Starting phenix.real_space_refine on Thu Feb 15 13:02:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dmp_30766/02_2024/7dmp_30766.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dmp_30766/02_2024/7dmp_30766.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/7dmp_30766/02_2024/7dmp_30766.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dmp_30766/02_2024/7dmp_30766.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dmp_30766/02_2024/7dmp_30766.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dmp_30766/02_2024/7dmp_30766.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= 0.001 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 38 5.16 5 C 7866 2.51 5 N 2090 2.21 5 O 2314 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 281": "OE1" <-> "OE2" Residue "B GLU 284": "OE1" <-> "OE2" Residue "B GLU 332": "OE1" <-> "OE2" Residue "B GLU 362": "OE1" <-> "OE2" Residue "B GLU 369": "OE1" <-> "OE2" Residue "B GLU 376": "OE1" <-> "OE2" Residue "B ARG 438": "NH1" <-> "NH2" Residue "B GLU 528": "OE1" <-> "OE2" Residue "B GLU 643": "OE1" <-> "OE2" Residue "b GLU 316": "OE1" <-> "OE2" Residue "b GLU 362": "OE1" <-> "OE2" Residue "b GLU 420": "OE1" <-> "OE2" Residue "b ARG 422": "NH1" <-> "NH2" Residue "b ARG 438": "NH1" <-> "NH2" Residue "b GLU 528": "OE1" <-> "OE2" Residue "b PHE 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 643": "OE1" <-> "OE2" Residue "b GLU 675": "OE1" <-> "OE2" Residue "b GLU 687": "OE1" <-> "OE2" Residue "A ARG 30": "NH1" <-> "NH2" Residue "A GLU 45": "OE1" <-> "OE2" Residue "A GLU 49": "OE1" <-> "OE2" Residue "A GLU 91": "OE1" <-> "OE2" Residue "A GLU 93": "OE1" <-> "OE2" Residue "A GLU 116": "OE1" <-> "OE2" Residue "A GLU 147": "OE1" <-> "OE2" Residue "A GLU 199": "OE1" <-> "OE2" Residue "A GLU 201": "OE1" <-> "OE2" Residue "a ARG 30": "NH1" <-> "NH2" Residue "a GLU 45": "OE1" <-> "OE2" Residue "a GLU 49": "OE1" <-> "OE2" Residue "a TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 200": "OE1" <-> "OE2" Residue "C ARG 37": "NH1" <-> "NH2" Residue "C ARG 40": "NH1" <-> "NH2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C ARG 71": "NH1" <-> "NH2" Residue "C GLU 110": "OE1" <-> "OE2" Residue "C GLU 112": "OE1" <-> "OE2" Residue "C ARG 139": "NH1" <-> "NH2" Residue "C ARG 156": "NH1" <-> "NH2" Residue "C ARG 191": "NH1" <-> "NH2" Residue "C GLU 218": "OE1" <-> "OE2" Residue "C GLU 231": "OE1" <-> "OE2" Residue "C GLU 267": "OE1" <-> "OE2" Residue "c GLU 11": "OE1" <-> "OE2" Residue "c ARG 37": "NH1" <-> "NH2" Residue "c ARG 40": "NH1" <-> "NH2" Residue "c ARG 43": "NH1" <-> "NH2" Residue "c GLU 65": "OE1" <-> "OE2" Residue "c ARG 71": "NH1" <-> "NH2" Residue "c GLU 81": "OE1" <-> "OE2" Residue "c GLU 91": "OE1" <-> "OE2" Residue "c GLU 110": "OE1" <-> "OE2" Residue "c ARG 139": "NH1" <-> "NH2" Residue "c ARG 156": "NH1" <-> "NH2" Residue "c ARG 171": "NH1" <-> "NH2" Residue "c ARG 191": "NH1" <-> "NH2" Residue "c GLU 267": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12308 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2704 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 31, 'TRANS': 304} Chain breaks: 4 Chain: "b" Number of atoms: 2704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2704 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 31, 'TRANS': 304} Chain breaks: 4 Chain: "A" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1521 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 4, 'TRANS': 181} Chain: "a" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1521 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 4, 'TRANS': 181} Chain: "C" Number of atoms: 1929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1929 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 12, 'TRANS': 229} Chain breaks: 2 Chain: "c" Number of atoms: 1929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1929 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 12, 'TRANS': 229} Chain breaks: 2 Time building chain proxies: 6.72, per 1000 atoms: 0.55 Number of scatterers: 12308 At special positions: 0 Unit cell: (110.16, 84.66, 223.38, 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 38 16.00 O 2314 8.00 N 2090 7.00 C 7866 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: 4.45 Conformation dependent library (CDL) restraints added in 2.1 seconds 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2780 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 16 sheets defined 17.1% alpha, 28.