Starting phenix.real_space_refine on Sun Mar 17 12:59:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lt0_0966/03_2024/6lt0_0966.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lt0_0966/03_2024/6lt0_0966.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lt0_0966/03_2024/6lt0_0966.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lt0_0966/03_2024/6lt0_0966.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lt0_0966/03_2024/6lt0_0966.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lt0_0966/03_2024/6lt0_0966.pdb" } resolution = 3.2 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= 0.003 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: 4 Type Number sf(0) Gaussians S 88 5.16 5 C 11438 2.51 5 N 3052 2.21 5 O 3196 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 47": "NH1" <-> "NH2" Residue "A ARG 144": "NH1" <-> "NH2" Residue "A ARG 199": "NH1" <-> "NH2" Residue "A ARG 217": "NH1" <-> "NH2" Residue "A ARG 436": "NH1" <-> "NH2" Residue "A ARG 441": "NH1" <-> "NH2" Residue "B ARG 731": "NH1" <-> "NH2" Residue "B ARG 802": "NH1" <-> "NH2" Residue "B ARG 883": "NH1" <-> "NH2" Residue "C ARG 42": "NH1" <-> "NH2" Residue "C ARG 143": "NH1" <-> "NH2" Residue "C ARG 249": "NH1" <-> "NH2" Residue "C PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 394": "NH1" <-> "NH2" Residue "D ARG 47": "NH1" <-> "NH2" Residue "D ARG 144": "NH1" <-> "NH2" Residue "D ARG 199": "NH1" <-> "NH2" Residue "D ARG 217": "NH1" <-> "NH2" Residue "D ARG 436": "NH1" <-> "NH2" Residue "D ARG 441": "NH1" <-> "NH2" Residue "E ARG 731": "NH1" <-> "NH2" Residue "E ARG 802": "NH1" <-> "NH2" Residue "E ARG 883": "NH1" <-> "NH2" Residue "F ARG 42": "NH1" <-> "NH2" Residue "F ARG 143": "NH1" <-> "NH2" Residue "F ARG 249": "NH1" <-> "NH2" Residue "F ARG 394": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17774 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2693 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 337} Chain breaks: 6 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 3134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3134 Classifications: {'peptide': 386} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 15, 'TRANS': 370} Chain breaks: 7 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 3060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3060 Classifications: {'peptide': 385} Link IDs: {'PTRANS': 16, 'TRANS': 368} Chain breaks: 5 Chain: "D" Number of atoms: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2693 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 337} Chain breaks: 6 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "E" Number of atoms: 3134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3134 Classifications: {'peptide': 386} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 15, 'TRANS': 370} Chain breaks: 7 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "F" Number of atoms: 3060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3060 Classifications: {'peptide': 385} Link IDs: {'PTRANS': 16, 'TRANS': 368} Chain breaks: 5 Time building chain proxies: 8.85, per 1000 atoms: 0.50 Number of scatterers: 17774 At special positions: 0 Unit cell: (157.028, 155.967, 89.124, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 88 16.00 O 3196 8.00 N 3052 7.00 C 11438 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 5.89 Conformation dependent library (CDL) restraints added in 2.7 seconds 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4224 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 28 sheets defined 36.9% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain 'A' and resid 440 through 453 removed outlier: 4.708A pdb=" N PHE A 446 " --> pdb=" O SER A 442 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN A 447 " --> pdb=" O LEU A 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 101 removed outlier: 3.991A pdb=" N GLN B 100 " --> pdb=" O SER B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 167 removed outlier: 4.236A pdb=" N ILE B 165 " --> pdb=" O ASP B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 174 removed outlier: 3.820A pdb=" N ALA B 174 " --> pdb=" O GLN B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 188 removed outlier: 4.180A pdb=" N LEU B 183 " --> pdb=" O ALA B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 345 removed outlier: 4.573A pdb=" N SER B 339 " --> pdb=" O LEU B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 365 Processing helix chain 'B' and resid 367 through 372 removed outlier: 3.850A pdb=" N PHE B 370 " --> pdb=" O ILE B 367 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU B 371 " --> pdb=" O THR B 368 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE B 372 " --> pdb=" O ASN B 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 367 through 372' Processing helix chain 'B' and resid 702 through 715 Processing helix chain 'B' and resid 720 through 730 Processing helix chain 'B' and resid 739 through 751 removed outlier: 3.765A pdb=" N VAL B 743 " --> pdb=" O ASP B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 754 No H-bonds generated for 'chain 'B' and resid 752 through 754' Processing helix chain 'B' and resid 775 through 780 removed outlier: 3.515A pdb=" N LYS B 779 " --> pdb=" O MET B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 796 through 801 Processing helix chain 'B' and resid 802 through 804 No H-bonds generated for 'chain 'B' and resid 802 through 804' Processing helix chain 'B' and resid 825 through 831 Processing helix chain 'B' and resid 840 through 864 removed outlier: 3.589A pdb=" N GLN B 853 " --> pdb=" O SER B 849 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 869 removed outlier: 3.802A pdb=" N HIS B 868 " --> pdb=" O CYS B 864 " (cutoff:3.500A) Processing helix chain 'B' and resid 876 through 891 Processing helix chain 'B' and resid 897 through 916 removed outlier: 4.042A pdb=" N GLU B 907 " --> pdb=" O GLN B 903 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN B 915 " --> pdb=" O LEU B 911 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 68 removed outlier: 3.803A pdb=" N ASN C 68 " --> pdb=" O ASN C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 126 No H-bonds generated for 'chain 'C' and resid 124 through 126' Processing helix chain 'C' and resid 127 through 148 removed outlier: 4.157A pdb=" N ASP C 133 " --> pdb=" O ARG C 129 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE C 138 " --> pdb=" O ARG C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 193 removed outlier: 4.531A pdb=" N GLY C 178 " --> pdb=" O PRO C 174 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N GLU C 179 " --> pdb=" O MET C 175 " (cutoff:3.500A) Proline residue: C 182 - end of helix removed outlier: 3.805A pdb=" N GLU C 185 " --> pdb=" O ILE C 181 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU C 187 " --> pdb=" O VAL C 183 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS C 191 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SER C 192 " --> pdb=" O SER C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 204 removed outlier: 3.631A pdb=" N ASP C 203 " --> pdb=" O ASP C 200 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR C 204 " --> pdb=" O ILE C 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 200 through 204' Processing helix chain 'C' and resid 215 through 230 removed outlier: 3.652A pdb=" N ILE C 224 " --> pdb=" O LEU C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 252 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 263 removed outlier: 3.566A pdb=" N LYS C 261 " --> pdb=" O PRO C 257 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N CYS C 262 " --> pdb=" O ALA C 258 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N SER C 263 " --> pdb=" O GLU C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 300 removed outlier: 3.804A pdb=" N MET C 299 " --> pdb=" O PHE C 295 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR C 300 " --> pdb=" O ARG C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 337 Processing helix chain 'C' and resid 375 through 385 removed outlier: 4.491A pdb=" N PHE C 