Starting phenix.real_space_refine on Wed Sep 25 12:04:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfh_24442/09_2024/7rfh_24442_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfh_24442/09_2024/7rfh_24442.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfh_24442/09_2024/7rfh_24442.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfh_24442/09_2024/7rfh_24442.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfh_24442/09_2024/7rfh_24442_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfh_24442/09_2024/7rfh_24442_trim.cif" } resolution = 3.7 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= 0.279 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: 6 Type Number sf(0) Gaussians P 48 5.49 5 S 169 5.16 5 C 17265 2.51 5 N 4717 2.21 5 O 5339 1.98 5 H 27603 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 163 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 55141 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 6823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 6823 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 17, 'TRANS': 431} Chain breaks: 5 Chain: "B" Number of atoms: 6823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 6823 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 17, 'TRANS': 431} Chain breaks: 5 Chain: "C" Number of atoms: 6823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 6823 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 17, 'TRANS': 431} Chain breaks: 5 Chain: "D" Number of atoms: 6823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 6823 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 17, 'TRANS': 431} Chain breaks: 5 Chain: "E" Number of atoms: 6823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 6823 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 17, 'TRANS': 431} Chain breaks: 5 Chain: "F" Number of atoms: 6823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 6823 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 17, 'TRANS': 431} Chain breaks: 5 Chain: "G" Number of atoms: 6845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 6845 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 17, 'TRANS': 432} Chain breaks: 5 Chain: "H" Number of atoms: 6862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 6862 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 17, 'TRANS': 433} Chain breaks: 5 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 20.14, per 1000 atoms: 0.37 Number of scatterers: 55141 At special positions: 0 Unit cell: (142.8, 142.8, 156.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 169 16.00 P 48 15.00 O 5339 8.00 N 4717 7.00 C 17265 6.00 H 27603 1.00 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=0, symmetry=0 Time building additional restraints: 10.21 Conformation dependent library (CDL) restraints added in 3.2 seconds 6998 Ramachandran restraints generated. 3499 Oldfield, 0 Emsley, 3499 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6502 Finding SS restraints... Secondary structure from input PDB file: 166 helices and 43 sheets defined 43.6% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.66 Creating SS restraints... Processing helix chain 'A' and resid -18 through -5 Processing helix chain 'A' and resid 3 through 8 Processing helix chain 'A' and resid 19 through 24 Processing helix chain 'A' and resid 25 through 27 No H-bonds generated for 'chain 'A' and resid 25 through 27' Processing helix chain 'A' and resid 75 through 85 Processing helix chain 'A' and resid 96 through 109 Processing helix chain 'A' and resid 127 through 132 Processing helix chain 'A' and resid 132 through 137 Processing helix chain 'A' and resid 159 through 163 Processing helix chain 'A' and resid 193 through 205 Processing helix chain 'A' and resid 224 through 228 Processing helix chain 'A' and resid 253 through 255 No H-bonds generated for 'chain 'A' and resid 253 through 255' Processing helix chain 'A' and resid 256 through 266 Processing helix chain 'A' and resid 280 through 294 Processing helix chain 'A' and resid 306 through 317 Processing helix chain 'A' and resid 342 through 355 Processing helix chain 'A' and resid 369 through 380 removed outlier: 3.636A pdb=" N GLY A 380 " --> pdb=" O ALA A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 452 through 471 Proline residue: A 458 - end of helix Processing helix chain 'A' and resid 475 through 485 Processing helix chain 'A' and resid 494 through 498 Processing helix chain 'B' and resid -18 through -5 Processing helix chain 'B' and resid 3 through 8 Processing helix chain 'B' and resid 19 through 24 Processing helix chain 'B' and resid 25 through 27 No H-bonds generated for 'chain 'B' and resid 25 through 27' Processing helix chain 'B' and resid 31 through 33 No H-bonds generated for 'chain 'B' and resid 31 through 33' Processing helix chain 'B' and resid 75 through 85 Processing helix chain 'B' and resid 96 through 109 Processing helix chain 'B' and resid 127 through 132 removed outlier: 3.819A pdb=" N GLU B 132 " --> pdb=" O GLY B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 137 Processing helix chain 'B' and resid 159 through 164 removed outlier: 3.500A pdb=" N ILE B 163 " --> pdb=" O THR B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 205 Processing helix chain 'B' and resid 224 through 228 Processing helix chain 'B' and resid 253 through 255 No H-bonds generated for 'chain 'B' and resid 253 through 255' Processing helix chain 'B' and resid 256 through 266 removed outlier: 3.547A pdb=" N ALA B 266 " --> pdb=" O LEU B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 294 Processing helix chain 'B' and resid 306 through 317 Processing helix chain 'B' and resid 342 through 355 Processing helix chain 'B' and resid 369 through 379 Processing helix chain 'B' and resid 387 through 391 Processing helix chain 'B' and resid 452 through 471 Proline residue: B 458 - end of helix Processing helix chain 'B' and resid 475 through 485 Processing helix chain 'B' and resid 494 through 500 removed outlier: 3.527A pdb=" N GLN B 498 " --> pdb=" O THR B 494 " (cutoff:3.500A) Processing helix chain 'C' and resid -18 through -5 removed outlier: 3.801A pdb=" N ALA C -6 " --> pdb=" O ARG C -10 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 8 removed outlier: 3.518A pdb=" N SER C 7 " --> pdb=" O ASP C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 24 Processing helix chain 'C' and resid 31 through 33 No H-bonds generated for 'chain 'C' and resid 31 through 33' Processing helix chain 'C' and resid 75 through 85 Processing helix chain 'C' and resid 96 through 109 Processing helix chain 'C' and resid 127 through 132 Processing helix chain 'C' and resid 132 through 137 Processing helix chain 'C' and resid 159 through 164 Processing helix chain 'C' and resid 193 through 205 Processing helix chain 'C' and resid 224 through 228 Processing helix chain 'C' and resid 253 through 255 No H-bonds generated for 'chain 'C' and resid 253 through 255' Processing helix chain 'C' and resid 256 through 266 Processing helix chain 'C' and resid 280 through 294 Processing helix chain 'C' and resid 306 through 317 Processing helix chain 'C' and resid 342 through 355 Processing helix chain 'C' and resid 369 through 380 removed outlier: 3.650A pdb=" N GLY C 380 " --> pdb=" O ALA C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 391 Processing helix chain 'C' and resid 452 through 471 Proline residue: C 458 - end of helix Processing helix chain 'C' and resid 475 through 485 Processing helix chain 'C' and resid 494 through 500 Processing helix chain 'D' and resid -18 through -5 Processing helix chain 'D' and resid 3 through 8 removed outlier: 3.703A pdb=" N SER D 7 " --> pdb=" O ASP D 3 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 24 Processing helix chain 'D' and resid 31 through 33 No H-bonds generated for 'chain 'D' and resid 31 through 33' Processing helix chain 'D' and resid 75 through 85 Processing helix chain 'D' and resid 96 through 109 removed outlier: 3.565A pdb=" N GLN D 100 " --> pdb=" O THR D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 132 Processing helix chain 'D' and resid 132 through 137 Processing helix chain 'D' and resid 159 through 163 Processing helix chain 'D' and resid 193 through 205 removed outlier: 3.672A pdb=" N GLN D 202 " --> pdb=" O ASN D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 228 Processing helix chain 'D' and resid 253 through 255 No H-bonds generated for 'chain 'D' and resid 253 through 255' Processing helix chain 'D' and resid 256 through 266 Processing helix chain 'D' and resid 280 through 294 Processing helix chain 'D' and resid 306 through 317 Processing helix chain 'D' and resid 342 through 355 Processing helix chain 'D' and resid 369 through 380 removed outlier: 3.635A pdb=" N GLY D 380 " --> pdb=" O ALA D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 391 Processing helix chain 'D' and resid 452 through 471 Proline residue: D 458 - end of helix Processing helix chain 'D' and resid 475 through 485 Processing helix chain 'D' and resid 494 through 499 Processing helix chain 'E' and resid -18 through -5 removed outlier: 3.549A pdb=" N GLN E -7 " --> pdb=" O ALA E -11 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA E -6 " --> pdb=" O ARG E -10 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 8 removed outlier: 3.727A pdb=" N SER E 7 " --> pdb=" O ASP E 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 24 Processing helix chain 'E' and resid 31 through 33 No H-bonds generated for 'chain 'E' and resid 31 through 33' Processing helix chain 'E' and resid 75 through 85 Processing helix chain 'E' and resid 96 through 109 Processing helix chain 'E' and resid 127 through 132 Processing helix chain 'E' and resid 132 through 137 Processing helix chain 'E' and resid 159 through 164 removed outlier: 3.570A pdb=" N ILE E 163 " --> pdb=" O THR E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 205 removed outlier: 3.582A pdb=" N GLU E 199 " --> pdb=" O LYS