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'B' and resid 277 through 291 removed outlier: 3.720A pdb=" N GLU B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR B 285 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N ALA B 288 " --> pdb=" O GLU B 284 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LEU B 289 " --> pdb=" O THR B 285 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N PHE B 290 " --> pdb=" O GLN B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 325 removed outlier: 3.652A pdb=" N TYR B 320 " --> pdb=" O GLU B 316 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE B 321 " --> pdb=" O SER B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 345 removed outlier: 3.576A pdb=" N ASP B 345 " --> pdb=" O LYS B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 492 removed outlier: 3.769A pdb=" N ARG B 484 " --> pdb=" O SER B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 538 removed outlier: 3.551A pdb=" N LEU B 535 " --> pdb=" O GLN B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 599 removed outlier: 3.963A pdb=" N GLU B 598 " --> pdb=" O PRO B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 688 removed outlier: 3.542A pdb=" N GLU B 687 " --> pdb=" O SER B 683 " (cutoff:3.500A) Processing helix chain 'b' and resid 278 through 285 removed outlier: 3.551A pdb=" N THR b 285 " --> pdb=" O GLU b 281 " (cutoff:3.500A) Processing helix chain 'b' and resid 286 through 289 Processing helix chain 'b' and resid 314 through 325 Processing helix chain 'b' and resid 334 through 345 Processing helix chain 'b' and resid 479 through 494 removed outlier: 3.589A pdb=" N LEU b 483 " --> pdb=" O GLU b 479 " (cutoff:3.500A) Processing helix chain 'b' and resid 533 through 538 removed outlier: 3.647A pdb=" N SER b 538 " --> pdb=" O ASP b 534 " (cutoff:3.500A) Processing helix chain 'b' and resid 595 through 599 removed outlier: 4.077A pdb=" N GLU b 598 " --> pdb=" O PRO b 595 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP b 599 " --> pdb=" O ILE b 596 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 595 through 599' Processing helix chain 'b' and resid 683 through 690 removed outlier: 3.561A pdb=" N PHE b 690 " --> pdb=" O GLU b 686 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 9 Processing helix chain 'C' and resid 24 through 39 removed outlier: 4.150A pdb=" N MET C 33 " --> pdb=" O LEU C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 96 removed outlier: 3.785A pdb=" N ALA C 93 " --> pdb=" O THR C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 99 No H-bonds generated for 'chain 'C' and resid 97 through 99' Processing helix chain 'C' and resid 135 through 149 Processing helix chain 'C' and resid 177 through 181 removed outlier: 3.580A pdb=" N GLU C 180 " --> pdb=" O PRO C 177 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL C 181 " --> pdb=" O LEU C 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 177 through 181' Processing helix chain 'C' and resid 271 through 276 Processing helix chain 'c' and resid 24 through 39 removed outlier: 3.504A pdb=" N LEU c 28 " --> pdb=" O ARG c 24 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N MET c 33 " --> pdb=" O LEU c 29 " (cutoff:3.500A) Processing helix chain 'c' and resid 64 through 68 removed outlier: 4.050A pdb=" N GLN c 67 " --> pdb=" O SER c 64 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LEU c 68 " --> pdb=" O GLU c 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 64 through 68' Processing helix chain 'c' and resid 89 through 96 removed outlier: 3.912A pdb=" N ILE c 96 " --> pdb=" O MET c 92 " (cutoff:3.500A) Processing helix chain 'c' and resid 136 through 151 Processing helix chain 'c' and resid 183 through 187 removed outlier: 3.627A pdb=" N SER c 186 " --> pdb=" O LYS c 183 " (cutoff:3.500A) Processing helix chain 'c' and resid 271 through 276 Processing sheet with id=AA1, first strand: chain 'B' and resid 441 through 442 removed outlier: 5.839A pdb=" N GLU B 369 " --> pdb=" O PHE B 354 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N PHE B 354 " --> pdb=" O GLU B 369 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N TRP B 355 " --> pdb=" O ASN B 644 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER B 637 " --> pdb=" O ALA B 623 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA B 623 " --> pdb=" O