385 " --> pdb=" O LEU C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 420 removed outlier: 3.568A pdb=" N THR C 420 " --> pdb=" O ILE C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 437 removed outlier: 3.653A pdb=" N LEU C 433 " --> pdb=" O SER C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 455 removed outlier: 4.544A pdb=" N ILE C 447 " --> pdb=" O GLY C 443 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE C 448 " --> pdb=" O ASP C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 464 removed outlier: 3.681A pdb=" N PHE C 462 " --> pdb=" O GLY C 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 453 removed outlier: 4.709A pdb=" N PHE D 446 " --> pdb=" O SER D 442 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN D 447 " --> pdb=" O LEU D 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 101 removed outlier: 3.991A pdb=" N GLN E 100 " --> pdb=" O SER E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 167 removed outlier: 4.236A pdb=" N ILE E 165 " --> pdb=" O ASP E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 174 removed outlier: 3.820A pdb=" N ALA E 174 " --> pdb=" O GLN E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 188 removed outlier: 4.180A pdb=" N LEU E 183 " --> pdb=" O ALA E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 345 removed outlier: 4.573A pdb=" N SER E 339 " --> pdb=" O LEU E 335 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 365 Processing helix chain 'E' and resid 367 through 372 removed outlier: 3.850A pdb=" N PHE E 370 " --> pdb=" O ILE E 367 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU E 371 " --> pdb=" O THR E 368 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE E 372 " --> pdb=" O ASN E 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 367 through 372' Processing helix chain 'E' and resid 702 through 715 Processing helix chain 'E' and resid 720 through 730 Processing helix chain 'E' and resid 739 through 751 removed outlier: 3.764A pdb=" N VAL E 743 " --> pdb=" O ASP E 739 " (cutoff:3.500A) Processing helix chain 'E' and resid 752 through 754 No H-bonds generated for 'chain 'E' and resid 752 through 754' Processing helix chain 'E' and resid 775 through 780 removed outlier: 3.514A pdb=" N LYS E 779 " --> pdb=" O MET E 775 " (cutoff:3.500A) Processing helix chain 'E' and resid 796 through 801 Processing helix chain 'E' and resid 802 through 804 No H-bonds generated for 'chain 'E' and resid 802 through 804' Processing helix chain 'E' and resid 825 through 831 Processing helix chain 'E' and resid 840 through 864 removed outlier: 3.589A pdb=" N GLN E 853 " --> pdb=" O SER E 849 " (cutoff:3.500A) Processing helix chain 'E' and resid 864 through 869 removed outlier: 3.802A pdb=" N HIS E 868 " --> pdb=" O CYS E 864 " (cutoff:3.500A) Processing helix chain 'E' and resid 876 through 891 Processing helix chain 'E' and resid 897 through 916 removed outlier: 4.042A pdb=" N GLU E 907 " --> pdb=" O GLN E 903 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN E 915 " --> pdb=" O LEU E 911 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 68 removed outlier: 3.803A pdb=" N ASN F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 126 No H-bonds generated for 'chain 'F' and resid 124 through 126' Processing helix chain 'F' and resid 127 through 148 removed outlier: 4.157A pdb=" N ASP F 133 " --> pdb=" O ARG F 129 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE F 138 " --> pdb=" O ARG F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 193 removed outlier: 4.532A pdb=" N GLY F 178 " --> pdb=" O PRO F 174 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLU F 179 " --> pdb=" O MET F 175 " (cutoff:3.500A) Proline residue: F 182 - end of helix removed outlier: 3.806A pdb=" N GLU F 185 " --> pdb=" O ILE F 181 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU F 187 " --> pdb=" O VAL F 183 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS F 191 " --> pdb=" O LEU F 187 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER F 192 " --> pdb=" O SER F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 204 removed outlier: 3.631A pdb=" N ASP F 203 " --> pdb=" O ASP F 200 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR F 204 " --> pdb=" O ILE F 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 200 through 204' Processing helix chain 'F' and resid 215 through 230 removed outlier: 3.652A pdb=" N ILE F 224 " --> pdb=" O LEU F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 241 through 252 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 263 removed outlier: 3.566A pdb=" N LYS F 261 " --> pdb=" O PRO F 257 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N CYS F 262 " --> pdb=" O ALA F 258 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N SER F 263 " --> pdb=" O GLU F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 300 removed outlier: 3.804A pdb=" N MET F 299 " --> pdb=" O PHE F 295 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR F 300 " --> pdb=" O ARG F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 320 through 337 Processing helix chain 'F' and resid 375 through 385 removed outlier: 4.492A pdb=" N PHE F 385 " --> pdb=" O LEU F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 420 removed outlier: 3.568A pdb=" N THR F 420 " --> pdb=" O ILE F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 437 removed outlier: 3.652A pdb=" N LEU F 433 " --> pdb=" O SER F 429 " (cutoff:3.500A) Processing helix chain 'F' and resid 441 through 455 removed outlier: 4.544A pdb=" N ILE F 447 " --> pdb=" O GLY F 443 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE F 448 " --> pdb=" O ASP F 444 " (cutoff:3.500A) Processing helix chain 'F' and resid 458 through 464 removed outlier: 3.682A pdb=" N PHE F 462 " --> pdb=" O GLY F 458 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 40 removed outlier: 4.947A pdb=" N LEU A 427 " --> pdb=" O SER A 423 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER A 423 " --> pdb=" O LEU A 427 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 419 " --> pdb=" O TRP A 431 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N MET A 410 " --> pdb=" O CYS A 422 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 46 through 53 removed outlier: 5.510A pdb=" N LEU A 49 " --> pdb=" O ALA A 60 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ALA A 60 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N GLN A 51 " --> pdb=" O ALA A 58 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ALA A 58 " --> pdb=" O GLN A 51 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP A 53 " --> pdb=" O ARG A 56 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU A 78 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ASN A 70 " --> pdb=" O LYS A 76 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LYS A 76 " --> pdb=" O ASN A 70 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 92 removed outlier: 4.068A pdb=" N ALA A 89 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN A 127 " --> pdb=" O VAL A 117 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 141 through 142 removed outlier: 3.625A pdb=" N VAL A 147 " --> pdb=" O LEU A 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 156 through 157 removed outlier: 3.976A pdb=" N LYS A 167 " --> pdb=" O VAL A 157 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 179 through 182 removed outlier: 3.600A pdb=" N VAL A 187 " --> pdb=" O ILE A 182 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 225 through 230 removed outlier: 3.605A pdb=" N SER A 227 " --> pdb=" O GLY A 239 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE A 246 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU A 245 " --> pdb=" O LYS A 276 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N LYS A 276 " --> pdb=" O LEU A 245 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE A 247 " --> pdb=" O GLU A 274 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 291 through 292 removed outlier: 4.217A pdb=" N VAL A 306 " --> pdb=" O ILE A 315 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 329 through 332 removed