E 195 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN E 202 " --> pdb=" O ASN E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 228 Processing helix chain 'E' and resid 253 through 255 No H-bonds generated for 'chain 'E' and resid 253 through 255' Processing helix chain 'E' and resid 256 through 266 removed outlier: 3.547A pdb=" N ALA E 266 " --> pdb=" O LEU E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 294 Processing helix chain 'E' and resid 306 through 317 Processing helix chain 'E' and resid 342 through 355 Processing helix chain 'E' and resid 369 through 380 removed outlier: 3.648A pdb=" N GLY E 380 " --> pdb=" O ALA E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 391 Processing helix chain 'E' and resid 452 through 471 Proline residue: E 458 - end of helix Processing helix chain 'E' and resid 475 through 485 Processing helix chain 'F' and resid -18 through -5 removed outlier: 3.885A pdb=" N ALA F -6 " --> pdb=" O ARG F -10 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 8 removed outlier: 3.687A pdb=" N SER F 7 " --> pdb=" O ASP F 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 24 Processing helix chain 'F' and resid 25 through 27 No H-bonds generated for 'chain 'F' and resid 25 through 27' Processing helix chain 'F' and resid 75 through 85 Processing helix chain 'F' and resid 96 through 109 Processing helix chain 'F' and resid 132 through 137 Processing helix chain 'F' and resid 159 through 164 removed outlier: 3.540A pdb=" N ILE F 163 " --> pdb=" O THR F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 205 Processing helix chain 'F' and resid 224 through 228 Processing helix chain 'F' and resid 253 through 255 No H-bonds generated for 'chain 'F' and resid 253 through 255' Processing helix chain 'F' and resid 256 through 266 Processing helix chain 'F' and resid 280 through 294 Processing helix chain 'F' and resid 306 through 317 Processing helix chain 'F' and resid 342 through 355 Processing helix chain 'F' and resid 370 through 380 removed outlier: 3.687A pdb=" N GLY F 380 " --> pdb=" O ALA F 376 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 391 Processing helix chain 'F' and resid 452 through 471 Proline residue: F 458 - end of helix Processing helix chain 'F' and resid 475 through 485 Processing helix chain 'F' and resid 495 through 498 Processing helix chain 'G' and resid -18 through -5 removed outlier: 3.979A pdb=" N ALA G -6 " --> pdb=" O ARG G -10 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 24 Processing helix chain 'G' and resid 31 through 33 No H-bonds generated for 'chain 'G' and resid 31 through 33' Processing helix chain 'G' and resid 45 through 49 Processing helix chain 'G' and resid 75 through 85 Processing helix chain 'G' and resid 96 through 109 Processing helix chain 'G' and resid 127 through 132 Processing helix chain 'G' and resid 132 through 137 Processing helix chain 'G' and resid 159 through 164 Processing helix chain 'G' and resid 193 through 205 removed outlier: 3.990A pdb=" N GLU G 199 " --> pdb=" O LYS G 195 " (cutoff:3.500A) Processing helix chain 'G' and resid 224 through 228 Processing helix chain 'G' and resid 253 through 255 No H-bonds generated for 'chain 'G' and resid 253 through 255' Processing helix chain 'G' and resid 256 through 266 Processing helix chain 'G' and resid 280 through 294 Processing helix chain 'G' and resid 306 through 317 Processing helix chain 'G' and resid 342 through 355 Processing helix chain 'G' and resid 369 through 380 removed outlier: 3.565A pdb=" N GLY G 380 " --> pdb=" O ALA G 376 " (cutoff:3.500A) Processing helix chain 'G' and resid 387 through 391 Processing helix chain 'G' and resid 452 through 472 Proline residue: G 458 - end of helix Processing helix chain 'G' and resid 475 through 485 Processing helix chain 'H' and resid -18 through -5 removed outlier: 3.502A pdb=" N GLN H -7 " --> pdb=" O ALA H -11 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA H -6 " --> pdb=" O ARG H -10 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 8 removed outlier: 3.506A pdb=" N SER H 7 " --> pdb=" O ASP H 3 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 24 Processing helix chain 'H' and resid 25 through 27 No H-bonds generated for 'chain 'H' and resid 25 through 27' Processing helix chain 'H' and resid 75 through 85 Processing helix chain 'H' and resid 96 through 108 Processing helix chain 'H' and resid 127 through 132 Processing helix chain 'H' and resid 132 through 137 Processing helix chain 'H' and resid 159 through 164 removed outlier: 3.534A pdb=" N ILE H 163 " --> pdb=" O THR H 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 193 through 205 removed outlier: 3.520A pdb=" N GLN H 202 " --> pdb=" O ASN H 198 " (cutoff:3.500A) Processing helix chain 'H' and resid 224 through 228 Processing helix chain 'H' and resid 253 through 255 No H-bonds generated for 'chain 'H' and resid 253 through 255' Processing helix chain 'H' and resid 256 through 266 removed outlier: 3.557A pdb=" N ALA H 266 " --> pdb=" O LEU H 262 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 294 Processing helix chain 'H' and resid 306 through 317 removed outlier: 3.560A pdb=" N ALA H 310 " --> pdb=" O THR H 306 " (cutoff:3.500A) Processing helix chain 'H' and resid 342 through 355 Processing helix chain 'H' and resid 369 through 379 Processing helix chain 'H' and resid 387 through 391 Processing helix chain 'H' and resid 452 through 471 Proline residue: H 458 - end of helix Processing helix chain 'H' and resid 475 through 485 Processing helix chain 'H' and resid 495 through 500 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 37 Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 65 through 67 removed outlier: 4.108A pdb=" N ILE A 88 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE A 90 " --> pdb=" O SER A 67 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N GLY A 89 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ALA A 249 " --> pdb=" O GLY A 89 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE A 91 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE A 271 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N GLY A 302 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N LEU A 273 " --> pdb=" O GLY A 302 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N VAL A 304 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ARG A 322 " --> pdb=" O GLY A 302 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP A 364 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N MET A 385 " --> pdb=" O ALA A 363 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE A 66 " --> pdb=" O MET A 386 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 143 Processing sheet with id=AA5, first strand: chain 'A' and resid 208 through 212 removed outlier: 6.645A pdb=" N LEU A 209 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ILE A 221 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE A 211 " --> pdb=" O VAL A 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 35 through 37 removed outlier: 7.869A pdb=" N GLY C 29 " --> pdb=" O PHE B 490 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LYS B 492 " --> pdb=" O GLY C 29 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA8, first strand: chain 'B' and resid 65 through 67 removed outlier: 6.552A pdb=" N ILE B 66 " --> pdb=" O MET B 386 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N MET B 385 " --> pdb=" O ALA B 363 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 90 through 91 removed outlier: 6.545A pdb=" N ILE B 91 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ALA B 248 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE B 271 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N GLY B 302 " --> pdb=" O ILE B 271 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N LEU B 273 " --> pdb=" O GLY B 302 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N VAL B 304 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N ARG B 322 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N GLY B 301 " --> pdb=" O ARG B 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 142 through 143 Processing sheet with id=AB2, first strand: chain 'B' and resid 208 through 212 removed outlier: 6.657A pdb=" N LEU B 209 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ILE B 221 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ILE B 211 " --> pdb=" O VAL B 219 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 35 through 37 removed outlier: 7.892A pdb=" N GLY D 29 " --> pdb=" O PHE C 490 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LYS C 492 " --> pdb=" O GLY D 29 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB5, first strand: chain 'C' and resid 65 through 67 removed outlier: 6.553A pdb=" N ILE C 66 " --> pdb=" O MET C 386 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N MET C 385 " --> pdb=" O ALA C 363 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 90 through 91 removed outlier: 6.735A pdb=" N ILE C 271 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N GLY C 302 " --> pdb=" O ILE C 271 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N LEU C 273 " --> pdb=" O GLY C 302 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N VAL C 304 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N ARG C 322 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N GLY C 301 " --> pdb=" O ARG C 322 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 142 through 143 Processing sheet with id=AB8, first strand: chain 'C' and resid 208 through 213 removed outlier: 6.698A pdb=" N LEU C 209 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ILE C 221 " --> pdb=" O LEU C 209 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ILE C 211 " --> pdb=" O VAL C 219 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU C 217 " --> pdb=" O ASN C 213 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 18 through 19 Processing sheet with id=AC1, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC2, first