SER B 637 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 496 through 498 Processing sheet with id=AA3, first strand: chain 'b' and resid 441 through 442 removed outlier: 3.614A pdb=" N PHE b 431 " --> pdb=" O ALA b 368 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N GLU b 369 " --> pdb=" O PHE b 354 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N PHE b 354 " --> pdb=" O GLU b 369 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N GLU b 371 " --> pdb=" O CYS b 352 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N CYS b 352 " --> pdb=" O GLU b 371 " (cutoff:3.500A) removed outlier: 15.264A pdb=" N PHE b 642 " --> pdb=" O ARG b 351 " (cutoff:3.500A) removed outlier: 10.789A pdb=" N ARG b 353 " --> pdb=" O PHE b 642 " (cutoff:3.500A) removed outlier: 9.937A pdb=" N ASN b 644 " --> pdb=" O ARG b 353 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N TRP b 355 " --> pdb=" O ASN b 644 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR b 646 " --> pdb=" O TRP b 355 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N ALA b 633 " --> pdb=" O SER b 627 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'b' and resid 497 through 498 Processing sheet with id=AA5, first strand: chain 'A' and resid 19 through 20 removed outlier: 5.854A pdb=" N GLN A 56 " --> pdb=" O SER A 47 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLU A 49 " --> pdb=" O HIS A 54 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N HIS A 54 " --> pdb=" O GLU A 49 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N GLN A 79 " --> pdb=" O ASP A 70 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N VAL A 72 " --> pdb=" O HIS A 77 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N HIS A 77 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ARG A 89 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL A 104 " --> pdb=" O ARG A 89 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N GLU A 91 " --> pdb=" O GLN A 102 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N GLN A 102 " --> pdb=" O GLU A 91 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N GLU A 93 " --> pdb=" O HIS A 100 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR A 114 " --> pdb=" O THR A 127 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N THR A 127 " --> pdb=" O THR A 114 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLU A 116 " --> pdb=" O GLN A 125 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N GLN A 125 " --> pdb=" O GLU A 116 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 19 through 20 removed outlier: 5.854A pdb=" N GLN A 56 " --> pdb=" O SER A 47 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLU A 49 " --> pdb=" O HIS A 54 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N HIS A 54 " --> pdb=" O GLU A 49 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N GLN A 79 " --> pdb=" O ASP A 70 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N VAL A 72 " --> pdb=" O HIS A 77 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N HIS A 77 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ARG A 89 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL A 104 " --> pdb=" O ARG A 89 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N GLU A 91 " --> pdb=" O GLN A 102 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N GLN A 102 " --> pdb=" O GLU A 91 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N GLU A 93 " --> pdb=" O HIS A 100 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR A 114 " --> pdb=" O THR A 127 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N THR A 127 " --> pdb=" O THR A 114 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLU A 116 " --> pdb=" O GLN A 125 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N GLN A 125 " --> pdb=" O GLU A 116 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N CYS A 180 " --> pdb=" O PHE A 176 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N GLU A 197 " --> pdb=" O HIS A 183 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'a' and resid 34 through 37 removed outlier: 3.574A pdb=" N SER a 47 " --> pdb=" O GLN a 56 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N GLN a 56 " --> pdb=" O SER a 47 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU a 49 " --> pdb=" O HIS a 54 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N HIS a 54 " --> pdb=" O GLU a 49 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N