outlier: 4.027A pdb=" N GLN A 336 " --> pdb=" O LEU A 332 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG A 347 " --> pdb=" O SER A 339 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE A 348 " --> pdb=" O ILE A 398 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 60 through 63 removed outlier: 3.867A pdb=" N SER B 61 " --> pdb=" O ALA B 156 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA B 156 " --> pdb=" O SER B 61 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE B 153 " --> pdb=" O HIS B 137 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR B 135 " --> pdb=" O MET B 155 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N PHE B 133 " --> pdb=" O TYR B 157 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N SER B 159 " --> pdb=" O GLY B 131 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N GLY B 131 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASN B 116 " --> pdb=" O ALA B 134 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU B 115 " --> pdb=" O VAL C 86 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP C 81 " --> pdb=" O ILE C 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 782 through 785 Processing sheet with id=AB3, first strand: chain 'B' and resid 817 through 819 removed outlier: 3.691A pdb=" N LEU B 817 " --> pdb=" O TYR B 935 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N CYS B 819 " --> pdb=" O PHE B 933 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 14 through 17 removed outlier: 6.263A pdb=" N THR C 15 " --> pdb=" O ALA C 46 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 280 through 281 Processing sheet with id=AB6, first strand: chain 'D' and resid 35 through 40 removed outlier: 4.947A pdb=" N LEU D 427 " --> pdb=" O SER D 423 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER D 423 " --> pdb=" O LEU D 427 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU D 419 " --> pdb=" O TRP D 431 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N MET D 410 " --> pdb=" O CYS D 422 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 46 through 53 removed outlier: 5.510A pdb=" N LEU D 49 " --> pdb=" O ALA D 60 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ALA D 60 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N GLN D 51 " --> pdb=" O ALA D 58 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ALA D 58 " --> pdb=" O GLN D 51 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP D 53 " --> pdb=" O ARG D 56 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU D 78 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ASN D 70 " --> pdb=" O LYS D 76 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LYS D 76 " --> pdb=" O ASN D 70 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 87 through 92 removed outlier: 4.069A pdb=" N ALA D 89 " --> pdb=" O ALA D 109 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN D 127 " --> pdb=" O VAL D 117 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 141 through 142 removed outlier: 3.625A pdb=" N VAL D 147 " --> pdb=" O LEU D 142 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 156 through 157 removed outlier: 3.975A pdb=" N LYS D 167 " --> pdb=" O VAL D 157 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 179 through 182 removed outlier: 3.600A pdb=" N VAL D 187 " --> pdb=" O ILE D 182 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 225 through 230 removed outlier: 3.605A pdb=" N SER D 227 " --> pdb=" O GLY D 239 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE D 246 " --> pdb=" O THR D 238 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU D 245 " --> pdb=" O LYS D 276 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N LYS D 276 " --> pdb=" O LEU D 245 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE D 247 " --> pdb=" O GLU D 274 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 291 through 292 removed outlier: 4.217A pdb=" N VAL D 306 " --> pdb=" O ILE D 315 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 329 through 332 removed outlier: 4.026A pdb=" N GLN D 336 " --> pdb=" O LEU D 332 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG D 347 " --> pdb=" O SER D 339 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE D 348 " --> pdb=" O ILE D 398 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 60 through 63 removed outlier: 3.867A pdb=" N SER E 61 " --> pdb=" O ALA E 156 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA E 156 " --> pdb=" O SER E 61 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE E 153 " --> pdb=" O HIS E 137 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR E 135 " --> pdb=" O MET E 155 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N PHE E 133 " --> pdb=" O TYR E 157 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N SER E 159 " --> pdb=" O GLY E 131 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLY E 131 " --> pdb=" O SER E 159 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASN E 116 " --> pdb=" O ALA E 134 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU E 115 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP F 81 " --> pdb=" O ILE F 98 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 782 through 785 Processing sheet with id=AC8, first strand: chain 'E' and resid 817 through 819 removed outlier: 3.692A pdb=" N LEU E 817 " --> pdb=" O TYR E 935 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N CYS E 819 " --> pdb=" O PHE E 933 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 14 through 17 removed outlier: 6.262A pdb=" N THR F 15 " --> pdb=" O ALA F 46 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'F' and resid 280 through 281 650 hydrogen bonds defined for protein. 1890 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.25 Time building geometry restraints manager: 6.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5474 1.34 - 1.46: 3097 1.46 - 1.57: 9439 1.57 - 1.69: 0 1.69 - 1.81: 126 Bond restraints: 18136 Sorted by residual: bond pdb=" C ILE F 181 " pdb=" N PRO F 182 " ideal model delta sigma weight residual 1.336 1.393 -0.057 1.20e-02 6.94e+03 2.22e+01 bond pdb=" C ILE C 181 " pdb=" N PRO C 182 " ideal model delta sigma weight residual 1.336 1.392 -0.056 1.20e-02 6.94e+03 2.22e+01 bond pdb=" C TYR E 112 " pdb=" N PRO E 113 " ideal model delta sigma weight residual 1.334 1.384 -0.050 2.34e-02 1.83e+03 4.53e+00 bond pdb=" C TYR B 112 " pdb=" N PRO B 113 " ideal model delta sigma weight residual 1.334 1.384 -0.050 2.34e-02 1.83e+03 4.50e+00 bond pdb=" C PRO E 107 " pdb=" N PRO E 108 " ideal model delta sigma weight residual 1.334 1.383 -0.049 2.34e-02 1.83e+03 4.42e+00 ... (remaining 18131 not shown) Histogram of bond angle deviations from ideal: 99.91 - 106.80: 512 106.80 - 113.69: 10168 113.69 - 120.58: 7203 120.58 - 127.47: 6405 127.47 - 134.35: 230 Bond angle restraints: 24518 Sorted by residual: angle pdb=" C ILE C 172 " pdb=" N ILE C 173 " pdb=" CA ILE C 173 " ideal model delta sigma weight residual 120.33 124.57 -4.24 8.00e-01 1.56e+00 2.81e+01 angle pdb=" C ILE F 172 " pdb=" N ILE F 173 " pdb=" CA ILE F 173 " ideal model delta sigma weight residual 120.33 124.55 -4.22 8.00e-01 1.56e+00 2.78e+01 angle pdb=" C LEU D 145 " pdb=" N ASP D 146 " pdb=" CA ASP D 146 " ideal model delta sigma weight residual 122.46 129.24 -6.78 1.41e+00 5.03e-01 2.31e+01 angle pdb=" C LEU A 145 " pdb=" N ASP A 146 " pdb=" CA ASP A 146 " ideal model delta sigma weight residual 122.46 129.21 -6.75 1.41e+00 5.03e-01 2.29e+01 angle pdb=" C GLY C 21 " pdb=" N LYS C 22 " pdb=" CA LYS C 22 " ideal model delta sigma weight residual 120.82 127.23 -6.41 1.47e+00 4.63e-01 1.90e+01 ... (remaining 24513 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.40: 9958 15.40 - 30.80: 610 30.80 - 46.21: 208 46.21 - 61.61: 10 61.61 - 77.01: 18 Dihedral angle restraints: 10804 sinusoidal: 4322 harmonic: 6482 Sorted by residual: dihedral pdb=" CA LEU A 218 " pdb=" C LEU A 218 " pdb=" N LEU A 219 " pdb=" CA LEU A 219 " ideal model delta harmonic sigma weight residual -180.00 -133.33 -46.67 0 5.00e+00 4.00e-02 8.71e+01 dihedral pdb=" CA LEU D 218 " pdb=" C LEU D 218 " pdb=" N