strand: chain 'D' and resid 65 through 67 removed outlier: 4.077A pdb=" N ILE D 88 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE D 90 " --> pdb=" O SER D 67 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N GLY D 89 " --> pdb=" O GLY D 247 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N ALA D 249 " --> pdb=" O GLY D 89 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE D 91 " --> pdb=" O ALA D 249 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE D 271 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N GLY D 302 " --> pdb=" O ILE D 271 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N LEU D 273 " --> pdb=" O GLY D 302 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N VAL D 304 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N ARG D 322 " --> pdb=" O VAL D 299 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N GLY D 301 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP D 364 " --> pdb=" O VAL D 323 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N MET D 385 " --> pdb=" O ALA D 363 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE D 66 " --> pdb=" O MET D 386 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 142 through 144 removed outlier: 3.664A pdb=" N GLY D 156 " --> pdb=" O ILE D 144 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 208 through 212 removed outlier: 6.600A pdb=" N LEU D 209 " --> pdb=" O ILE D 221 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ILE D 221 " --> pdb=" O LEU D 209 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE D 211 " --> pdb=" O VAL D 219 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 28 through 29 Processing sheet with id=AC6, first strand: chain 'E' and resid 35 through 37 Processing sheet with id=AC7, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC8, first strand: chain 'E' and resid 65 through 67 removed outlier: 6.549A pdb=" N ILE E 66 " --> pdb=" O MET E 386 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N MET E 385 " --> pdb=" O ALA E 363 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 90 through 91 removed outlier: 6.498A pdb=" N ILE E 91 " --> pdb=" O ALA E 249 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ALA E 248 " --> pdb=" O VAL E 272 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE E 271 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N GLY E 302 " --> pdb=" O ILE E 271 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N LEU E 273 " --> pdb=" O GLY E 302 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N VAL E 304 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N ARG E 322 " --> pdb=" O VAL E 299 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N GLY E 301 " --> pdb=" O ARG E 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'E' and resid 142 through 144 removed outlier: 4.501A pdb=" N GLY E 156 " --> pdb=" O ILE E 144 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 208 through 212 Processing sheet with id=AD3, first strand: chain 'F' and resid 35 through 37 removed outlier: 7.972A pdb=" N GLY G 29 " --> pdb=" O PHE F 490 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LYS F 492 " --> pdb=" O GLY G 29 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AD5, first strand: chain 'F' and resid 65 through 67 removed outlier: 3.774A pdb=" N ILE F 88 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ALA F 248 " --> pdb=" O VAL F 272 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY F 320 " --> pdb=" O VAL F 299 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ASN F 303 " --> pdb=" O ARG F 322 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR F 383 " --> pdb=" O ILE F 361 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N MET F 385 " --> pdb=" O ALA F 363 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE F 66 " --> pdb=" O MET F 386 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 142 through 143 Processing sheet with id=AD7, first strand: chain 'F' and resid 208 through 213 removed outlier: 6.606A pdb=" N LEU F 209 " --> pdb=" O ILE F 221 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ILE F 221 " --> pdb=" O LEU F 209 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ILE F 211 " --> pdb=" O VAL F 219 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU F 217 " --> pdb=" O ASN F 213 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 18 through 19 Processing sheet with id=AD9, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AE1, first strand: chain 'G' and resid 65 through 67 removed outlier: 3.849A pdb=" N ILE G 88 " --> pdb=" O LEU G 65 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE G 90 " --> pdb=" O SER G 67 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE G 271 " --> pdb=" O ILE G 300 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N GLY G 302 " --> pdb=" O ILE G 271 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N LEU G 273 " --> pdb=" O GLY G 302 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N VAL G 304 " --> pdb=" O LEU G 273 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ARG G 322 " --> pdb=" O GLY G 302 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU G 321 " --> pdb=" O ILE G 362 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ASP G 364 " --> pdb=" O LEU G 321 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N VAL G 323 " --> pdb=" O ASP G 364 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N MET G 385 " --> pdb=" O ALA G 363 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE G 66 " --> pdb=" O MET G 386 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 142 through 143 Processing sheet with id=AE3, first strand: chain 'G' and resid 208 through 212 removed outlier: 6.429A pdb=" N LEU G 209 " --> pdb=" O ILE G 221 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ILE G 221 " --> pdb=" O LEU G 209 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE G 211 " --> pdb=" O VAL G 219 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 53 through 54 Processing sheet with id=AE5, first strand: chain 'H' and resid 65 through 67 removed outlier: 4.079A pdb=" N ILE H 88 " --> pdb=" O LEU H 65 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE H 90 " --> pdb=" O SER H 67 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLY H 89 " --> pdb=" O GLY H 247 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ALA H 249 " --> pdb=" O GLY H 89 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE H 91 " --> pdb=" O ALA H 249 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ALA H 248 " --> pdb=" O VAL H 272 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY H 320 " --> pdb=" O VAL H 299 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ASN H 303 " --> pdb=" O ARG H 322 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR H 383 " --> pdb=" O ILE H 361 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET H 385 " --> pdb=" O ALA H 363 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE H 66 " --> pdb=" O MET H 386 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 142 through 143 Processing sheet with id=AE7, first strand: chain 'H' and resid 208 through 212 removed outlier: 3.605A pdb=" N ALA H 220 " --> pdb=" O ILE H 211 " (cutoff:3.500A) 1002 hydrogen bonds defined for protein. 2865 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: 18.06 Time building geometry restraints manager: 12.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.91 - 1.09: 27555 1.09 - 1.27: 4588 1.27 - 1.46: 7881 1.46 - 1.64: 15243 1.64 - 1.82: 290 Bond restraints: 55557 Sorted by residual: bond pdb=" N SER H 237 " pdb=" H SER H 237 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" CE1 TYR E 282 " pdb=" HE1 TYR E 282 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N VAL G 373 " pdb=" H VAL G 373 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N LYS F 238 " pdb=" H LYS F 238 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N LEU B 174 " pdb=" H LEU B 174 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 ... (remaining 55552 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.94: 93286 3.94 - 7.87: 7020 7.87 - 11.81: 230 11.81 - 15.75: 39 15.75 - 19.68: 20 Bond angle restraints: 100595 Sorted by residual: angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 120.19 19.68 1.00e+00 1.00e+00 3.87e+02 angle pdb=" PB ATP G 602 " pdb=" O3B ATP G 602 " pdb=" PG ATP G 602 " ideal model delta sigma weight residual 139.87 120.24 19.63 1.00e+00 1.00e+00 3.85e+02 angle pdb=" PB ATP F 602 " pdb=" O3B ATP F 602 " pdb=" PG ATP F 602 " ideal model delta sigma weight residual 139.87 120.63 19.24 1.00e+00 1.00e+00 3.70e+02 angle pdb=" PA ATP D 601 " pdb=" O3A ATP D 601 " pdb=" PB ATP D 601 " ideal model delta sigma weight residual 136.83 117.78 19.05 1.00e+00 1.00e+00 3.63e+02 angle pdb=" PB ATP C 602 " pdb=" O3B ATP C 602 " pdb=" PG ATP C 602 " ideal model delta sigma weight residual 139.87 120.90 18.97 1.00e+00 1.00e+00 3.60e+02 ... (remaining 100590 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 22923 17.83 - 35.66: 1854 35.66 - 53.49: 831 53.49 - 71.31: 527 71.31 - 89.14: 107 Dihedral angle restraints: 26242 sinusoidal: 14873 harmonic: 11369 Sorted by residual: dihedral pdb=" C VAL E 503 " pdb=" N VAL E 503 " pdb=" CA VAL E 503 " pdb=" CB VAL E 503 " ideal model delta harmonic sigma weight residual -122.00 -137.80 15.80 0 2.50e+00 1.60e-01 3.99e+01 dihedral pdb=" C VAL D 503 " pdb=" N VAL D 503 " pdb=" CA VAL D 503 " pdb=" CB VAL D 503 " ideal model delta harmonic sigma weight residual -122.00 -137.68 15.68 0 2.50e+00 1.60e-01 3.93e+01 dihedral pdb=" N VAL E 503 " pdb=" C VAL E 503 " pdb=" CA VAL E 503 " pdb=" CB VAL E 503 " ideal model delta harmonic sigma weight residual 123.40 138.09 -14.69 0 2.50e+00 1.60e-01 3.45e+01 ... (remaining 26239 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 3698 0.120 - 0.239: 641 0.239 - 0.359: 93 0.359 - 0.479: 24 0.479 - 0.599: 3 Chirality restraints: 4459 Sorted by residual: chirality pdb=" CA VAL E 503 " pdb=" N VAL E 503 " pdb=" C VAL E 503 " pdb=" CB VAL E 503 " both_signs ideal model delta sigma weight residual False 2.44 1.84 0.60 2.00e-01 2.50e+01 8.96e+00 chirality pdb=" CA VAL D 503 " pdb=" N VAL D 503 " pdb=" C VAL D 503 " pdb=" CB VAL D 503 " both_signs ideal model delta sigma weight residual False 2.44 1.85 0.59 2.00e-01 2.50e+01 8.75e+00 chirality pdb=" CG LEU E 18 " pdb=" CB LEU E 18 " pdb=" CD1 LEU E 18 " pdb=" CD2 LEU E 18 " both_signs ideal model delta sigma weight residual False -2.59 -2.00 -0.59 2.00e-01 2.50e+01 8.74e+00 ... (remaining 4456 not shown) Planarity restraints: 8174 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 139 " -0.190 2.00e-02 2.50e+03 8.17e-02 2.00e+02 pdb=" CG PHE B 139 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE B 139 " 0.063 2.00e-02 2.50e+03 pdb=" CD2 PHE B 139 " 0.045 2.00e-02 2.50e+03 pdb=" CE1 PHE B 139 " 0.025 2.00e-02 2.50e+03 pdb=" CE2 PHE B 139 " 0.036 2.00e-02 2.50e+03 pdb=" CZ PHE B 139 " -0.036 2.00e-02 2.50e+03 pdb=" HD1 PHE B 139 " 0.073 2.00e-02 2.50e+03 pdb=" HD2 PHE B 139 " 0.038 2.00e-02 2.50e+03 pdb=" HE1 PHE B 139 " 0.016 2.00e-02 2.50e+03 pdb=" HE2 PHE B 139 " 0.056 2.00e-02 2.50e+03 pdb=" HZ PHE B 139 " -0.154 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 139 " -0.197 2.00e-02 2.50e+03 8.15e-02 1.99e+02 pdb=" CG PHE C 139 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE C 139 " 0.062 2.00e-02 2.50e+03 pdb=" CD2 PHE C 139 " 0.053 2.00e-02 2.50e+03 pdb=" CE1 PHE C 139 " 0.027 2.00e-02 2.50e+03 pdb=" CE2 PHE C 139 " 0.036 2.00e-02 2.50e+03 pdb=" CZ PHE C 139 " -0.032 2.00e-02 2.50e+03 pdb=" HD1 PHE C 139 " 0.072 2.00e-02 2.50e+03 pdb=" HD2 PHE C 139 " 0.048 2.00e-02 2.50e+03 pdb=" HE1 PHE C 139 " 0.013 2.00e-02 2.50e+03 pdb=" HE2 PHE C 139 " 0.036 2.00e-02 2.50e+03 pdb=" HZ PHE C 139 " -0.147 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 161 " 0.022 9.50e-02 1.11e+02 9.11e-02 1.86e+02 pdb=" NE ARG A 161 " -0.033 2.00e-02 2.50e+03 pdb=" CZ ARG A 161 " -0.058 2.00e-02 2.50e+03 pdb=" NH1 ARG A 161 " -0.091 2.00e-02 2.50e+03 pdb=" NH2 ARG A 161 " -0.021 2.00e-02 2.50e+03 pdb="HH11 ARG A 161 " 0.044 2.00e-02 2.50e+03 pdb="HH12 ARG A 161 " 0.136 2.00e-02 2.50e+03 pdb="HH21 ARG A 161 " 0.153 2.00e-02 2.50e+03 pdb="HH22 ARG A 161 " -0.132 2.00e-02 2.50e+03 ... (remaining 8171 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.06: 1984 2.06 - 2.70: 76180 2.70 - 3.33: 164951 3.33 - 3.97: 212769 3.97 - 4.60: 320523 Nonbonded interactions: 776407 Sorted by model distance: nonbonded pdb=" OE1 GLU B 146 " pdb=" H GLU B 146 " model vdw 1.426 2.450 nonbonded pdb=" H GLY H 128 " pdb=" H ASP H 129 " model vdw 1.480 2.100 nonbonded pdb=" HG3 LYS F 134 " pdb=" HZ3 LYS F 134 " model vdw 1.496 2.270 nonbonded pdb=" HB2 CYS B 95 " pdb=" HD2 PHE B 99 " model vdw 1.500 2.270 nonbonded pdb=" H GLY F 128 " pdb=" H ASP F 129 " model vdw 1.500 2.100 ... (remaining 776402 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = (chain 'G' and (resid -20 through 149 or resid 154 through 504 or resid 601 thro \ ugh 602)) selection = (chain 'H' and (resid -20 through 149 or resid 154 through 504 or resid 601 thro \ ugh 602)) } 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 group one per residue 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: 1.180 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: 0.730 Extract box with map and model: 1.520 Check model and map are aligned: 0.300 Set scattering table: 0.380 Process input model: 86.070 Find NCS groups from input model: 1.790 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 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 : 0.013 0.135 27954 Z= 0.834 Angle : 1.861 19.683 37896 Z= 1.279 Chirality : 0.098 0.599 4459 Planarity : 0.013 0.123 4763 Dihedral : 16.782 89.142 10622 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 1.09 % Allowed : 8.75 % Favored : 90.17 % Rotamer: Outliers : 2.73 % Allowed : 9.31 % Favored : 87.96 % Cbeta Deviations : 1.11 % 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: -3.02 (0.13), residues: 3499 helix: -2.39 (0.11), residues: 1357 sheet: -1.10 (0.26), residues: 281 loop : -1.80 (0.15), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS B 288 PHE 0.109 0.013 PHE C 139 TYR 0.132 0.019 TYR B 282 ARG 0.009 0.001 ARG G 161 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6998 Ramachandran restraints generated. 3499 Oldfield, 0 Emsley, 3499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6998 Ramachandran restraints generated. 3499 Oldfield, 0 Emsley, 3499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 865 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 786 time to evaluate : 3.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.6868 (t0) cc_final: 0.6483 (t0) REVERT: A 102 ASN cc_start: 0.8114 (t0) cc_final: 0.7893 (t0) REVERT: A 226 ASP cc_start: 0.7466 (m-30) cc_final: 0.7181 (m-30) REVERT: A 230 ASN cc_start: 0.6804 (p0) cc_final: 0.6384 (p0) REVERT: A 253 ARG cc_start: 0.7617 (mmt90) cc_final: 0.7319 (mmm160) REVERT: A 500 GLU cc_start: 0.7850 (tm-30) cc_final: 0.6414 (tt0) REVERT: B 47 ASP cc_start: 0.6906 (t0) cc_final: 0.6541 (t0) REVERT: B 85 MET cc_start: 0.8409 (mmm) cc_final: 0.8183 (mmt) REVERT: B 109 LYS cc_start: 0.7930 (mttm) cc_final: 0.7722 (mtpt) REVERT: B 230 ASN cc_start: 0.6845 (p0) cc_final: 0.6402 (p0) REVERT: B 245 LEU cc_start: 0.8794 (mt) cc_final: 0.8565 (mt) REVERT: B 483 MET cc_start: 0.9207 (tmm) cc_final: 0.8923 (tmm) REVERT: C 42 ILE cc_start: 0.9006 (mt) cc_final: 0.8597 (mt) REVERT: C 47 ASP cc_start: 0.6905 (t0) cc_final: 0.6540 (t0) REVERT: C 94 ASN cc_start: 0.7663 (t0) cc_final: 0.7247 (t0) REVERT: C 98 GLU cc_start: 0.7349 (tp30) cc_final: 0.7039 (tp30) REVERT: C 194 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7407 (tt) REVERT: C 238 LYS cc_start: 0.7969 (mttt) cc_final: 0.7604 (mtpt) REVERT: C 245 LEU cc_start: 0.8824 (mt) cc_final: 0.8577 (mt) REVERT: C 253 ARG cc_start: 0.7560 (mmt90) cc_final: 0.7341 (mmm160) REVERT: C 455 LYS cc_start: 0.8074 (OUTLIER) cc_final: 0.7631 (tmmt) REVERT: D 34 ASP cc_start: 0.8072 (OUTLIER) cc_final: 0.7831 (t0) REVERT: D 47 ASP cc_start: 0.6906 (t0) cc_final: 0.6523 (t0) REVERT: D 102 ASN cc_start: 0.8110 (t0) cc_final: 0.7860 (t0) REVERT: D 109 LYS cc_start: 0.7903 (mttm) cc_final: 0.7695 (mtmm) REVERT: D 146 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7373 (pm20) REVERT: D 179 MET cc_start: 0.7182 (mpp) cc_final: 0.6455 (mpp) REVERT: D 239 ASP cc_start: 0.7805 (p0) cc_final: 0.7553 (p0) REVERT: E 47 ASP cc_start: 0.6939 (t0) cc_final: 0.6530 (t0) REVERT: E 109 LYS cc_start: 0.7873 (mttm) cc_final: 0.7629 (mtpt) REVERT: E 226 ASP cc_start: 0.7254 (m-30) cc_final: 0.6862 (m-30) REVERT: E 293 LYS cc_start: 0.8489 (ttmm) cc_final: 0.8002 (ttmm) REVERT: F 47 ASP cc_start: 0.6935 (t0) cc_final: 0.6607 (t0) REVERT: F 102 ASN cc_start: 0.8159 (t0) cc_final: 0.7748 (t0) REVERT: F 455 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7709 (tmmt) REVERT: F 504 HIS cc_start: 0.6417 (OUTLIER) cc_final: 0.6052 (m-70) REVERT: G 42 ILE cc_start: 0.9016 (mt) cc_final: 0.8733 (mt) REVERT: G 102 ASN cc_start: 0.8076 (t0) cc_final: 0.7764 (t0) REVERT: G 483 MET cc_start: 0.9089 (tmm) cc_final: 0.8860 (tmm) REVERT: H 47 ASP cc_start: 0.6862 (t0) cc_final: 0.6527 (t0) REVERT: H 238 LYS cc_start: 0.7906 (mttt) cc_final: 0.7529 (mtmt) REVERT: H 455 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7801 (tmtt) outliers start: 79 outliers final: 28 residues processed: 843 average time/residue: 0.7765 time to fit residues: 1023.1500 Evaluate side-chains 752 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 717 time to evaluate : 3.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 504 HIS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 146 GLU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 504 HIS Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 455 LYS Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain F residue 504 HIS Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 455 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 298 optimal weight: 0.6980 chunk 268 optimal weight: 0.9990 chunk 148 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 180 optimal weight: 0.8980 chunk 143 optimal weight: 0.9990 chunk 277 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 168 optimal weight: 0.8980 chunk 206 optimal weight: 0.9980 chunk 321 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN A 466 HIS B 241 GLN B 466 HIS B 498 GLN C 230 ASN C 466 HIS D 466 HIS E 466 HIS F 22 GLN F 466 HIS F 469 GLN G 230 ASN H 230 ASN H 466 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 27954 Z= 0.249 Angle : 0.709 7.749 37896 Z= 0.380 Chirality : 0.044 0.184 4459 Planarity : 0.005 0.064 4763 Dihedral : 15.118 89.149 4435 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.92 % Favored : 92.63 % Rotamer: Outliers : 2.48 % Allowed : 12.59 % Favored : 84.93 % 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: -2.19 (0.13), residues: 3499 helix: -0.87 (0.12), residues: 1353 sheet: -1.15 (0.25), residues: 331 loop : -1.98 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS C 125 PHE 0.014 0.002 PHE G 490 TYR 0.037 0.002 TYR F 282 ARG 0.004 0.000 ARG C 105 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6998 Ramachandran restraints generated. 3499 Oldfield, 0 Emsley, 3499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6998 Ramachandran restraints generated. 3499 Oldfield, 0 Emsley, 3499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 832 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 760 time to evaluate : 3.