 222 optimal weight: 5.9990 chunk 134 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 174 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 201 optimal weight: 0.8980 chunk 210 optimal weight: 0.9990 chunk 221 optimal weight: 3.9990 chunk 146 optimal weight: 0.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 62 ASN H 62 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20638 Z= 0.201 Angle : 0.564 11.078 27970 Z= 0.286 Chirality : 0.042 0.163 3170 Planarity : 0.005 0.046 3548 Dihedral : 7.514 93.013 2846 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.56 % Favored : 94.36 % Rotamer: Outliers : 1.75 % Allowed : 12.99 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.17), residues: 2516 helix: 2.12 (0.15), residues: 1216 sheet: 0.30 (0.34), residues: 266 loop : -1.56 (0.19), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 294 HIS 0.002 0.001 HIS B 78 PHE 0.017 0.001 PHE E 256 TYR 0.016 0.001 TYR B 510 ARG 0.005 0.000 ARG C 20 *********************** 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 263 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 224 time to evaluate : 2.492 Fit side-chains REVERT: A 136 THR cc_start: 0.8557 (OUTLIER) cc_final: 0.8294 (m) REVERT: A 533 MET cc_start: 0.7159 (mtm) cc_final: 0.6804 (mtm) REVERT: B 119 ASP cc_start: 0.7973 (t70) cc_final: 0.7353 (t0) REVERT: B 158 MET cc_start: 0.8748 (ttp) cc_final: 0.8291 (ttm) REVERT: D 111 MET cc_start: 0.7356 (mmt) cc_final: 0.7098 (mmt) REVERT: C 51 MET cc_start: 0.8883 (mtt) cc_final: 0.8654 (mtt) REVERT: E 136 THR cc_start: 0.8564 (OUTLIER) cc_final: 0.8299 (m) REVERT: E 533 MET cc_start: 0.7272 (mtm) cc_final: 0.6904 (mtm) REVERT: F 119 ASP cc_start: 0.7977 (t70) cc_final: 0.7367 (t0) REVERT: F 158 MET cc_start: 0.8753 (ttp) cc_final: 0.8294 (ttm) REVERT: H 111 MET cc_start: 0.7367 (mmt) cc_final: 0.7102 (mmt) REVERT: H 137 ASP cc_start: 0.8287 (OUTLIER) cc_final: 0.7858 (m-30) REVERT: G 51 MET cc_start: 0.8892 (mtt) cc_final: 0.8687 (mtt) outliers start: 39 outliers final: 33 residues processed: 246 average time/residue: 0.3223 time to fit residues: 126.8884 Evaluate side-chains 255 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 219 time to evaluate : 2.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 437 THR Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 504 THR Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 120 MET Chi-restraints excluded: chain H residue 137 ASP Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain G residue 66 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 235 optimal weight: 1.9990 chunk 143 optimal weight: 0.6980 chunk 111 optimal weight: 0.3980 chunk 163 optimal weight: 2.9990 chunk 247 optimal weight: 2.9990 chunk 227 optimal weight: 4.9990 chunk 196 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 156 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 62 ASN H 62 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 20638 Z= 0.170 Angle : 0.546 10.399 27970 Z= 0.278 Chirality : 0.042 0.165 3170 Planarity : 0.005 0.046 3548 Dihedral : 7.397 92.541 2846 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.09 % Favored : 94.83 % Rotamer: Outliers : 1.61 % Allowed : 13.08 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.17), residues: 2516 helix: 2.17 (0.15), residues: 1218 sheet: 0.16 (0.33), residues: 280 loop : -1.53 (0.19), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 294 HIS 0.003 0.001 HIS E 374 PHE 0.016 0.001 PHE E 256 TYR 0.013 0.001 TYR B 510 ARG 0.005 0.000 ARG C 20 ********************** 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 258 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 222 time to evaluate : 2.531 Fit side-chains REVERT: A 136 THR cc_start: 0.8601 (OUTLIER) cc_final: 0.8334 (m) REVERT: A 533 MET cc_start: 0.7268 (mtm) cc_final: 0.6883 (mtm) REVERT: B 119 ASP cc_start: 0.8011 (t70) cc_final: 0.7386 (t0) REVERT: B 158 MET cc_start: 0.8747 (ttp) cc_final: 0.8270 (ttm) REVERT: D 110 ASN cc_start: 0.7827 (t0) cc_final: 0.7610 (t0) REVERT: D 111 MET cc_start: 0.7313 (mmt) cc_final: 0.7066 (mmt) REVERT: C 51 MET cc_start: 0.8871 (mtt) cc_final: 0.8646 (mtt) REVERT: E 136 THR cc_start: 0.8612 (OUTLIER) cc_final: 0.8344 (m) REVERT: E 533 MET cc_start: 0.7268 (mtm) cc_final: 0.6885 (mtm) REVERT: F 119 ASP cc_start: 0.8015 (t70) cc_final: 0.7385 (t0) REVERT: F 158 MET cc_start: 0.8749 (ttp) cc_final: 0.8270 (ttm) REVERT: H 110 ASN cc_start: 0.7824 (t0) cc_final: 0.7605 (t0) REVERT: H 111 MET cc_start: 0.7355 (mmt) cc_final: 0.7106 (mmt) REVERT: H 137 ASP cc_start: 0.8322 (OUTLIER) cc_final: 0.7838 (m-30) REVERT: G 51 MET cc_start: 0.8902 (mtt) cc_final: 0.8693 (mtt) outliers start: 36 outliers final: 30 residues processed: 242 average time/residue: 0.3148 time to fit residues: 121.1365 Evaluate side-chains 247 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 214 time to evaluate : 2.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 437 THR Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 504 THR Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 120 MET Chi-restraints excluded: chain H residue 137 ASP Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain G residue 66 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 chunk 181 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 197 optimal weight: 6.9990 chunk 82 optimal weight: 10.0000 chunk 202 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 173 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN D 62 ASN E 274 GLN H 62 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.131076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.104067 restraints weight = 27591.133| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.70 r_work: 0.2986 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20638 Z= 0.216 Angle : 0.569 11.001 27970 Z= 0.289 Chirality : 0.042 0.164 3170 Planarity : 0.005 0.047 3548 Dihedral : 7.497 91.975 2846 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.64 % Favored : 94.28 % Rotamer: Outliers : 1.61 % Allowed : 13.44 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.17), residues: 2516 helix: 2.10 (0.15), residues: 1230 sheet: 0.30 (0.34), residues: 266 loop : -1.58 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 294 HIS 0.003 0.001 HIS B 78 PHE 0.018 0.001 PHE E 256 TYR 0.017 0.001 TYR F 510 ARG 0.005 0.000 ARG G 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4095.04 seconds wall clock time: 76 minutes 3.63 seconds (4563.63 seconds total)