LEU D 219 " pdb=" CA LEU D 219 " ideal model delta harmonic sigma weight residual -180.00 -133.39 -46.61 0 5.00e+00 4.00e-02 8.69e+01 dihedral pdb=" CA ASP D 292 " pdb=" C ASP D 292 " pdb=" N GLU D 293 " pdb=" CA GLU D 293 " ideal model delta harmonic sigma weight residual -180.00 -144.21 -35.79 0 5.00e+00 4.00e-02 5.12e+01 ... (remaining 10801 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1927 0.052 - 0.103: 659 0.103 - 0.155: 215 0.155 - 0.207: 29 0.207 - 0.258: 8 Chirality restraints: 2838 Sorted by residual: chirality pdb=" CB VAL C 195 " pdb=" CA VAL C 195 " pdb=" CG1 VAL C 195 " pdb=" CG2 VAL C 195 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CB VAL F 195 " pdb=" CA VAL F 195 " pdb=" CG1 VAL F 195 " pdb=" CG2 VAL F 195 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CB VAL E 104 " pdb=" CA VAL E 104 " pdb=" CG1 VAL E 104 " pdb=" CG2 VAL E 104 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 2835 not shown) Planarity restraints: 3058 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO E 107 " 0.053 5.00e-02 4.00e+02 8.11e-02 1.05e+01 pdb=" N PRO E 108 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO E 108 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO E 108 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 107 " -0.053 5.00e-02 4.00e+02 8.10e-02 1.05e+01 pdb=" N PRO B 108 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO B 108 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 108 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 218 " 0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C LEU D 218 " -0.055 2.00e-02 2.50e+03 pdb=" O LEU D 218 " 0.020 2.00e-02 2.50e+03 pdb=" N LEU D 219 " 0.019 2.00e-02 2.50e+03 ... (remaining 3055 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 61 2.50 - 3.10: 11297 3.10 - 3.70: 26318 3.70 - 4.30: 36526 4.30 - 4.90: 61858 Nonbonded interactions: 136060 Sorted by model distance: nonbonded pdb=" O ARG B 834 " pdb=" NH2 ARG F 431 " model vdw 1.898 2.520 nonbonded pdb=" CG ASN B 896 " pdb=" OE1 GLN F 368 " model vdw 1.912 3.270 nonbonded pdb=" NH2 ARG C 431 " pdb=" OD2 ASP E 832 " model vdw 1.957 2.520 nonbonded pdb=" ND2 ASN B 896 " pdb=" OE1 GLN F 368 " model vdw 2.007 2.520 nonbonded pdb=" O GLU E 181 " pdb=" OG1 THR E 185 " model vdw 2.276 2.440 ... (remaining 136055 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.300 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: 0.000 Extract box with map and model: 5.850 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 44.150 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.100 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:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5624 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 : 0.005 0.060 18136 Z= 0.359 Angle : 1.085 13.626 24518 Z= 0.567 Chirality : 0.058 0.258 2838 Planarity : 0.007 0.081 3058 Dihedral : 11.856 77.009 6580 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.28 % Allowed : 13.34 % Favored : 86.38 % Rotamer: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.28 % 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: -5.35 (0.14), residues: 2144 helix: -3.40 (0.12), residues: 708 sheet: -2.99 (0.21), residues: 498 loop : -3.91 (0.16), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP A 118 HIS 0.013 0.002 HIS A 221 PHE 0.022 0.003 PHE F 99 TYR 0.025 0.002 TYR B 757 ARG 0.006 0.001 ARG D 56 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 1984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 492 time to evaluate : 2.184 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: A 107 LEU cc_start: 0.8387 (mp) cc_final: 0.8186 (pp) REVERT: A 118 TRP cc_start: 0.7579 (m-10) cc_final: 0.6995 (m-10) REVERT: A 200 LEU cc_start: 0.7215 (tt) cc_final: 0.6888 (mt) REVERT: B 363 LYS cc_start: 0.6737 (mmtp) cc_final: 0.6341 (tttp) REVERT: B 767 TRP cc_start: 0.6338 (t60) cc_final: 0.5914 (t60) REVERT: C 64 ASN cc_start: 0.7286 (m110) cc_final: 0.7054 (m-40) REVERT: C 184 MET cc_start: 0.8523 (tmt) cc_final: 0.8226 (tmm) REVERT: C 191 LYS cc_start: 0.7387 (ttpt) cc_final: 0.6944 (tmtt) REVERT: C 414 LYS cc_start: 0.7940 (mmmt) cc_final: 0.7590 (mmmt) REVERT: D 94 PRO cc_start: 0.2150 (Cg_exo) cc_final: 0.1751 (Cg_endo) REVERT: D 311 MET cc_start: 0.4390 (ttm) cc_final: 0.2802 (mmt) REVERT: E 155 MET cc_start: 0.4543 (ptt) cc_final: 0.4069 (mtp) REVERT: E 162 GLN cc_start: 0.5024 (tp-100) cc_final: 0.4588 (pm20) REVERT: E 888 LEU cc_start: 0.4505 (mp) cc_final: 0.4266 (mp) REVERT: F 49 THR cc_start: 0.3656 (p) cc_final: 0.3332 (t) REVERT: F 94 ILE cc_start: 0.7359 (mt) cc_final: 0.6141 (mt) REVERT: F 184 MET cc_start: 0.5608 (tmt) cc_final: 0.5308 (tmm) outliers start: 0 outliers final: 0 residues processed: 492 average time/residue: 0.3403 time to fit residues: 237.7239 Evaluate side-chains 252 residues out of total 1984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 252 time to evaluate : 2.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 9.9990 chunk 166 optimal weight: 9.9990 chunk 92 optimal weight: 1.9990 chunk 56 optimal weight: 0.0980 chunk 112 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 172 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 104 optimal weight: 0.9980 chunk 128 optimal weight: 0.9980 chunk 199 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 HIS A 426 HIS B 106 HIS ** B 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 922 HIS C 65 HIS C 137 HIS C 281 GLN C 460 HIS D 143 GLN ** D 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 GLN D 426 HIS D 433 ASN E 106 HIS E 163 HIS E 340 HIS E 366 HIS ** E 721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 798 HIS E 846 HIS E 872 HIS E 922 HIS ** F 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 297 GLN F 460 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5777 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18136 Z= 0.211 Angle : 0.720 9.197 24518 Z= 0.366 Chirality : 0.046 0.183 2838 Planarity : 0.005 0.061 3058 Dihedral : 6.293 45.071 2372 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.40 % Favored : 89.51 % Rotamer: Outliers : 3.31 % Allowed : 11.47 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -4.00 (0.16), residues: 2144 helix: -1.44 (0.16), residues: 746 sheet: -2.40 (0.23), residues: 456 loop : -3.82 (0.16), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 33 HIS 0.014 0.001 HIS E 366 PHE 0.029 0.002 PHE C 61 TYR 0.019 0.001 TYR D 55 ARG 0.007 0.001 ARG D 441 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 286 time to evaluate : 2.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 TRP cc_start: 0.7564 (m-10) cc_final: 0.6712 (m-90) REVERT: B 363 LYS cc_start: 0.7090 (mmtp) cc_final: 0.6724 (tttp) REVERT: B 767 TRP cc_start: 0.6489 (t60) cc_final: 0.5945 (t60) REVERT: C 64 ASN cc_start: 0.7293 (m110) cc_final: 0.6779 (m-40) REVERT: C 98 ILE cc_start: 0.7125 (mm) cc_final: 0.6651 (pt) REVERT: C 184 MET cc_start: 0.8526 (tmt) cc_final: 0.8046 (tmm) REVERT: C 191 LYS cc_start: 0.7244 (ttpt) cc_final: 0.6772 (tmtt) REVERT: C 298 VAL cc_start: 0.9151 (t) cc_final: 0.8744 (m) REVERT: C 334 SER cc_start: 0.7711 (OUTLIER) cc_final: 0.7191 (m) REVERT: C 414 LYS cc_start: 0.8053 (mmmt) cc_final: 0.7705 (mmmt) REVERT: D 311 MET cc_start: 0.4298 (ttm) cc_final: 0.2865 (mmt) REVERT: D 349 TRP cc_start: 0.1737 (m-90) cc_final: 0.1200 (m-90) REVERT: E 116 ASN cc_start: 0.6071 (p0) cc_final: 0.5596 (m-40) REVERT: E 155 MET cc_start: 0.4965 (ptt) cc_final: 0.3899 (mtp) REVERT: F 49 THR cc_start: 0.3265 (p) cc_final: 0.2972 (t) REVERT: F 85 PHE cc_start: 0.4058 (t80) cc_final: 0.3530 (t80) REVERT: F 184 MET cc_start: 0.5138 (tmt) cc_final: 0.4826 (tmm) REVERT: F 318 MET cc_start: 0.6664 (mmm) cc_final: 0.6195 (ttm) outliers start: 65 outliers final: 41 residues processed: 334 average time/residue: 0.3004 time to fit residues: 152.3057 Evaluate side-chains 268 residues out of total 1984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 226 time to evaluate : 2.