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.6784 (t0) cc_final: 0.6429 (t0) REVERT: A 102 ASN cc_start: 0.8083 (t0) cc_final: 0.7846 (t0) REVERT: A 109 LYS cc_start: 0.7749 (mttm) cc_final: 0.7544 (mtpt) REVERT: A 226 ASP cc_start: 0.7384 (m-30) cc_final: 0.7166 (m-30) REVERT: A 242 LYS cc_start: 0.7717 (mttt) cc_final: 0.7158 (ttmm) REVERT: A 253 ARG cc_start: 0.7743 (mmt90) cc_final: 0.7401 (mmp-170) REVERT: A 368 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7918 (pt0) REVERT: B 34 ASP cc_start: 0.7875 (t70) cc_final: 0.7611 (t0) REVERT: B 47 ASP cc_start: 0.6867 (t0) cc_final: 0.6459 (t0) REVERT: B 109 LYS cc_start: 0.7838 (mttm) cc_final: 0.7564 (mtpt) REVERT: B 241 GLN cc_start: 0.7972 (mm110) cc_final: 0.7696 (mm110) REVERT: B 242 LYS cc_start: 0.7767 (mttt) cc_final: 0.7388 (ttmt) REVERT: B 455 LYS cc_start: 0.7947 (OUTLIER) cc_final: 0.7609 (tmmt) REVERT: C 47 ASP cc_start: 0.6830 (t0) cc_final: 0.6454 (t0) REVERT: C 94 ASN cc_start: 0.7740 (t0) cc_final: 0.7239 (t0) REVERT: C 98 GLU cc_start: 0.7408 (tp30) cc_final: 0.7093 (tp30) REVERT: C 125 HIS cc_start: 0.6721 (t70) cc_final: 0.6337 (t70) REVERT: C 130 VAL cc_start: 0.8052 (OUTLIER) cc_final: 0.7846 (t) REVERT: C 226 ASP cc_start: 0.7553 (m-30) cc_final: 0.7319 (m-30) REVERT: C 253 ARG cc_start: 0.7687 (mmt90) cc_final: 0.7447 (mmp-170) REVERT: C 494 THR cc_start: 0.8525 (t) cc_final: 0.8306 (t) REVERT: C 498 GLN cc_start: 0.8469 (pt0) cc_final: 0.8259 (pt0) REVERT: D 47 ASP cc_start: 0.6853 (t0) cc_final: 0.6461 (t0) REVERT: D 88 ILE cc_start: 0.9082 (OUTLIER) cc_final: 0.8795 (tt) REVERT: D 102 ASN cc_start: 0.8080 (t0) cc_final: 0.7849 (t0) REVERT: D 109 LYS cc_start: 0.7810 (mttm) cc_final: 0.7553 (mtpt) REVERT: D 238 LYS cc_start: 0.7828 (mttt) cc_final: 0.7491 (mtpt) REVERT: D 239 ASP cc_start: 0.7772 (p0) cc_final: 0.7560 (p0) REVERT: D 293 LYS cc_start: 0.8256 (ttmm) cc_final: 0.7816 (ttmm) REVERT: D 395 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7557 (mm-30) REVERT: E 47 ASP cc_start: 0.6794 (t0) cc_final: 0.6407 (t0) REVERT: E 109 LYS cc_start: 0.7893 (mttm) cc_final: 0.7541 (mtpt) REVERT: E 242 LYS cc_start: 0.7848 (mttt) cc_final: 0.7492 (ttmt) REVERT: E 504 HIS cc_start: 0.7089 (OUTLIER) cc_final: 0.6756 (m90) REVERT: F 34 ASP cc_start: 0.8016 (t0) cc_final: 0.7754 (t0) REVERT: F 47 ASP cc_start: 0.6935 (t0) cc_final: 0.6578 (t0) REVERT: F 98 GLU cc_start: 0.7031 (tp30) cc_final: 0.6795 (tp30) REVERT: F 230 ASN cc_start: 0.7316 (m110) cc_final: 0.7054 (m110) REVERT: F 504 HIS cc_start: 0.6509 (OUTLIER) cc_final: 0.6130 (m-70) REVERT: G 102 ASN cc_start: 0.7994 (t0) cc_final: 0.7647 (t0) REVERT: G 109 LYS cc_start: 0.7938 (mttt) cc_final: 0.7709 (mtmm) REVERT: G 199 GLU cc_start: 0.7465 (tm-30) cc_final: 0.7239 (tm-30) REVERT: G 242 LYS cc_start: 0.7694 (mttt) cc_final: 0.7378 (ttmt) REVERT: G 454 GLN cc_start: 0.7976 (mm-40) cc_final: 0.7694 (tp40) REVERT: H 34 ASP cc_start: 0.8159 (t0) cc_final: 0.7913 (t0) REVERT: H 47 ASP cc_start: 0.6839 (t0) cc_final: 0.6455 (t0) REVERT: H 109 LYS cc_start: 0.8007 (mttm) cc_final: 0.7796 (mttt) REVERT: H 238 LYS cc_start: 0.7913 (mttt) cc_final: 0.7445 (mtmt) REVERT: H 286 MET cc_start: 0.8258 (tpp) cc_final: 0.8021 (tpp) outliers start: 72 outliers final: 45 residues processed: 808 average time/residue: 0.7983 time to fit residues: 1023.3968 Evaluate side-chains 764 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 713 time to evaluate : 3.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 368 GLN Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 368 GLN Chi-restraints excluded: chain B residue 455 LYS Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 504 HIS Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 274 ASP Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain F residue 504 HIS Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 461 ILE Chi-restraints excluded: chain G residue 471 ILE Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 457 VAL Chi-restraints excluded: chain H residue 485 SER Chi-restraints excluded: chain H residue 504 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 178 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 267 optimal weight: 0.8980 chunk 218 optimal weight: 1.9990 chunk 88 optimal weight: 10.0000 chunk 322 optimal weight: 0.8980 chunk 347 optimal weight: 3.9990 chunk 286 optimal weight: 6.9990 chunk 319 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 258 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN B 454 GLN C 213 ASN C 230 ASN E 94 ASN H 94 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 27954 Z= 0.276 Angle : 0.638 7.762 37896 Z= 0.337 Chirality : 0.044 0.163 4459 Planarity : 0.004 0.046 4763 Dihedral : 14.345 89.748 4393 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.20 % Favored : 92.45 % Rotamer: Outliers : 2.62 % Allowed : 14.00 % Favored : 83.37 % 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: -1.76 (0.14), residues: 3499 helix: -0.12 (0.14), residues: 1368 sheet: -1.40 (0.24), residues: 341 loop : -2.00 (0.15), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 92 PHE 0.014 0.002 PHE G 490 TYR 0.028 0.002 TYR G 282 ARG 0.006 0.000 ARG H 341 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6998 Ramachandran restraints generated. 3499 Oldfield, 0 Emsley, 3499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6998 Ramachandran restraints generated. 3499 Oldfield, 0 Emsley, 3499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 786 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 710 time to evaluate : 3.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.6875 (t0) cc_final: 0.6509 (t0) REVERT: A 94 ASN cc_start: 0.7886 (t0) cc_final: 0.7356 (t0) REVERT: A 102 ASN cc_start: 0.8080 (t0) cc_final: 0.7873 (t0) REVERT: A 132 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.6372 (pp20) REVERT: A 242 LYS cc_start: 0.7767 (mttt) cc_final: 0.7394 (mttm) REVERT: A 500 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7942 (tm-30) REVERT: B 34 ASP cc_start: 0.7956 (t70) cc_final: 0.7682 (t0) REVERT: B 47 ASP cc_start: 0.6927 (t0) cc_final: 0.6675 (t0) REVERT: B 109 LYS cc_start: 0.7757 (mttm) cc_final: 0.7495 (mtpt) REVERT: B 177 GLU cc_start: 0.6357 (OUTLIER) cc_final: 0.4722 (pm20) REVERT: B 242 LYS cc_start: 0.7725 (mttt) cc_final: 0.7381 (ttmt) REVERT: B 253 ARG cc_start: 0.7794 (tpp80) cc_final: 0.7003 (mmp-170) REVERT: B 269 ASP cc_start: 0.8446 (OUTLIER) cc_final: 0.8238 (t0) REVERT: B 455 LYS cc_start: 0.7931 (OUTLIER) cc_final: 0.7616 (tmmt) REVERT: C 47 ASP cc_start: 0.6961 (t0) cc_final: 0.6733 (t0) REVERT: C 94 ASN cc_start: 0.7846 (t0) cc_final: 0.7320 (t0) REVERT: C 98 GLU cc_start: 0.7316 (tp30) cc_final: 0.6967 (tp30) REVERT: C 206 LYS cc_start: 0.7800 (mmtp) cc_final: 0.7555 (mmtp) REVERT: C 238 LYS cc_start: 0.7870 (mttt) cc_final: 0.7582 (mtmt) REVERT: C 253 ARG cc_start: 0.7582 (mmt90) cc_final: 0.7269 (mmp-170) REVERT: C 293 LYS cc_start: 0.8184 (ttmm) cc_final: 0.7894 (ttmm) REVERT: D 47 ASP cc_start: 0.6933 (t0) cc_final: 0.6704 (t0) REVERT: D 238 LYS cc_start: 0.7852 (mttt) cc_final: 0.7540 (mtpt) REVERT: D 395 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7660 (mm-30) REVERT: E 47 ASP cc_start: 0.6946 (t0) cc_final: 0.6719 (t0) REVERT: E 109 LYS cc_start: 0.7896 (mttm) cc_final: 0.7555 (mtpt) REVERT: E 213 ASN cc_start: 0.7884 (p0) cc_final: 0.7677 (p0) REVERT: E 238 LYS cc_start: 0.7857 (mttt) cc_final: 0.7553 (mtmt) REVERT: E 504 HIS cc_start: 0.7039 (OUTLIER) cc_final: 0.6756 (m90) REVERT: F 34 ASP cc_start: 0.8044 (t0) cc_final: 0.7762 (t0) REVERT: F 47 ASP cc_start: 0.6996 (t0) cc_final: 0.6762 (t0) REVERT: F 132 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.6411 (pp20) REVERT: F 504 HIS cc_start: 0.6606 (OUTLIER) cc_final: 0.6293 (m-70) REVERT: G 102 ASN cc_start: 0.8011 (t0) cc_final: 0.7728 (t0) REVERT: G 109 LYS cc_start: 0.7796 (mttt) cc_final: 0.7505 (mtmm) REVERT: G 242 LYS cc_start: 0.7742 (mttt) cc_final: 0.7421 (ttmt) REVERT: H 34 ASP cc_start: 0.8209 (t0) cc_final: 0.7921 (t0) REVERT: H 47 ASP cc_start: 0.6893 (t0) cc_final: 0.6533 (t0) REVERT: H 109 LYS cc_start: 0.8007 (mttm) cc_final: 0.7764 (mtmt) REVERT: H 154 LEU cc_start: 0.4145 (OUTLIER) cc_final: 0.3871 (tt) REVERT: H 238 LYS cc_start: 0.7940 (mttt) cc_final: 0.7592 (mtmt) outliers start: 76 outliers final: 50 residues processed: 749 average time/residue: 0.7596 time to fit residues: 896.6520 Evaluate side-chains 734 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 676 time to evaluate : 3.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 454 GLN Chi-restraints excluded: chain B residue 455 LYS Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 499 ILE Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 485 SER Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 261 ASP Chi-restraints excluded: chain E residue 504 HIS Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 274 ASP Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain F residue 504 HIS Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain G residue 274 ASP Chi-restraints excluded: chain G residue 461 ILE Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 457 VAL Chi-restraints excluded: chain H residue 485 SER Chi-restraints excluded: chain H residue 504 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 318 optimal weight: 2.9990 chunk 242 optimal weight: 5.9990 chunk 167 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 216 optimal weight: 0.8980 chunk 323 optimal weight: 10.0000 chunk 342 optimal weight: 3.9990 chunk 168 optimal weight: 1.9990 chunk 306 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 ASN C 213 ASN C 230 ASN E 94 ASN H 94 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 27954 Z= 0.244 Angle : 0.597 7.305 37896 Z= 0.316 Chirality : 0.043 0.160 4459 Planarity : 0.004 0.045 4763 Dihedral : 13.857 89.283 4390 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.06 % Favored : 92.63 % Rotamer: Outliers : 2.62 % Allowed : 15.14 % Favored : 82.24 % 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: -1.43 (0.14), residues: 3499 helix: 0.42 (0.14), residues: 1356 sheet: -1.49 (0.24), residues: 341 loop : -1.96 (0.15), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 92 PHE 0.011 0.001 PHE G 490 TYR 0.024 0.002 TYR G 282 ARG 0.006 0.000 ARG D 203 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6998 Ramachandran restraints generated. 