GLN a 79 " --> pdb=" O ASP a 70 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL a 72 " --> pdb=" O HIS a 77 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N HIS a 77 " --> pdb=" O VAL a 72 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N GLN a 102 " --> pdb=" O GLU a 93 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ALA a 95 " --> pdb=" O HIS a 100 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N HIS a 100 " --> pdb=" O ALA a 95 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N GLN a 125 " --> pdb=" O GLU a 116 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'a' and resid 34 through 37 removed outlier: 3.574A pdb=" N SER a 47 " --> pdb=" O GLN a 56 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N GLN a 56 " --> pdb=" O SER a 47 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU a 49 " --> pdb=" O HIS a 54 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N HIS a 54 " --> pdb=" O GLU a 49 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N GLN a 79 " --> pdb=" O ASP a 70 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL a 72 " --> pdb=" O HIS a 77 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N HIS a 77 " --> pdb=" O VAL a 72 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N GLN a 102 " --> pdb=" O GLU a 93 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ALA a 95 " --> pdb=" O HIS a 100 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N HIS a 100 " --> pdb=" O ALA a 95 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N GLN a 125 " --> pdb=" O GLU a 116 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N CYS a 180 " --> pdb=" O PHE a 176 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLU a 181 " --> pdb=" O GLU a 198 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLU a 198 " --> pdb=" O GLU a 181 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'a' and resid 163 through 164 Processing sheet with id=AB1, first strand: chain 'C' and resid 44 through 48 removed outlier: 6.670A pdb=" N ILE C 59 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS C 72 " --> pdb=" O GLY C 62 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR C 75 " --> pdb=" O SER C 83 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER C 83 " --> pdb=" O TYR C 75 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 153 through 154 Processing sheet with id=AB3, first strand: chain 'C' and resid 226 through 230 removed outlier: 5.109A pdb=" N LEU C 247 " --> pdb=" O SER C 241 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'c' and resid 43 through 48 removed outlier: 5.442A pdb=" N VAL c 44 " --> pdb=" O LEU c 63 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU c 63 " --> pdb=" O VAL c 44 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N PHE c 46 " --> pdb=" O GLN c 61 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N GLN c 61 " --> pdb=" O PHE c 46 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'c' and resid 110 through 113 Processing sheet with id=AB6, first strand: chain 'c' and resid 153 through 154 Processing sheet with id=AB7, first strand: chain 'c' and resid 226 through 230 removed outlier: 4.815A pdb=" N LEU c 247 " --> pdb=" O SER c 241 " (cutoff:3.500A) 455 hydrogen bonds defined for protein. 1203 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.13 Time building geometry restraints manager: 4.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3461 1.33 - 1.45: 2386 1.45 - 1.57: 6734 1.57 - 1.69: 1 1.69 - 1.81: 64 Bond restraints: 12646 Sorted by residual: bond pdb=" C ILE C 221 " pdb=" N PRO C 222 " ideal model delta sigma weight residual 1.332 1.372 -0.040 8.20e-03 1.49e+04 2.38e+01 bond pdb=" C ILE c 221 " pdb=" N PRO c 222 " ideal model delta sigma weight residual 1.337 1.376 -0.039 1.24e-02 6.50e+03 9.85e+00 bond pdb=" C TRP b 630 " pdb=" O TRP b 630 " ideal model delta sigma weight residual 1.246 1.225 0.021 9.20e-03 1.18e+04 5.37e+00 bond pdb=" C VAL B 314 " pdb=" O VAL B 314 " ideal model delta sigma weight residual 1.237 1.213 0.024 1.17e-02 7.31e+03 4.17e+00 bond pdb=" C SER c 21 " pdb=" N PRO c 22 " ideal model delta sigma weight residual 1.334 1.380 -0.046 2.34e-02 1.83e+03 3.82e+00 ... (remaining 12641 not shown) Histogram of bond angle deviations from ideal: 99.99 - 106.80: 484 106.80 - 113.60: 6392 113.60 - 120.41: 4857 120.41 - 127.22: 5241 127.22 - 134.03: 178 Bond