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain B residue 182 CYS Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 369 ASN Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 266 CYS Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 422 CYS Chi-restraints excluded: chain E residue 713 PHE Chi-restraints excluded: chain E residue 754 VAL Chi-restraints excluded: chain E residue 798 HIS Chi-restraints excluded: chain E residue 841 SER Chi-restraints excluded: chain E residue 894 LEU Chi-restraints excluded: chain E residue 895 VAL Chi-restraints excluded: chain E residue 911 LEU Chi-restraints excluded: chain E residue 917 SER Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 263 SER Chi-restraints excluded: chain F residue 286 ASP Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 396 THR Chi-restraints excluded: chain F residue 460 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 111 optimal weight: 30.0000 chunk 62 optimal weight: 6.9990 chunk 166 optimal weight: 1.9990 chunk 136 optimal weight: 9.9990 chunk 55 optimal weight: 0.0970 chunk 200 optimal weight: 30.0000 chunk 216 optimal weight: 2.9990 chunk 178 optimal weight: 8.9990 chunk 198 optimal weight: 10.0000 chunk 68 optimal weight: 0.7980 chunk 160 optimal weight: 10.0000 overall best weight: 2.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 221 HIS B 137 HIS B 162 GLN B 369 ASN C 65 HIS ** D 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 846 HIS ** F 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 383 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5943 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 18136 Z= 0.338 Angle : 0.771 10.940 24518 Z= 0.389 Chirality : 0.048 0.264 2838 Planarity : 0.005 0.057 3058 Dihedral : 6.116 43.927 2372 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.57 % Favored : 88.34 % Rotamer: Outliers : 4.54 % Allowed : 13.56 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -3.46 (0.17), residues: 2144 helix: -0.77 (0.18), residues: 746 sheet: -2.36 (0.22), residues: 464 loop : -3.58 (0.17), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 148 HIS 0.021 0.002 HIS F 460 PHE 0.023 0.002 PHE F 61 TYR 0.021 0.002 TYR B 935 ARG 0.005 0.001 ARG D 302 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 247 time to evaluate : 2.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7743 (pt) REVERT: A 78 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7389 (pp) REVERT: B 117 PHE cc_start: 0.7427 (t80) cc_final: 0.7029 (t80) REVERT: B 363 LYS cc_start: 0.7127 (mmtp) cc_final: 0.6780 (tttp) REVERT: B 898 ASP cc_start: 0.7403 (OUTLIER) cc_final: 0.7057 (m-30) REVERT: C 64 ASN cc_start: 0.7460 (m110) cc_final: 0.6927 (m-40) REVERT: C 184 MET cc_start: 0.8492 (tmt) cc_final: 0.8017 (tmm) REVERT: C 191 LYS cc_start: 0.7418 (ttpt) cc_final: 0.7012 (tmtt) REVERT: C 414 LYS cc_start: 0.8197 (mmmt) cc_final: 0.7803 (mmmt) REVERT: D 349 TRP cc_start: 0.1852 (m-90) cc_final: 0.1218 (m-90) REVERT: E 116 ASN cc_start: 0.6789 (p0) cc_final: 0.6014 (m-40) REVERT: E 155 MET cc_start: 0.5036 (ptt) cc_final: 0.3781 (mtm) REVERT: F 17 ILE cc_start: 0.3626 (OUTLIER) cc_final: 0.3411 (mp) REVERT: F 49 THR cc_start: 0.3288 (p) cc_final: 0.2961 (t) REVERT: F 51 GLN cc_start: 0.6036 (tm-30) cc_final: 0.5181 (tt0) REVERT: F 85 PHE cc_start: 0.4004 (t80) cc_final: 0.3314 (t80) REVERT: F 184 MET cc_start: 0.5282 (tmt) cc_final: 0.4868 (tmm) REVERT: F 242 GLU cc_start: 0.2928 (mp0) cc_final: 0.2242 (mm-30) outliers start: 89 outliers final: 55 residues processed: 308 average time/residue: 0.2760 time to fit residues: 131.8424 Evaluate side-chains 270 residues out of total 1984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 211 time to evaluate : 2.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 148 TRP Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain B residue 182 CYS Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 898 ASP Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 266 CYS Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 315 ILE Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain E residue 368 THR Chi-restraints excluded: chain E residue 713 PHE Chi-restraints excluded: chain E residue 754 VAL Chi-restraints excluded: chain E residue 841 SER Chi-restraints excluded: chain E residue 894 LEU Chi-restraints excluded: chain E residue 895 VAL Chi-restraints excluded: chain E residue 917 SER Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 286 ASP Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 396 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 197 optimal weight: 10.0000 chunk 150 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 95 optimal weight: 0.0570 chunk 134 optimal weight: 0.9980 chunk 200 optimal weight: 20.0000 chunk 212 optimal weight: 10.0000 chunk 104 optimal weight: 0.6980 chunk 190 optimal weight: 10.0000 chunk 57 optimal weight: 0.6980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS C 65 HIS ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 HIS ** D 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 HIS E 846 HIS E 868 HIS F 51 GLN ** F 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 460 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5857 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18136 Z= 0.170 Angle : 0.656 14.435 24518 Z= 0.328 Chirality : 0.045 0.170 2838 Planarity : 0.004 0.045 3058 Dihedral : 5.622 43.402 2372 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.28 % Favored : 90.62 % Rotamer: Outliers : 2.96 % Allowed : 16.26 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.95 (0.17), residues: 2144 helix: -0.18 (0.19), residues: 746 sheet: -1.98 (0.23), residues: 436 loop : -3.47 (0.17), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 148 HIS 0.007 0.001 HIS D 221 PHE 0.024 0.001 PHE F 401 TYR 0.018 0.001 TYR D 55 ARG 0.005 0.000 ARG E 839 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 248 time to evaluate : 2.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7367 (pt) REVERT: A 78 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7365 (pp) REVERT: A 139 LEU cc_start: 0.8995 (mt) cc_final: 0.8772 (mt) REVERT: B 117 PHE cc_start: 0.7452 (t80) cc_final: 0.7075 (t80) REVERT: B 363 LYS cc_start: 0.7107 (mmtp) cc_final: 0.6726 (tttp) REVERT: C 64 ASN cc_start: 0.7355 (m110) cc_final: 0.6784 (m-40) REVERT: C 98 ILE cc_start: 0.7089 (mm) cc_final: 0.6554 (pt) REVERT: C 184 MET cc_start: 0.8400 (tmt) cc_final: 0.7845 (tmm) REVERT: C 191 LYS cc_start: 0.7250 (ttpt) cc_final: 0.6810 (tmtt) REVERT: C 414 LYS cc_start: 0.8098 (mmmt) cc_final: 0.7738 (mmmt) REVERT: D 349 TRP cc_start: 0.1681 (m-90) cc_final: 0.1248 (m-90) REVERT: E 117 PHE cc_start: 0.3183 (OUTLIER) cc_final: 0.2685 (t80) REVERT: E 155 MET cc_start: 0.4883 (ptt) cc_final: 0.3665 (mtm) REVERT: E 898 ASP cc_start: -0.0080 (OUTLIER) cc_final: -0.0811 (m-30) REVERT: F 49 THR cc_start: 0.2918 (p) cc_final: 0.2678 (t) REVERT: F 51 GLN cc_start: 0.5953 (tm130) cc_final: 0.5217 (tt0) REVERT: F 85 PHE cc_start: 0.3917 (t80) cc_final: 0.3253 (t80) REVERT: F 184 MET cc_start: 0.5208 (tmt) cc_final: 0.4843 (tmm) REVERT: F 242 GLU cc_start: 0.2796 (mp0) cc_final: 0.2106 (mm-30) outliers start: 58 outliers final: 35 residues processed: 286 average time/residue: 0.2840 time to fit residues: 124.7522 Evaluate side-chains 244 residues out of total 1984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 205 time to evaluate : 2.