3499 Oldfield, 0 Emsley, 3499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6998 Ramachandran restraints generated. 3499 Oldfield, 0 Emsley, 3499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 780 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 704 time to evaluate : 3.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.6919 (t0) cc_final: 0.6702 (t0) REVERT: A 94 ASN cc_start: 0.7933 (t0) cc_final: 0.7391 (t0) REVERT: A 102 ASN cc_start: 0.8082 (t0) cc_final: 0.7798 (t0) REVERT: A 155 VAL cc_start: 0.6443 (OUTLIER) cc_final: 0.6067 (t) REVERT: A 242 LYS cc_start: 0.7760 (mttt) cc_final: 0.7390 (mttm) REVERT: A 253 ARG cc_start: 0.7729 (mmt90) cc_final: 0.7335 (mmp-170) REVERT: A 500 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7958 (tm-30) REVERT: B 34 ASP cc_start: 0.8057 (t70) cc_final: 0.7763 (t0) REVERT: B 47 ASP cc_start: 0.6976 (t0) cc_final: 0.6739 (t0) REVERT: B 109 LYS cc_start: 0.7729 (mttm) cc_final: 0.7434 (mtpt) REVERT: B 177 GLU cc_start: 0.6330 (OUTLIER) cc_final: 0.4717 (pm20) REVERT: B 241 GLN cc_start: 0.7970 (mm110) cc_final: 0.7725 (mm110) REVERT: B 242 LYS cc_start: 0.7782 (mttt) cc_final: 0.7432 (ttmt) REVERT: B 253 ARG cc_start: 0.7827 (tpp80) cc_final: 0.7027 (mmp-170) REVERT: B 455 LYS cc_start: 0.7918 (OUTLIER) cc_final: 0.7557 (tmmt) REVERT: B 456 PHE cc_start: 0.8392 (t80) cc_final: 0.8109 (t80) REVERT: C 47 ASP cc_start: 0.6966 (t0) cc_final: 0.6739 (t0) REVERT: C 94 ASN cc_start: 0.7956 (t0) cc_final: 0.7444 (t0) REVERT: C 238 LYS cc_start: 0.7896 (mttt) cc_final: 0.7527 (mtmt) REVERT: C 253 ARG cc_start: 0.7513 (mmt90) cc_final: 0.7213 (mmp-170) REVERT: C 293 LYS cc_start: 0.8222 (ttmm) cc_final: 0.7868 (ttmm) REVERT: D 47 ASP cc_start: 0.7015 (t0) cc_final: 0.6758 (t0) REVERT: D 242 LYS cc_start: 0.7697 (mttp) cc_final: 0.7313 (ttmt) REVERT: D 395 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7630 (mm-30) REVERT: E 47 ASP cc_start: 0.7013 (t0) cc_final: 0.6770 (t0) REVERT: E 109 LYS cc_start: 0.7834 (mttm) cc_final: 0.7483 (mtpt) REVERT: E 213 ASN cc_start: 0.7765 (p0) cc_final: 0.7503 (p0) REVERT: E 238 LYS cc_start: 0.7872 (mttt) cc_final: 0.7573 (mtmt) REVERT: E 504 HIS cc_start: 0.7021 (OUTLIER) cc_final: 0.6778 (m90) REVERT: F 34 ASP cc_start: 0.8042 (t0) cc_final: 0.7767 (t0) REVERT: F 47 ASP cc_start: 0.7042 (t0) cc_final: 0.6799 (t0) REVERT: F 94 ASN cc_start: 0.8035 (t0) cc_final: 0.7531 (t0) REVERT: F 132 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.6334 (pp20) REVERT: F 504 HIS cc_start: 0.6753 (OUTLIER) cc_final: 0.6489 (m-70) REVERT: G 94 ASN cc_start: 0.7954 (t0) cc_final: 0.7501 (t0) REVERT: G 102 ASN cc_start: 0.7990 (t0) cc_final: 0.7703 (t0) REVERT: G 109 LYS cc_start: 0.7774 (mttt) cc_final: 0.7528 (mtmm) REVERT: G 242 LYS cc_start: 0.7734 (mttt) cc_final: 0.7432 (ttmt) REVERT: G 253 ARG cc_start: 0.7833 (tpp80) cc_final: 0.6969 (mmp-170) REVERT: H 34 ASP cc_start: 0.8222 (t0) cc_final: 0.7931 (t0) REVERT: H 47 ASP cc_start: 0.6960 (t0) cc_final: 0.6730 (t0) REVERT: H 154 LEU cc_start: 0.4014 (OUTLIER) cc_final: 0.3766 (tp) REVERT: H 238 LYS cc_start: 0.7921 (mttt) cc_final: 0.7546 (mtmt) REVERT: H 253 ARG cc_start: 0.7914 (tpp80) cc_final: 0.7100 (mmp-170) outliers start: 76 outliers final: 58 residues processed: 744 average time/residue: 0.7511 time to fit residues: 875.2954 Evaluate side-chains 740 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 675 time to evaluate : 3.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 368 GLN Chi-restraints excluded: chain B residue 455 LYS Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 499 ILE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 132 GLU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 485 SER Chi-restraints excluded: chain E residue 504 HIS Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 274 ASP Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain F residue 504 HIS Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain G residue 274 ASP Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 457 VAL Chi-restraints excluded: chain H residue 504 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 284 optimal weight: 4.9990 chunk 194 optimal weight: 0.3980 chunk 4 optimal weight: 1.9990 chunk 254 optimal weight: 0.9980 chunk 141 optimal weight: 4.9990 chunk 291 optimal weight: 1.9990 chunk 236 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 174 optimal weight: 0.9990 chunk 307 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 ASN E 94 ASN H 94 ASN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 27954 Z= 0.203 Angle : 0.561 7.103 37896 Z= 0.295 Chirality : 0.042 0.154 4459 Planarity : 0.004 0.044 4763 Dihedral : 13.268 87.905 4390 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.97 % Favored : 92.66 % Rotamer: Outliers : 2.90 % Allowed : 14.94 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.14), residues: 3499 helix: 0.60 (0.14), residues: 1425 sheet: -1.46 (0.26), residues: 317 loop : -1.96 (0.15), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 92 PHE 0.017 0.001 PHE G 456 TYR 0.021 0.002 TYR G 282 ARG 0.004 0.000 ARG D 203 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6998 Ramachandran restraints generated. 3499 Oldfield, 0 Emsley, 3499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6998 Ramachandran restraints generated. 3499 Oldfield, 0 Emsley, 3499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 777 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 693 time to evaluate : 3.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.6965 (t0) cc_final: 0.6723 (t0) REVERT: A 78 MET cc_start: 0.8656 (tpp) cc_final: 0.8438 (tpt) REVERT: A 94 ASN cc_start: 0.7978 (t0) cc_final: 0.7476 (t0) REVERT: A 98 GLU cc_start: 0.7117 (OUTLIER) cc_final: 0.6418 (mm-30) REVERT: A 102 ASN cc_start: 0.8045 (t0) cc_final: 0.7586 (t0) REVERT: A 109 LYS cc_start: 0.7626 (mttm) cc_final: 0.7227 (mtpt) REVERT: A 500 GLU cc_start: 0.8055 (tm-30) cc_final: 0.7806 (tm-30) REVERT: B 34 ASP cc_start: 0.8076 (t70) cc_final: 0.7806 (t0) REVERT: B 47 ASP cc_start: 0.6939 (t0) cc_final: 0.6682 (t0) REVERT: B 177 GLU cc_start: 0.6660 (OUTLIER) cc_final: 0.4654 (tp30) REVERT: B 242 LYS cc_start: 0.7766 (mttt) cc_final: 0.7417 (ttmt) REVERT: B 253 ARG cc_start: 0.7870 (tpp80) cc_final: 0.7077 (mmp-170) REVERT: C 47 ASP cc_start: 0.6848 (t0) cc_final: 0.6596 (t0) REVERT: C 94 ASN cc_start: 0.7939 (t0) cc_final: 0.7456 (t0) REVERT: C 238 LYS cc_start: 0.7829 (mttt) cc_final: 0.7484 (mtpt) REVERT: C 253 ARG cc_start: 0.7510 (mmt90) cc_final: 0.7141 (mmp-170) REVERT: D 47 ASP cc_start: 0.6917 (t0) cc_final: 0.6675 (t0) REVERT: D 242 LYS cc_start: 0.7740 (mttp) cc_final: 0.7199 (ttmm) REVERT: D 395 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7755 (mm-30) REVERT: E 47 ASP cc_start: 0.6979 (t0) cc_final: 0.6726 (t0) REVERT: E 213 ASN cc_start: 0.7781 (p0) cc_final: 0.7579 (p0) REVERT: E 238 LYS cc_start: 0.7856 (mttt) cc_final: 0.7538 (mtmt) REVERT: F 34 ASP cc_start: 0.8047 (t0) cc_final: 0.7757 (t0) REVERT: F 47 ASP cc_start: 0.7015 (t0) cc_final: 0.6770 (t0) REVERT: F 94 ASN cc_start: 0.8130 (t0) cc_final: 0.7670 (t0) REVERT: F 132 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.6211 (pp20) REVERT: F 242 LYS cc_start: 0.7752 (mttt) cc_final: 0.7451 (ttmt) REVERT: F 504 HIS cc_start: 0.6747 (OUTLIER) cc_final: 0.6535 (m-70) REVERT: G 94 ASN cc_start: 0.8007 (t0) cc_final: 0.7598 (t0) REVERT: G 102 ASN cc_start: 0.7939 (t0) cc_final: 0.7666 (t0) REVERT: G 109 LYS cc_start: 0.7753 (mttt) cc_final: 0.7468 (mtmm) REVERT: G 242 LYS cc_start: 0.7730 (mttt) cc_final: 0.7438 (ttmt) REVERT: G 456 PHE cc_start: 0.8196 (t80) cc_final: 0.7994 (t80) REVERT: H 34 ASP cc_start: 0.8241 (t0) cc_final: 0.7926 (t0) REVERT: H 47 ASP cc_start: 0.6918 (t0) cc_final: 0.6679 (t0) REVERT: H 154 LEU cc_start: 0.4003 (OUTLIER) cc_final: 0.3762 (tp) REVERT: H 206 LYS cc_start: 0.7727 (mmtp) cc_final: 0.7527 (mmtp) REVERT: H 238 LYS cc_start: 0.7914 (mttt) cc_final: 0.7496 (mtmt) outliers start: 84 outliers final: 67 residues processed: 740 average time/residue: 0.7377 time to fit residues: 853.5006 Evaluate side-chains 742 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 670 time to evaluate : 3.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 132 GLU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 274 ASP Chi-restraints excluded: chain F residue 476 LEU Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain F residue 504 HIS Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 94 ASN Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 476 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 115 optimal weight: 2.9990 chunk 308 optimal weight: 0.0010 chunk 67 optimal weight: 1.9990 chunk 200 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 342 optimal weight: 3.9990 chunk 284 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 179 optimal weight: 0.6980 overall best weight: 0.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 GLN B 94 ASN B 454 GLN C 213 ASN D 230 ASN E 94 ASN F 230 ASN F 454 GLN H 94 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27954 Z= 0.188 Angle : 0.550 7.528 37896 Z= 0.290 Chirality : 0.042 0.151 4459 Planarity : 0.004 0.043 4763 Dihedral : 12.845 89.066 4388 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.74 % Favored : 92.91 % Rotamer: Outliers : 2.93 % Allowed : 15.28 % Favored : 81.79 % 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: -1.11 (0.14), residues: 3499 helix: 0.73 (0.14), residues: 1473 sheet: -1.82 (0.26), residues: 312 loop : -1.88 (0.15), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS C 125 PHE 0.010 0.001 PHE G 456 TYR 0.019 0.001 TYR G 282 ARG 0.003 0.000 ARG F 203 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6998 Ramachandran restraints generated. 3499 Oldfield, 0 Emsley, 3499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6998 Ramachandran restraints generated. 3499 Oldfield, 0 Emsley, 3499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 764 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 679 time to evaluate : 3.