angle restraints: 17152 Sorted by residual: angle pdb=" N VAL a 27 " pdb=" CA VAL a 27 " pdb=" C VAL a 27 " ideal model delta sigma weight residual 113.71 109.11 4.60 9.50e-01 1.11e+00 2.34e+01 angle pdb=" C ALA a 95 " pdb=" N ASP a 96 " pdb=" CA ASP a 96 " ideal model delta sigma weight residual 121.54 130.68 -9.14 1.91e+00 2.74e-01 2.29e+01 angle pdb=" C ILE b 617 " pdb=" N PRO b 618 " pdb=" CA PRO b 618 " ideal model delta sigma weight residual 119.05 124.17 -5.12 1.11e+00 8.12e-01 2.13e+01 angle pdb=" C ASN B 478 " pdb=" N GLU B 479 " pdb=" CA GLU B 479 " ideal model delta sigma weight residual 121.54 129.83 -8.29 1.91e+00 2.74e-01 1.89e+01 angle pdb=" N TYR b 620 " pdb=" CA TYR b 620 " pdb=" C TYR b 620 " ideal model delta sigma weight residual 109.11 115.08 -5.97 1.42e+00 4.96e-01 1.77e+01 ... (remaining 17147 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 6672 18.01 - 36.01: 603 36.01 - 54.02: 100 54.02 - 72.03: 29 72.03 - 90.03: 22 Dihedral angle restraints: 7426 sinusoidal: 3038 harmonic: 4388 Sorted by residual: dihedral pdb=" CA SER C 21 " pdb=" C SER C 21 " pdb=" N PRO C 22 " pdb=" CA PRO C 22 " ideal model delta harmonic sigma weight residual 180.00 157.33 22.67 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" C ASN a 165 " pdb=" N ASN a 165 " pdb=" CA ASN a 165 " pdb=" CB ASN a 165 " ideal model delta harmonic sigma weight residual -122.60 -133.48 10.88 0 2.50e+00 1.60e-01 1.90e+01 dihedral pdb=" CA PRO C 22 " pdb=" C PRO C 22 " pdb=" N ASP C 23 " pdb=" CA ASP C 23 " ideal model delta harmonic sigma weight residual -180.00 -159.32 -20.68 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 7423 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1502 0.072 - 0.144: 244 0.144 - 0.217: 16 0.217 - 0.289: 3 0.289 - 0.361: 1 Chirality restraints: 1766 Sorted by residual: chirality pdb=" CA ASN a 165 " pdb=" N ASN a 165 " pdb=" C ASN a 165 " pdb=" CB ASN a 165 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.26e+00 chirality pdb=" CA LYS a 166 " pdb=" N LYS a 166 " pdb=" C LYS a 166 " pdb=" CB LYS a 166 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CA ASP a 96 " pdb=" N ASP a 96 " pdb=" C ASP a 96 " pdb=" CB ASP a 96 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 1763 not shown) Planarity restraints: 2248 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 435 " -0.040 5.00e-02 4.00e+02 5.99e-02 5.74e+00 pdb=" N PRO B 436 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 436 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 436 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA c 69 " 0.038 5.00e-02 4.00e+02 5.72e-02 5.24e+00 pdb=" N PRO c 70 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO c 70 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO c 70 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER c 21 " 0.035 5.00e-02 4.00e+02 5.37e-02 4.62e+00 pdb=" N PRO c 22 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO c 22 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO c 22 " 0.030 5.00e-02 4.00e+02 ... (remaining 2245 not shown) Histogram of nonbonded interaction distances: 1.02 - 1.80: 1 1.80 - 2.57: 111 2.57 - 3.35: 14164 3.35 - 4.12: 31027 4.12 - 4.90: 55617 Nonbonded interactions: 100920 Sorted by model distance: nonbonded pdb=" OH TYR b 634 " pdb=" CG GLN c 18 " model vdw 1.020 3.440 nonbonded pdb=" OH TYR b 634 " pdb=" CD GLN c 18 " model vdw 1.948 3.270 nonbonded pdb=" OD1 ASN b 615 " pdb=" OD2 ASP c 23 " model vdw 1.987 3.040 nonbonded pdb=" CG2 VAL b 326 " pdb=" CE1 TYR b 634 " model vdw 2.052 3.760 nonbonded pdb=" OE2 GLU B 316 " pdb=" NZ LYS B 641 " model vdw 2.119 2.520 ... (remaining 100915 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 'a' } ncs_group { reference = chain 'B' selection = chain 'b' } ncs_group { reference = chain 'C' selection = chain 'c' } 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: 3.