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 148 TRP Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain B residue 182 CYS Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain C residue 266 CYS Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 315 ILE Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain E residue 117 PHE Chi-restraints excluded: chain E residue 713 PHE Chi-restraints excluded: chain E residue 754 VAL Chi-restraints excluded: chain E residue 894 LEU Chi-restraints excluded: chain E residue 898 ASP Chi-restraints excluded: chain E residue 917 SER Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 263 SER Chi-restraints excluded: chain F residue 440 THR Chi-restraints excluded: chain F residue 460 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 177 optimal weight: 2.9990 chunk 120 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 158 optimal weight: 20.0000 chunk 87 optimal weight: 3.9990 chunk 181 optimal weight: 20.0000 chunk 146 optimal weight: 20.0000 chunk 0 optimal weight: 4.9990 chunk 108 optimal weight: 0.8980 chunk 190 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 846 HIS ** F 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 368 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5998 moved from start: 0.4775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 18136 Z= 0.353 Angle : 0.740 12.303 24518 Z= 0.373 Chirality : 0.048 0.311 2838 Planarity : 0.005 0.051 3058 Dihedral : 5.805 44.039 2372 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.31 % Favored : 87.59 % Rotamer: Outliers : 4.69 % Allowed : 16.31 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.05 (0.17), residues: 2144 helix: -0.36 (0.19), residues: 756 sheet: -2.06 (0.23), residues: 466 loop : -3.48 (0.18), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 148 HIS 0.018 0.001 HIS F 460 PHE 0.045 0.002 PHE F 219 TYR 0.017 0.002 TYR B 935 ARG 0.004 0.000 ARG B 823 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 223 time to evaluate : 2.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7723 (pt) REVERT: A 78 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7438 (pp) REVERT: B 363 LYS cc_start: 0.6856 (mmtp) cc_final: 0.6509 (tttp) REVERT: B 898 ASP cc_start: 0.7365 (OUTLIER) cc_final: 0.7093 (m-30) REVERT: C 64 ASN cc_start: 0.7606 (m110) cc_final: 0.7021 (m-40) REVERT: C 184 MET cc_start: 0.8398 (tmt) cc_final: 0.7931 (tmm) REVERT: C 191 LYS cc_start: 0.7481 (ttpt) cc_final: 0.7060 (tmtt) REVERT: C 372 HIS cc_start: 0.7691 (OUTLIER) cc_final: 0.6994 (p-80) REVERT: C 414 LYS cc_start: 0.8112 (mmmt) cc_final: 0.7724 (mmmt) REVERT: D 349 TRP cc_start: 0.1840 (m-90) cc_final: 0.1361 (m-90) REVERT: E 155 MET cc_start: 0.4727 (ptt) cc_final: 0.3415 (mtt) REVERT: E 857 LYS cc_start: 0.5989 (mmtt) cc_final: 0.5775 (mmtt) REVERT: F 49 THR cc_start: 0.3073 (p) cc_final: 0.2844 (t) REVERT: F 184 MET cc_start: 0.5282 (tmt) cc_final: 0.4890 (tmm) REVERT: F 242 GLU cc_start: 0.2896 (mp0) cc_final: 0.2128 (mm-30) REVERT: F 286 ASP cc_start: 0.4211 (OUTLIER) cc_final: 0.3854 (p0) outliers start: 92 outliers final: 68 residues processed: 294 average time/residue: 0.2838 time to fit residues: 128.2878 Evaluate side-chains 271 residues out of total 1984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 198 time to evaluate : 2.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 118 TRP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 148 TRP Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain B residue 182 CYS Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 898 ASP Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain C residue 266 CYS Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 372 HIS Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 315 ILE Chi-restraints excluded: chain D residue 323 ASP Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 713 PHE Chi-restraints excluded: chain E residue 734 VAL Chi-restraints excluded: chain E residue 754 VAL Chi-restraints excluded: chain E residue 841 SER Chi-restraints excluded: chain E residue 851 LEU Chi-restraints excluded: chain E residue 866 HIS Chi-restraints excluded: chain E residue 894 LEU Chi-restraints excluded: chain E residue 895 VAL Chi-restraints excluded: chain E residue 911 LEU Chi-restraints excluded: chain E residue 917 SER Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 263 SER Chi-restraints excluded: chain F residue 286 ASP Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 396 THR Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain F residue 440 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 71 optimal weight: 0.7980 chunk 191 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 124 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 chunk 212 optimal weight: 40.0000 chunk 176 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 chunk 111 optimal weight: 20.0000 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 ASN B 100 GLN ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 GLN ** D 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 325 ASN E 766 HIS E 846 HIS E 903 GLN ** F 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 460 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6005 moved from start: 0.5171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 18136 Z= 0.302 Angle : 0.718 12.986 24518 Z= 0.360 Chirality : 0.047 0.267 2838 Planarity : 0.005 0.044 3058 Dihedral : 5.730 43.923 2372 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.19 % Favored : 88.71 % Rotamer: Outliers : 4.79 % Allowed : 17.69 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.93 (0.17), residues: 2144 helix: -0.34 (0.19), residues: 762 sheet: -1.91 (0.23), residues: 454 loop : -3.38 (0.18), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 148 HIS 0.007 0.001 HIS B 846 PHE 0.021 0.002 PHE F 219 TYR 0.020 0.002 TYR E 861 ARG 0.004 0.000 ARG B 823 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 212 time to evaluate : 2.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7642 (pt) REVERT: A 78 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7427 (pp) REVERT: B 95 MET cc_start: 0.4598 (ptm) cc_final: 0.4376 (tmm) REVERT: B 363 LYS cc_start: 0.6884 (mmtp) cc_final: 0.6520 (tttp) REVERT: B 898 ASP cc_start: 0.7180 (OUTLIER) cc_final: 0.6884 (m-30) REVERT: C 64 ASN cc_start: 0.7657 (m110) cc_final: 0.7065 (m-40) REVERT: C 98 ILE cc_start: 0.7272 (mm) cc_final: 0.6801 (pt) REVERT: C 184 MET cc_start: 0.8449 (tmt) cc_final: 0.8027 (tmm) REVERT: C 191 LYS cc_start: 0.7404 (ttpt) cc_final: 0.6977 (tmtt) REVERT: C 372 HIS cc_start: 0.7635 (OUTLIER) cc_final: 0.6905 (p-80) REVERT: C 414 LYS cc_start: 0.8147 (mmmt) cc_final: 0.7765 (mmmt) REVERT: D 349 TRP cc_start: 0.1805 (m-90) cc_final: 0.1344 (m-90) REVERT: E 155 MET cc_start: 0.4926 (ptt) cc_final: 0.3486 (mtt) REVERT: E 869 LEU cc_start: 0.6091 (mp) cc_final: 0.5889 (pt) REVERT: F 49 THR cc_start: 0.3135 (p) cc_final: 0.2900 (t) REVERT: F 184 MET cc_start: 0.5334 (tmt) cc_final: 0.4942 (tmm) REVERT: F 242 GLU cc_start: 0.2957 (mp0) cc_final: 0.2216 (mm-30) REVERT: F 260 ARG cc_start: 0.6655 (mtt90) cc_final: 0.4409 (ttp80) REVERT: F 286 ASP cc_start: 0.4331 (OUTLIER) cc_final: 0.3810 (m-30) outliers start: 94 outliers final: 69 residues processed: 282 average time/residue: 0.2974 time to fit residues: 128.6071 Evaluate side-chains 272 residues out of total 1984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 198 time to evaluate : 2.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 118 TRP Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 148 TRP Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 182 CYS Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 898 ASP Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain C residue 266 CYS Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 372 HIS Chi-restraints excluded: chain C residue 382 ASP Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 315 ILE Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 734 VAL Chi-restraints excluded: chain E residue 841 SER Chi-restraints excluded: chain E residue 851 LEU Chi-restraints excluded: chain E residue 894 LEU Chi-restraints excluded: chain E residue 895 VAL Chi-restraints excluded: chain E residue 911 LEU Chi-restraints excluded: chain E residue 917 SER Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 263 SER Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain F residue 286 ASP Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 396 THR Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain F residue 460 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 205 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 121 optimal weight: 40.0000 chunk 155 optimal weight: 20.0000 chunk 120 optimal weight: 20.0000 chunk 179 optimal weight: 4.9990 chunk 118 optimal weight: 30.0000 chunk 212 optimal weight: 0.0000 chunk 132 optimal weight: 1.9990 chunk 129 optimal weight: 40.0000 chunk 97 optimal weight: 0.2980 overall best weight: 1.8590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 846 HIS F 51 GLN ** F 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 460 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6005 moved from start: 0.5389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18136 Z= 0.263 Angle : 0.693 13.592 24518 Z= 0.348 Chirality : 0.046 0.242 2838 Planarity : 0.005 0.047 3058 Dihedral : 5.618 44.129 2372 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.24 % Favored : 88.67 % Rotamer: Outliers : 4.79 % Allowed : 17.64 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.77 (0.17), residues: 2144 helix: -0.16 (0.19), residues: 760 sheet: -1.91 (0.23), residues: 466 loop : -3.30 (0.18), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 148 HIS 0.009 0.001 HIS F 460 PHE 0.018 0.002 PHE C 295 TYR 0.015 0.001 TYR E 760 ARG 0.005 0.000 ARG D 441 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 212 time to evaluate : 1.