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.6942 (t0) cc_final: 0.6703 (t0) REVERT: A 94 ASN cc_start: 0.7979 (t0) cc_final: 0.7472 (t0) REVERT: A 98 GLU cc_start: 0.7078 (OUTLIER) cc_final: 0.6333 (mm-30) REVERT: A 102 ASN cc_start: 0.7955 (t0) cc_final: 0.7718 (t0) REVERT: A 109 LYS cc_start: 0.7584 (mttm) cc_final: 0.7223 (mtpt) REVERT: A 155 VAL cc_start: 0.6483 (OUTLIER) cc_final: 0.6097 (t) REVERT: B 34 ASP cc_start: 0.8034 (t70) cc_final: 0.7784 (t0) REVERT: B 47 ASP cc_start: 0.6927 (t0) cc_final: 0.6675 (t0) REVERT: B 177 GLU cc_start: 0.6579 (OUTLIER) cc_final: 0.5383 (tp30) REVERT: B 242 LYS cc_start: 0.7765 (mttt) cc_final: 0.7419 (ttmt) REVERT: B 253 ARG cc_start: 0.7872 (tpp80) cc_final: 0.7050 (mmp-170) REVERT: B 455 LYS cc_start: 0.7932 (OUTLIER) cc_final: 0.7551 (tmmt) REVERT: B 456 PHE cc_start: 0.8318 (t80) cc_final: 0.8003 (t80) REVERT: C 47 ASP cc_start: 0.6862 (t0) cc_final: 0.6603 (t0) REVERT: C 78 MET cc_start: 0.8812 (tpp) cc_final: 0.8559 (tpt) REVERT: C 94 ASN cc_start: 0.7966 (t0) cc_final: 0.7492 (t0) REVERT: C 238 LYS cc_start: 0.7789 (mttt) cc_final: 0.7485 (mtpt) REVERT: C 253 ARG cc_start: 0.7567 (mmt90) cc_final: 0.7234 (mmp-170) REVERT: D 47 ASP cc_start: 0.6885 (t0) cc_final: 0.6650 (t0) REVERT: D 94 ASN cc_start: 0.7940 (t0) cc_final: 0.7401 (t0) REVERT: D 242 LYS cc_start: 0.7765 (mttp) cc_final: 0.7453 (ttmt) REVERT: D 395 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7581 (mm-30) REVERT: E 47 ASP cc_start: 0.6973 (t0) cc_final: 0.6703 (t0) REVERT: E 75 GLU cc_start: 0.6625 (OUTLIER) cc_final: 0.6297 (tt0) REVERT: E 213 ASN cc_start: 0.7727 (p0) cc_final: 0.7508 (p0) REVERT: E 242 LYS cc_start: 0.7698 (mttp) cc_final: 0.7457 (ttmt) REVERT: F 34 ASP cc_start: 0.8037 (t0) cc_final: 0.7765 (t0) REVERT: F 47 ASP cc_start: 0.7013 (t0) cc_final: 0.6752 (t0) REVERT: F 78 MET cc_start: 0.8598 (tpp) cc_final: 0.8263 (tpp) REVERT: F 94 ASN cc_start: 0.8133 (t0) cc_final: 0.7669 (t0) REVERT: F 109 LYS cc_start: 0.7660 (mtpt) cc_final: 0.7395 (mtmm) REVERT: F 179 MET cc_start: 0.7175 (mpp) cc_final: 0.6869 (mpp) REVERT: F 242 LYS cc_start: 0.7745 (mttt) cc_final: 0.7435 (ttmt) REVERT: F 265 GLN cc_start: 0.7809 (tp40) cc_final: 0.7552 (tp-100) REVERT: F 368 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.7707 (pt0) REVERT: G 94 ASN cc_start: 0.7987 (t0) cc_final: 0.7568 (t0) REVERT: G 102 ASN cc_start: 0.7970 (t0) cc_final: 0.7649 (t0) REVERT: G 109 LYS cc_start: 0.7712 (mttt) cc_final: 0.7417 (mtmm) REVERT: G 242 LYS cc_start: 0.7713 (mttt) cc_final: 0.7447 (ttmt) REVERT: H 34 ASP cc_start: 0.8230 (t0) cc_final: 0.7876 (t0) REVERT: H 47 ASP cc_start: 0.6932 (t0) cc_final: 0.6694 (t0) REVERT: H 75 GLU cc_start: 0.6793 (OUTLIER) cc_final: 0.6429 (tt0) REVERT: H 154 LEU cc_start: 0.4099 (OUTLIER) cc_final: 0.3897 (tp) REVERT: H 179 MET cc_start: 0.8232 (mpp) cc_final: 0.7973 (mmt) REVERT: H 238 LYS cc_start: 0.7905 (mttt) cc_final: 0.7494 (mtmt) REVERT: H 253 ARG cc_start: 0.7881 (tpp80) cc_final: 0.7048 (mmp-170) REVERT: H 456 PHE cc_start: 0.8176 (t80) cc_final: 0.7816 (t80) outliers start: 85 outliers final: 63 residues processed: 734 average time/residue: 0.7773 time to fit residues: 896.8401 Evaluate side-chains 738 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 667 time to evaluate : 3.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain B residue 455 LYS Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 132 GLU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 504 HIS Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 368 GLN Chi-restraints excluded: chain F residue 476 LEU Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 460 LEU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 476 LEU Chi-restraints excluded: chain H residue 504 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 330 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 195 optimal weight: 4.9990 chunk 250 optimal weight: 1.9990 chunk 193 optimal weight: 2.9990 chunk 288 optimal weight: 2.9990 chunk 191 optimal weight: 3.9990 chunk 341 optimal weight: 1.9990 chunk 213 optimal weight: 1.9990 chunk 208 optimal weight: 0.6980 chunk 157 optimal weight: 4.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 GLN B 94 ASN B 454 GLN C 213 ASN E 94 ASN F 454 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 27954 Z= 0.325 Angle : 0.583 5.875 37896 Z= 0.309 Chirality : 0.043 0.147 4459 Planarity : 0.004 0.041 4763 Dihedral : 13.021 89.336 4386 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.09 % Favored : 91.60 % Rotamer: Outliers : 3.38 % Allowed : 14.94 % Favored : 81.68 % 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: -1.15 (0.14), residues: 3499 helix: 0.78 (0.14), residues: 1436 sheet: -2.08 (0.23), residues: 403 loop : -1.84 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS E 93 PHE 0.010 0.001 PHE G 490 TYR 0.024 0.002 TYR B 282 ARG 0.005 0.000 ARG C 105 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6998 Ramachandran restraints generated. 3499 Oldfield, 0 Emsley, 3499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6998 Ramachandran restraints generated. 3499 Oldfield, 0 Emsley, 3499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 771 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 673 time to evaluate : 3.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.6900 (t0) cc_final: 0.6652 (t0) REVERT: A 94 ASN cc_start: 0.8018 (t0) cc_final: 0.7507 (t0) REVERT: A 98 GLU cc_start: 0.7145 (OUTLIER) cc_final: 0.6383 (mm-30) REVERT: A 102 ASN cc_start: 0.8006 (t0) cc_final: 0.7789 (t0) REVERT: A 109 LYS cc_start: 0.7595 (mttm) cc_final: 0.7311 (mtpt) REVERT: A 253 ARG cc_start: 0.7638 (mmt90) cc_final: 0.7256 (mmp-170) REVERT: A 293 LYS cc_start: 0.8227 (ttmm) cc_final: 0.8003 (ttmm) REVERT: B 34 ASP cc_start: 0.8097 (t70) cc_final: 0.7810 (t0) REVERT: B 47 ASP cc_start: 0.6948 (t0) cc_final: 0.6699 (t0) REVERT: B 75 GLU cc_start: 0.6608 (OUTLIER) cc_final: 0.6319 (tt0) REVERT: B 109 LYS cc_start: 0.7671 (mttm) cc_final: 0.7392 (mtmm) REVERT: B 242 LYS cc_start: 0.7768 (mttt) cc_final: 0.7295 (ttmm) REVERT: B 253 ARG cc_start: 0.7883 (tpp80) cc_final: 0.7080 (mmp-170) REVERT: B 292 GLN cc_start: 0.8329 (tm-30) cc_final: 0.8004 (tm-30) REVERT: B 455 LYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7599 (tmmt) REVERT: B 456 PHE cc_start: 0.8330 (t80) cc_final: 0.8041 (t80) REVERT: C 47 ASP cc_start: 0.6869 (t0) cc_final: 0.6637 (t0) REVERT: C 78 MET cc_start: 0.8827 (tpp) cc_final: 0.8582 (tpt) REVERT: C 85 MET cc_start: 0.8305 (mmm) cc_final: 0.8029 (mmt) REVERT: C 94 ASN cc_start: 0.8032 (t0) cc_final: 0.7595 (t0) REVERT: C 238 LYS cc_start: 0.7868 (mttt) cc_final: 0.7588 (mtpt) REVERT: C 253 ARG cc_start: 0.7578 (mmt90) cc_final: 0.7367 (mmp-170) REVERT: D 47 ASP cc_start: 0.6927 (t0) cc_final: 0.6659 (t0) REVERT: D 94 ASN cc_start: 0.7941 (t0) cc_final: 0.7429 (t0) REVERT: D 109 LYS cc_start: 0.7536 (mttm) cc_final: 0.7326 (mtpt) REVERT: D 242 LYS cc_start: 0.7682 (mttp) cc_final: 0.7406 (ttmt) REVERT: D 293 LYS cc_start: 0.8245 (ttmm) cc_final: 0.7999 (ttmm) REVERT: D 395 GLU cc_start: 0.8306 (mm-30) cc_final: 0.7613 (mm-30) REVERT: E 47 ASP cc_start: 0.7006 (t0) cc_final: 0.6744 (t0) REVERT: E 75 GLU cc_start: 0.6692 (OUTLIER) cc_final: 0.6259 (tt0) REVERT: E 109 LYS cc_start: 0.7781 (mttm) cc_final: 0.7484 (mtmt) REVERT: E 213 ASN cc_start: 0.7729 (p0) cc_final: 0.7509 (p0) REVERT: E 242 LYS cc_start: 0.7704 (mttp) cc_final: 0.7281 (ttmm) REVERT: F 34 ASP cc_start: 0.8123 (t0) cc_final: 0.7845 (t0) REVERT: F 47 ASP cc_start: 0.7026 (t0) cc_final: 0.6771 (t0) REVERT: F 78 MET cc_start: 0.8652 (tpp) cc_final: 0.8321 (tpp) REVERT: F 94 ASN cc_start: 0.8174 (t0) cc_final: 0.7692 (t0) REVERT: F 105 ARG cc_start: 0.7915 (ttp-170) cc_final: 0.7581 (ttp80) REVERT: F 179 MET cc_start: 0.7332 (mpp) cc_final: 0.7059 (mpp) REVERT: F 242 LYS cc_start: 0.7771 (mttt) cc_final: 0.7324 (ttmm) REVERT: F 265 GLN cc_start: 0.7821 (tp40) cc_final: 0.7602 (tp-100) REVERT: F 368 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7722 (pt0) REVERT: G 94 ASN cc_start: 0.7998 (t0) cc_final: 0.7614 (t0) REVERT: G 98 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.5940 (tp30) REVERT: G 102 ASN cc_start: 0.7974 (t0) cc_final: 0.7533 (t0) REVERT: G 109 LYS cc_start: 0.7748 (mttt) cc_final: 0.7434 (mtmm) REVERT: G 242 LYS cc_start: 0.7716 (mttt) cc_final: 0.7466 (ttmt) REVERT: G 293 LYS cc_start: 0.8217 (ttmm) cc_final: 0.7993 (ttmm) REVERT: H 34 ASP cc_start: 0.8189 (t0) cc_final: 0.7855 (t0) REVERT: H 47 ASP cc_start: 0.6939 (t0) cc_final: 0.6687 (t0) REVERT: H 75 GLU cc_start: 0.6789 (OUTLIER) cc_final: 0.6354 (tt0) REVERT: H 154 LEU cc_start: 0.4094 (OUTLIER) cc_final: 0.3846 (tp) REVERT: H 179 MET cc_start: 0.8301 (mpp) cc_final: 0.8058 (mmt) REVERT: H 238 LYS cc_start: 0.7958 (mttt) cc_final: 0.7538 (mtmt) REVERT: H 253 ARG cc_start: 0.7881 (tpp80) cc_final: 0.7034 (mmp-170) REVERT: H 456 PHE cc_start: 0.8166 (t80) cc_final: 0.7830 (t80) outliers start: 98 outliers final: 73 residues processed: 733 average time/residue: 0.7594 time to fit residues: 867.5524 Evaluate side-chains 749 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 668 time to evaluate : 3.