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 13.310 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 35.160 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6681 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 : 0.003 0.046 12646 Z= 0.217 Angle : 0.758 9.135 17152 Z= 0.438 Chirality : 0.052 0.361 1766 Planarity : 0.006 0.060 2248 Dihedral : 14.924 90.032 4646 Min Nonbonded Distance : 1.020 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 1.61 % Allowed : 7.12 % Favored : 91.27 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.33 (0.17), residues: 1492 helix: -3.09 (0.24), residues: 218 sheet: -2.68 (0.23), residues: 372 loop : -3.01 (0.16), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 542 HIS 0.004 0.001 HIS A 120 PHE 0.015 0.001 PHE B 636 TYR 0.014 0.001 TYR b 334 ARG 0.002 0.000 ARG b 484 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 297 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 351 ARG cc_start: 0.6407 (ttp80) cc_final: 0.5807 (ttp80) REVERT: b 619 GLN cc_start: 0.6054 (OUTLIER) cc_final: 0.5829 (tt0) REVERT: A 89 ARG cc_start: 0.8233 (ptt90) cc_final: 0.7690 (ptt-90) REVERT: A 102 GLN cc_start: 0.7474 (mm-40) cc_final: 0.7204 (mm110) REVERT: A 155 LEU cc_start: 0.8164 (mt) cc_final: 0.7933 (mt) REVERT: a 109 ASN cc_start: 0.8196 (p0) cc_final: 0.7904 (p0) REVERT: a 110 ASN cc_start: 0.6173 (t0) cc_final: 0.5917 (t0) REVERT: a 164 MET cc_start: 0.7802 (mmm) cc_final: 0.7601 (mmm) REVERT: C 20 LEU cc_start: 0.6258 (mt) cc_final: 0.5969 (mt) REVERT: C 270 MET cc_start: 0.5713 (mmt) cc_final: 0.5376 (mmt) REVERT: c 94 MET cc_start: 0.6583 (ptp) cc_final: 0.6109 (mtm) REVERT: c 104 MET cc_start: 0.7583 (tpt) cc_final: 0.7337 (tpp) REVERT: c 134 ILE cc_start: 0.6809 (tp) cc_final: 0.6397 (tp) REVERT: c 230 MET cc_start: 0.6623 (mmm) cc_final: 0.6269 (mmt) REVERT: c 270 MET cc_start: 0.5249 (mmm) cc_final: 0.4925 (mmm) outliers start: 21 outliers final: 12 residues processed: 314 average time/residue: 0.2991 time to fit residues: 126.8489 Evaluate side-chains 203 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 190 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 315 MET Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 617 ILE Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain b residue 310 SER Chi-restraints excluded: chain b residue 612 LEU Chi-restraints excluded: chain b residue 619 GLN Chi-restraints excluded: chain b residue 622 ILE Chi-restraints excluded: chain b residue 625 LEU Chi-restraints excluded: chain b residue 627 SER Chi-restraints excluded: chain b residue 636 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 136 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 323 GLN ** B 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 495 HIS B 541 ASN B 619 GLN ** b 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 544 HIS ** b 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 619 GLN ** b 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 31 HIS A 110 ASN ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 GLN a 31 HIS a 123 HIS ** a 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 189 HIS c 251 HIS c 257 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 12646 Z= 0.410 Angle : 0.741 7.628 17152 Z= 0.382 Chirality : 0.048 0.205 1766 Planarity : 0.006 0.044 2248 Dihedral : 6.368 58.928 1717 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 3.45 % Allowed : 14.85 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.66 (0.18), residues: 1492 helix: -1.72 (0.29), residues: 220 sheet: -2.69 (0.23), residues: 364 loop : -2.58 (0.17), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP a 141 HIS 0.007 0.002 HIS a 120 PHE 0.019 0.003 PHE B 321 TYR 0.026 0.003 TYR b 634 ARG 0.009 0.001 ARG b 438 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 222 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ARG cc_start: 0.7533 (ttm110) cc_final: 0.7045 (ttp-110) REVERT: A 89 ARG cc_start: 0.8148 (ptt90) cc_final: 0.7430 (ptt90) REVERT: a 37 ARG cc_start: 0.7546 (ttm110) cc_final: 0.6563 (mtm110) REVERT: a 38 LEU cc_start: 0.7479 (mm) cc_final: 0.6925 (mp) REVERT: a 109 ASN cc_start: 0.8156 (p0) cc_final: 0.7855 (p0) REVERT: C 148 ASP cc_start: 0.7381 (m-30) cc_final: 0.7071 (m-30) REVERT: c 29 LEU cc_start: 0.8431 (mm) cc_final: 0.8187 (mm) REVERT: c 92 MET cc_start: 0.7334 (ptm) cc_final: 0.7050 (ttp) REVERT: c 94 MET cc_start: 0.6719 (ptp) cc_final: 0.6166 (mtm) REVERT: c 149 LYS cc_start: 0.7223 (mmmt) cc_final: 0.7018 (mmtm) REVERT: c 230 MET cc_start: 0.7347 (mmm) cc_final: 0.7062 (mmt) REVERT: c 250 TYR cc_start: 0.6677 (p90) cc_final: 0.5973 (p90) outliers start: 45 outliers final: 26 residues processed: 248 average time/residue: 0.2670 time to fit residues: 92.5589 Evaluate side-chains 208 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 182 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain b residue 