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7633 (pt) REVERT: A 78 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7435 (pp) REVERT: B 363 LYS cc_start: 0.6868 (mmtp) cc_final: 0.6514 (tttp) REVERT: B 898 ASP cc_start: 0.7236 (OUTLIER) cc_final: 0.6903 (m-30) REVERT: C 64 ASN cc_start: 0.7457 (m110) cc_final: 0.6818 (m-40) REVERT: C 98 ILE cc_start: 0.7272 (mm) cc_final: 0.6801 (pt) REVERT: C 184 MET cc_start: 0.8476 (tmt) cc_final: 0.8049 (tmm) REVERT: C 191 LYS cc_start: 0.7464 (ttpt) cc_final: 0.7040 (tmtt) REVERT: C 372 HIS cc_start: 0.7660 (OUTLIER) cc_final: 0.6870 (p-80) REVERT: C 414 LYS cc_start: 0.8171 (mmmt) cc_final: 0.7787 (mmmt) REVERT: D 349 TRP cc_start: 0.1852 (m-90) cc_final: 0.1400 (m-90) REVERT: F 49 THR cc_start: 0.3131 (p) cc_final: 0.2895 (t) REVERT: F 184 MET cc_start: 0.5492 (tmt) cc_final: 0.4967 (tmm) REVERT: F 242 GLU cc_start: 0.2859 (mp0) cc_final: 0.2122 (mm-30) REVERT: F 286 ASP cc_start: 0.4561 (OUTLIER) cc_final: 0.3944 (m-30) REVERT: F 449 MET cc_start: 0.4837 (tpp) cc_final: 0.4623 (tpp) outliers start: 94 outliers final: 72 residues processed: 285 average time/residue: 0.2710 time to fit residues: 119.8758 Evaluate side-chains 276 residues out of total 1984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 199 time to evaluate : 1.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 118 TRP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 148 TRP Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 182 CYS Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 898 ASP Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 266 CYS Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 372 HIS Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 315 ILE Chi-restraints excluded: chain D residue 323 ASP Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 437 GLU Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 726 SER Chi-restraints excluded: chain E residue 734 VAL Chi-restraints excluded: chain E residue 841 SER Chi-restraints excluded: chain E residue 885 MET Chi-restraints excluded: chain E residue 894 LEU Chi-restraints excluded: chain E residue 895 VAL Chi-restraints excluded: chain E residue 917 SER Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 263 SER Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain F residue 286 ASP Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 396 THR Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain F residue 460 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 131 optimal weight: 0.7980 chunk 84 optimal weight: 5.9990 chunk 126 optimal weight: 50.0000 chunk 63 optimal weight: 0.6980 chunk 41 optimal weight: 10.0000 chunk 134 optimal weight: 0.3980 chunk 144 optimal weight: 20.0000 chunk 104 optimal weight: 0.9980 chunk 19 optimal weight: 8.9990 chunk 166 optimal weight: 8.9990 chunk 192 optimal weight: 3.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 GLN B 167 GLN ** B 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 GLN ** D 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 778 GLN E 846 HIS ** E 884 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 400 GLN F 460 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5986 moved from start: 0.5539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18136 Z= 0.223 Angle : 0.678 14.304 24518 Z= 0.339 Chirality : 0.045 0.259 2838 Planarity : 0.004 0.045 3058 Dihedral : 5.498 44.817 2372 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.59 % Favored : 89.32 % Rotamer: Outliers : 4.33 % Allowed : 18.25 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.58 (0.18), residues: 2144 helix: 0.01 (0.19), residues: 758 sheet: -1.76 (0.23), residues: 454 loop : -3.21 (0.18), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 148 HIS 0.008 0.001 HIS F 460 PHE 0.013 0.001 PHE D 297 TYR 0.015 0.001 TYR B 822 ARG 0.003 0.000 ARG C 129 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 210 time to evaluate : 1.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7537 (pt) REVERT: A 78 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7385 (pp) REVERT: A 139 LEU cc_start: 0.9089 (mt) cc_final: 0.8882 (mt) REVERT: B 363 LYS cc_start: 0.6838 (mmtp) cc_final: 0.6479 (tttp) REVERT: B 898 ASP cc_start: 0.7208 (OUTLIER) cc_final: 0.6892 (m-30) REVERT: C 64 ASN cc_start: 0.7475 (m110) cc_final: 0.6829 (m-40) REVERT: C 98 ILE cc_start: 0.7256 (mm) cc_final: 0.6785 (pt) REVERT: C 184 MET cc_start: 0.8475 (tmt) cc_final: 0.8064 (tmm) REVERT: C 191 LYS cc_start: 0.7379 (ttpt) cc_final: 0.6989 (tmtt) REVERT: C 372 HIS cc_start: 0.7553 (OUTLIER) cc_final: 0.6775 (p-80) REVERT: C 414 LYS cc_start: 0.8123 (mmmt) cc_final: 0.7744 (mmmt) REVERT: D 349 TRP cc_start: 0.1572 (m-90) cc_final: 0.1278 (m-90) REVERT: D 411 PHE cc_start: 0.3702 (OUTLIER) cc_final: 0.3367 (p90) REVERT: E 103 PHE cc_start: 0.2186 (m-10) cc_final: 0.1455 (m-80) REVERT: E 155 MET cc_start: 0.4134 (ptt) cc_final: 0.3213 (mtt) REVERT: F 184 MET cc_start: 0.5280 (tmt) cc_final: 0.4882 (tmm) REVERT: F 242 GLU cc_start: 0.2853 (mp0) cc_final: 0.2099 (mm-30) REVERT: F 286 ASP cc_start: 0.4949 (OUTLIER) cc_final: 0.4113 (m-30) outliers start: 85 outliers final: 68 residues processed: 274 average time/residue: 0.2709 time to fit residues: 115.2525 Evaluate side-chains 271 residues out of total 1984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 197 time to evaluate : 2.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 118 TRP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 148 TRP Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain B residue 182 CYS Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 869 LEU Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 898 ASP Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 266 CYS Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 372 HIS Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 315 ILE Chi-restraints excluded: chain D residue 323 ASP Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 411 PHE Chi-restraints excluded: chain D residue 437 GLU Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 734 VAL Chi-restraints excluded: chain E residue 841 SER Chi-restraints excluded: chain E residue 866 HIS Chi-restraints excluded: chain E residue 894 LEU Chi-restraints excluded: chain E residue 895 VAL Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 263 SER Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain F residue 286 ASP Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 396 THR Chi-restraints excluded: chain F residue 460 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 203 optimal weight: 10.0000 chunk 185 optimal weight: 1.9990 chunk 197 optimal weight: 8.9990 chunk 118 optimal weight: 20.0000 chunk 86 optimal weight: 0.0270 chunk 155 optimal weight: 20.0000 chunk 60 optimal weight: 3.9990 chunk 178 optimal weight: 7.9990 chunk 186 optimal weight: 9.9990 chunk 196 optimal weight: 3.9990 chunk 129 optimal weight: 20.0000 overall best weight: 3.