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain B residue 455 LYS Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 485 SER Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 132 GLU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 476 LEU Chi-restraints excluded: chain E residue 485 SER Chi-restraints excluded: chain E residue 504 HIS Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 274 ASP Chi-restraints excluded: chain F residue 368 GLN Chi-restraints excluded: chain F residue 476 LEU Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 98 GLU Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain G residue 274 ASP Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 504 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 211 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 chunk 203 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 216 optimal weight: 0.9990 chunk 232 optimal weight: 4.9990 chunk 168 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 268 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 213 ASN C 283 GLN D 22 GLN D 230 ASN F 454 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 27954 Z= 0.246 Angle : 0.566 8.929 37896 Z= 0.299 Chirality : 0.043 0.173 4459 Planarity : 0.004 0.041 4763 Dihedral : 12.730 88.546 4384 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.46 % Favored : 92.23 % Rotamer: Outliers : 3.28 % Allowed : 15.28 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.06 (0.14), residues: 3499 helix: 0.90 (0.14), residues: 1436 sheet: -2.03 (0.23), residues: 403 loop : -1.84 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS C 125 PHE 0.010 0.001 PHE G 456 TYR 0.022 0.002 TYR H 289 ARG 0.005 0.000 ARG C 105 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6998 Ramachandran restraints generated. 3499 Oldfield, 0 Emsley, 3499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6998 Ramachandran restraints generated. 3499 Oldfield, 0 Emsley, 3499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 773 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 678 time to evaluate : 3.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.6891 (t0) cc_final: 0.6656 (t0) REVERT: A 94 ASN cc_start: 0.7995 (t0) cc_final: 0.7505 (t0) REVERT: A 98 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.6350 (mm-30) REVERT: A 102 ASN cc_start: 0.7998 (t0) cc_final: 0.7750 (t0) REVERT: A 109 LYS cc_start: 0.7572 (mttm) cc_final: 0.7305 (mtpt) REVERT: A 155 VAL cc_start: 0.6414 (OUTLIER) cc_final: 0.6048 (t) REVERT: A 242 LYS cc_start: 0.7648 (mttp) cc_final: 0.7335 (mtpp) REVERT: B 34 ASP cc_start: 0.8045 (t70) cc_final: 0.7805 (t0) REVERT: B 47 ASP cc_start: 0.6861 (t0) cc_final: 0.6606 (t0) REVERT: B 75 GLU cc_start: 0.6629 (OUTLIER) cc_final: 0.6279 (tt0) REVERT: B 109 LYS cc_start: 0.7735 (mttm) cc_final: 0.7418 (mtmm) REVERT: B 242 LYS cc_start: 0.7770 (mttt) cc_final: 0.7291 (ttmm) REVERT: B 253 ARG cc_start: 0.7887 (tpp80) cc_final: 0.7077 (mmp-170) REVERT: B 292 GLN cc_start: 0.8312 (tm-30) cc_final: 0.8004 (tm-30) REVERT: B 455 LYS cc_start: 0.7947 (OUTLIER) cc_final: 0.7601 (tmmt) REVERT: B 456 PHE cc_start: 0.8311 (t80) cc_final: 0.8035 (t80) REVERT: C 47 ASP cc_start: 0.6874 (t0) cc_final: 0.6633 (t0) REVERT: C 85 MET cc_start: 0.8314 (mmm) cc_final: 0.8052 (mmt) REVERT: C 94 ASN cc_start: 0.8020 (t0) cc_final: 0.7550 (t0) REVERT: C 105 ARG cc_start: 0.8108 (ttp80) cc_final: 0.7807 (ttp80) REVERT: C 238 LYS cc_start: 0.7845 (mttt) cc_final: 0.7492 (mtpt) REVERT: C 253 ARG cc_start: 0.7528 (mmt90) cc_final: 0.7199 (mmp-170) REVERT: D 47 ASP cc_start: 0.6919 (t0) cc_final: 0.6648 (t0) REVERT: D 78 MET cc_start: 0.8697 (tpp) cc_final: 0.8458 (tpt) REVERT: D 94 ASN cc_start: 0.7931 (t0) cc_final: 0.7428 (t0) REVERT: D 109 LYS cc_start: 0.7522 (mttm) cc_final: 0.7304 (mtpt) REVERT: D 242 LYS cc_start: 0.7697 (mttp) cc_final: 0.7417 (ttmt) REVERT: D 395 GLU cc_start: 0.8310 (mm-30) cc_final: 0.7586 (mm-30) REVERT: E 47 ASP cc_start: 0.6926 (t0) cc_final: 0.6669 (t0) REVERT: E 75 GLU cc_start: 0.6569 (OUTLIER) cc_final: 0.6119 (tt0) REVERT: E 109 LYS cc_start: 0.7746 (mttm) cc_final: 0.7454 (mtmm) REVERT: E 242 LYS cc_start: 0.7703 (mttp) cc_final: 0.7274 (ttmm) REVERT: F 34 ASP cc_start: 0.8137 (t0) cc_final: 0.7853 (t0) REVERT: F 47 ASP cc_start: 0.6924 (t0) cc_final: 0.6666 (t0) REVERT: F 78 MET cc_start: 0.8639 (tpp) cc_final: 0.8300 (tpp) REVERT: F 94 ASN cc_start: 0.8165 (t0) cc_final: 0.7697 (t0) REVERT: F 105 ARG cc_start: 0.7910 (ttp-170) cc_final: 0.7577 (ttp80) REVERT: F 179 MET cc_start: 0.7252 (mpp) cc_final: 0.6991 (mpp) REVERT: F 242 LYS cc_start: 0.7778 (mttt) cc_final: 0.7303 (ttmm) REVERT: F 265 GLN cc_start: 0.7825 (tp40) cc_final: 0.7601 (tp-100) REVERT: F 292 GLN cc_start: 0.8215 (tm-30) cc_final: 0.7877 (tm-30) REVERT: F 368 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.7743 (pt0) REVERT: G 94 ASN cc_start: 0.7988 (t0) cc_final: 0.7581 (t0) REVERT: G 98 GLU cc_start: 0.7011 (OUTLIER) cc_final: 0.5926 (tp30) REVERT: G 102 ASN cc_start: 0.7920 (t0) cc_final: 0.7676 (t0) REVERT: G 242 LYS cc_start: 0.7717 (mttt) cc_final: 0.7297 (ttmm) REVERT: G 456 PHE cc_start: 0.8117 (t80) cc_final: 0.7902 (t80) REVERT: H 34 ASP cc_start: 0.8169 (t0) cc_final: 0.7832 (t0) REVERT: H 47 ASP cc_start: 0.6842 (t0) cc_final: 0.6599 (t0) REVERT: H 154 LEU cc_start: 0.4095 (OUTLIER) cc_final: 0.3858 (tp) REVERT: H 179 MET cc_start: 0.8255 (mpp) cc_final: 0.8037 (mmt) REVERT: H 238 LYS cc_start: 0.7940 (mttt) cc_final: 0.7511 (mtpt) REVERT: H 253 ARG cc_start: 0.7893 (tpp80) cc_final: 0.7000 (mmp-170) REVERT: H 292 GLN cc_start: 0.8260 (tm-30) cc_final: 0.7945 (tm-30) outliers start: 95 outliers final: 76 residues processed: 732 average time/residue: 0.7746 time to fit residues: 887.4069 Evaluate side-chains 745 residues out of total 2899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 661 time to evaluate : 3.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain B residue 455 LYS Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 274 ASP Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 485 SER Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 132 GLU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 485 SER Chi-restraints excluded: chain E residue 504 HIS Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 274 ASP Chi-restraints excluded: chain F residue 368 GLN Chi-restraints excluded: chain F residue 476 LEU Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 98 GLU Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain G residue 274 ASP Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 274 ASP Chi-restraints excluded: chain H residue 485 SER Chi-restraints excluded: chain H residue 504 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.888 > 50: distance: 62 - 74: 9.867 distance: 74 - 75: 8.965 distance: 74 - 82: 6.947 distance: 75 - 76: 6.582 distance: 75 - 78: 15.699 distance: 75 - 83: 11.784 distance: 76 - 77: 25.318 distance: 76 - 86: 11.262 distance: 78 - 79: 24.345 distance: 78 - 84: 13.863 distance: 78 - 85: 15.587 distance: 79 - 80: 16.052 distance: 79 - 81: 9.928 distance: 86 - 87: 9.305 distance: 86 - 97: 15.209 distance: 87 - 88: 20.015 distance: 87 - 90: 17.415 distance: 87 - 98: 22.374 distance: 88 - 89: 32.940 distance: 88 - 106: 18.511 distance: 90 - 91: 6.287 distance: 90 - 99: 7.102 distance: 90 - 100: 16.915 distance: 91 - 92: 9.894 distance: 91 - 93: 11.129 distance: 92 - 101: 4.475 distance: 93 - 102: 9.929 distance: 94 - 96: 7.652 distance: 94 - 103: 11.205 distance: 95 - 96: 11.783 distance: 95 - 104: 13.784 distance: 96 - 105: 5.139 distance: 106 - 107: 15.593 distance: 106 - 114: 11.965 distance: 107 - 108: 18.073 distance: 107 - 110: 32.337 distance: 107 - 115: 22.597 distance: 108 - 109: 21.614 distance: 108 - 125: 25.944 distance: 110 - 111: 7.242 distance: 110 - 112: 6.326 distance: 110 - 116: 13.739 distance: 111 - 113: 10.489 distance: 111 - 117: 13.002 distance: 111 - 118: 13.249 distance: 112 - 119: 7.712 distance: 112 - 120: 6.160 distance: 112 - 121: 4.985 distance: 113 - 122: 3.170 distance: 113 - 124: 10.512 distance: 125 - 126: 19.736 distance: 125 - 130: 26.543 distance: 126 - 127: 48.517 distance: 126 - 129: 27.729 distance: 126 - 131: 8.591 distance: 127 - 128: 20.213 distance: 127 - 135: 45.100 distance: 129 - 132: 20.735 distance: 129 - 133: 15.776 distance: 129 - 134: 10.932 distance: 135 - 136: 21.161 distance: 135 - 143: 20.811 distance: 136 - 137: 22.395 distance: 136 - 139: 15.334 distance: 136 - 144: 27.457 distance: 137 - 138: 22.586 distance: 137 - 147: 17.408 distance: 139 - 140: 43.111 distance: 139 - 145: 14.310 distance: 139 - 146: 10.439 distance: 140 - 141: 12.903 distance: 140 - 142: 6.747 distance: 147 - 148: 6.297 distance: 147 - 156: 18.546 distance: 148 - 149: 25.872 distance: 148 - 151: 24.483 distance: 148 - 157: 28.148 distance: 149 - 150: 25.165 distance: 149 - 162: 19.108 distance: 151 - 152: 25.564 distance: 151 - 158: 23.212 distance: 151 - 159: 29.773 distance: 152 - 153: 16.859 distance: 152 - 160: 39.980 distance: 152 - 161: 13.720 distance: 153 - 154: 9.247 distance: 153 - 155: 20.765 distance: 162 - 163: 6.569 distance: 162 - 169: 15.473 distance: 163 - 164: 28.334 distance: 163 - 166: 17.035 distance: 163 - 170: 32.733 distance: 164 - 165: 15.271 distance: 164 - 178: 12.543 distance: 166 - 167: 5.574 distance: 166 - 168: 33.589 distance: 166 - 171: 19.264 distance: 167 - 172: 8.601 distance: 167 - 173: 5.371 distance: 168 - 175: 7.584 distance: 168 - 176: 29.516 distance: 168 - 177: 33.060 distance: 178 - 179: 17.549 distance: 178 - 186: 19.422 distance: 179 - 180: 12.194 distance: 179 - 182: 21.614 distance: 179 - 187: 9.997 distance: 180 - 181: 16.791 distance: 180 - 190: 21.727 distance: 182 - 183: 27.682 distance: 182 - 188: 24.084 distance: 182 - 189: 26.982 distance: 183 - 184: 21.100 distance: 183 - 185: 7.024 distance: 190 - 191: 8.599 distance: 190 - 198: 3.296 distance: 191 - 192: 6.772 distance: 191 - 194: 8.494 distance: 191 - 199: 5.382 distance: 192 - 193: 15.246 distance: 192 - 209: 22.399 distance: 194 - 195: 11.088 distance: 194 - 200: 12.354 distance: 194 - 201: 12.502 distance: 195 - 196: 13.871 distance: 195 - 197: 32.470 distance: 195 - 202: 10.537 distance: 196 - 203: 14.999 distance: 196 - 204: 3.722 distance: 196 - 205: 3.662 distance: 197 - 206: 5.034 distance: 197 - 208: 13.778 distance: 209 - 210: 9.094 distance: 209 - 216: 15.618 distance: 210 - 211: 9.320 distance: 210 - 213: 6.791 distance: 210 - 217: 18.880 distance: 211 - 212: 23.560 distance: 211 - 223: 4.871 distance: 213 - 214: 9.230 distance: 213 - 215: 6.319 distance: 213 - 218: 8.827 distance: 214 - 219: 28.660 distance: 215 - 220: 7.509 distance: 215 - 221: 13.724 distance: 215 - 222: 8.267