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 GLN B 167 GLN ** B 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 ASN ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 846 HIS ** E 884 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6113 moved from start: 0.6069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 18136 Z= 0.445 Angle : 0.842 14.190 24518 Z= 0.422 Chirality : 0.051 0.338 2838 Planarity : 0.006 0.062 3058 Dihedral : 6.055 44.565 2372 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 17.53 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.64 % Favored : 87.22 % Rotamer: Outliers : 4.38 % Allowed : 18.40 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.96 (0.17), residues: 2144 helix: -0.48 (0.19), residues: 760 sheet: -1.87 (0.23), residues: 454 loop : -3.31 (0.18), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 148 HIS 0.030 0.002 HIS F 460 PHE 0.025 0.002 PHE A 48 TYR 0.020 0.002 TYR B 843 ARG 0.010 0.001 ARG F 394 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 202 time to evaluate : 2.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.7818 (pt) REVERT: A 78 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7329 (pp) REVERT: B 363 LYS cc_start: 0.6972 (mmtp) cc_final: 0.6614 (tttp) REVERT: B 898 ASP cc_start: 0.7617 (OUTLIER) cc_final: 0.7041 (m-30) REVERT: C 64 ASN cc_start: 0.7716 (m-40) cc_final: 0.7106 (m-40) REVERT: C 184 MET cc_start: 0.8578 (tmt) cc_final: 0.8175 (tmm) REVERT: C 191 LYS cc_start: 0.7637 (ttpt) cc_final: 0.7293 (tmtt) REVERT: C 372 HIS cc_start: 0.7956 (OUTLIER) cc_final: 0.6983 (p-80) REVERT: C 414 LYS cc_start: 0.8181 (mmmt) cc_final: 0.7768 (mmmt) REVERT: D 319 LYS cc_start: 0.3975 (mppt) cc_final: 0.3625 (pptt) REVERT: D 349 TRP cc_start: 0.1994 (m-90) cc_final: 0.1321 (m-90) REVERT: E 155 MET cc_start: 0.4543 (ptt) cc_final: 0.3892 (mtt) REVERT: F 184 MET cc_start: 0.5462 (tmt) cc_final: 0.5004 (tmm) REVERT: F 286 ASP cc_start: 0.5046 (OUTLIER) cc_final: 0.4320 (m-30) REVERT: F 297 GLN cc_start: 0.4719 (pt0) cc_final: 0.3678 (tt0) outliers start: 86 outliers final: 71 residues processed: 267 average time/residue: 0.2729 time to fit residues: 114.7850 Evaluate side-chains 255 residues out of total 1984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 179 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 118 TRP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 148 TRP Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 182 CYS Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 898 ASP Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 372 HIS Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 315 ILE Chi-restraints excluded: chain D residue 323 ASP Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 433 ASN Chi-restraints excluded: chain D residue 437 GLU Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 344 MET Chi-restraints excluded: chain E residue 841 SER Chi-restraints excluded: chain E residue 885 MET Chi-restraints excluded: chain E residue 894 LEU Chi-restraints excluded: chain E residue 895 VAL Chi-restraints excluded: chain E residue 898 ASP Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 263 SER Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain F residue 286 ASP Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 318 MET Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 396 THR Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain F residue 460 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 208 optimal weight: 0.0770 chunk 127 optimal weight: 8.9990 chunk 99 optimal weight: 0.9990 chunk 145 optimal weight: 5.9990 chunk 219 optimal weight: 0.9990 chunk 201 optimal weight: 0.9980 chunk 174 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 134 optimal weight: 6.9990 chunk 107 optimal weight: 0.9980 chunk 138 optimal weight: 0.0980 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 GLN E 766 HIS E 846 HIS E 848 GLN ** E 884 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 400 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5978 moved from start: 0.6050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18136 Z= 0.179 Angle : 0.690 15.766 24518 Z= 0.342 Chirality : 0.046 0.244 2838 Planarity : 0.004 0.049 3058 Dihedral : 5.476 44.987 2372 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.89 % Favored : 90.02 % Rotamer: Outliers : 2.70 % Allowed : 20.85 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.48 (0.18), residues: 2144 helix: 0.05 (0.19), residues: 756 sheet: -1.50 (0.24), residues: 436 loop : -3.21 (0.18), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 148 HIS 0.006 0.001 HIS D 328 PHE 0.015 0.001 PHE F 99 TYR 0.016 0.001 TYR E 822 ARG 0.006 0.000 ARG F 394 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 213 time to evaluate : 1.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7440 (pt) REVERT: A 78 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7359 (pp) REVERT: B 363 LYS cc_start: 0.6836 (mmtp) cc_final: 0.6475 (tttp) REVERT: B 898 ASP cc_start: 0.7073 (OUTLIER) cc_final: 0.6744 (m-30) REVERT: C 64 ASN cc_start: 0.7691 (m-40) cc_final: 0.6988 (m-40) REVERT: C 98 ILE cc_start: 0.7249 (mm) cc_final: 0.6769 (pt) REVERT: C 184 MET cc_start: 0.8563 (tmt) cc_final: 0.8156 (tmm) REVERT: C 191 LYS cc_start: 0.7428 (ttpt) cc_final: 0.7023 (tmtt) REVERT: C 372 HIS cc_start: 0.7234 (OUTLIER) cc_final: 0.6458 (p-80) REVERT: E 878 GLU cc_start: 0.5833 (pp20) cc_final: 0.4766 (pm20) REVERT: E 885 MET cc_start: 0.2156 (OUTLIER) cc_final: 0.1637 (tpt) REVERT: F 184 MET cc_start: 0.5454 (tmt) cc_final: 0.5063 (tmm) REVERT: F 297 GLN cc_start: 0.4591 (pt0) cc_final: 0.3656 (tt0) outliers start: 53 outliers final: 43 residues processed: 251 average time/residue: 0.2670 time to fit residues: 104.7291 Evaluate side-chains 242 residues out of total 1984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 194 time to evaluate : 2.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain B residue 182 CYS Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 898 ASP Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 372 HIS Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 315 ILE Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 841 SER Chi-restraints excluded: chain E residue 885 MET Chi-restraints excluded: chain E residue 894 LEU Chi-restraints excluded: chain E residue 911 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 318 MET Chi-restraints excluded: chain F residue 384 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 160 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 174 optimal weight: 5.9990 chunk 73 optimal weight: 0.6980 chunk 179 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 153 optimal weight: 0.1980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 168 GLN B 814 ASN ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 814 ASN E 846 HIS ** E 884 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 51 GLN ** F 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 383 GLN F 460 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4768 r_free = 0.4768 target = 0.220143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.152281 restraints weight = 29611.666| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 3.18 r_work: 0.3721 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.6197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18136 Z= 0.223 Angle : 0.695 15.428 24518 Z= 0.346 Chirality : 0.046 0.287 2838 Planarity : 0.004 0.046 3058 Dihedral : 5.442 44.802 2372 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.63 % Favored : 89.27 % Rotamer: Outliers : 2.91 % Allowed : 20.74 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.45 (0.18), residues: 2144 helix: 0.08 (0.19), residues: 758 sheet: -1.58 (0.23), residues: 448 loop : -3.16 (0.18), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP D 349 HIS 0.007 0.001 HIS D 328 PHE 0.030 0.002 PHE E 719 TYR 0.015 0.001 TYR E 760 ARG 0.006 0.000 ARG F 394 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4044.49 seconds wall clock time: 73 minutes 42.07 seconds (4422.07 seconds total)