310 SER Chi-restraints excluded: chain b residue 370 VAL Chi-restraints excluded: chain b residue 491 SER Chi-restraints excluded: chain b residue 501 PHE Chi-restraints excluded: chain b residue 519 ASP Chi-restraints excluded: chain b residue 544 HIS Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain a residue 40 ASN Chi-restraints excluded: chain a residue 70 ASP Chi-restraints excluded: chain a residue 74 ASN Chi-restraints excluded: chain a residue 114 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain c residue 89 THR Chi-restraints excluded: chain c residue 136 GLU Chi-restraints excluded: chain c residue 168 HIS Chi-restraints excluded: chain c residue 214 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 136 optimal weight: 1.9990 chunk 147 optimal weight: 0.3980 chunk 121 optimal weight: 0.8980 chunk 135 optimal weight: 0.4980 chunk 46 optimal weight: 0.0870 chunk 109 optimal weight: 0.8980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 544 HIS ** b 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 680 ASN A 157 HIS ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 31 HIS ** a 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 ASN ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12646 Z= 0.242 Angle : 0.597 7.434 17152 Z= 0.302 Chirality : 0.044 0.172 1766 Planarity : 0.004 0.043 2248 Dihedral : 5.043 55.903 1695 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 3.75 % Allowed : 17.23 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.19), residues: 1492 helix: -1.21 (0.32), residues: 232 sheet: -2.59 (0.24), residues: 360 loop : -2.25 (0.18), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP b 440 HIS 0.010 0.001 HIS b 544 PHE 0.021 0.002 PHE C 46 TYR 0.021 0.002 TYR B 365 ARG 0.005 0.000 ARG b 438 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 203 time to evaluate : 1.527 Fit side-chains revert: symmetry clash REVERT: B 366 ILE cc_start: 0.8726 (OUTLIER) cc_final: 0.8289 (mp) REVERT: A 37 ARG cc_start: 0.7515 (ttm110) cc_final: 0.7147 (ttp-110) REVERT: A 66 ARG cc_start: 0.7916 (mtm110) cc_final: 0.7701 (mtp85) REVERT: a 37 ARG cc_start: 0.7535 (ttm110) cc_final: 0.6538 (mtm110) REVERT: a 38 LEU cc_start: 0.7435 (mm) cc_final: 0.6816 (mp) REVERT: a 109 ASN cc_start: 0.8227 (p0) cc_final: 0.7904 (p0) REVERT: C 32 LEU cc_start: 0.7675 (mt) cc_final: 0.7443 (mt) REVERT: C 188 PHE cc_start: 0.7186 (m-10) cc_final: 0.6983 (m-10) REVERT: c 29 LEU cc_start: 0.8443 (mm) cc_final: 0.8198 (mm) REVERT: c 94 MET cc_start: 0.6767 (ptp) cc_final: 0.6234 (mtm) REVERT: c 149 LYS cc_start: 0.7321 (mmmt) cc_final: 0.7062 (mmtm) REVERT: c 230 MET cc_start: 0.7229 (mmm) cc_final: 0.6964 (mmt) REVERT: c 250 TYR cc_start: 0.6836 (p90) cc_final: 0.6085 (p90) REVERT: c 256 LYS cc_start: 0.8444 (ptpp) cc_final: 0.8112 (ptmt) outliers start: 49 outliers final: 32 residues processed: 233 average time/residue: 0.2583 time to fit residues: 85.2866 Evaluate side-chains 215 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 182 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 319 TYR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain b residue 447 THR Chi-restraints excluded: chain b residue 469 VAL Chi-restraints excluded: chain b residue 491 SER Chi-restraints excluded: chain b residue 501 PHE Chi-restraints excluded: chain b residue 519 ASP Chi-restraints excluded: chain b residue 544 HIS Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain a residue 31 HIS Chi-restraints excluded: chain a residue 40 ASN Chi-restraints excluded: chain a residue 70 ASP Chi-restraints excluded: chain a residue 74 ASN Chi-restraints excluded: chain a residue 114 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain c residue 51 LEU Chi-restraints excluded: chain c residue 83 SER Chi-restraints excluded: chain c residue 89 THR Chi-restraints excluded: chain c residue 130 VAL Chi-restraints excluded: chain c residue 214 LEU Chi-restraints excluded: chain c residue 221 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 65 optimal weight: 0.4980 chunk 91 optimal weight: 3.9990 chunk 136 optimal weight: 0.0770 chunk 144 optimal weight: 0.0980 chunk 71 optimal weight: 0.7980 chunk 129 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 544 HIS ** b 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 31 HIS a 110 ASN ** a 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12646 Z= 0.228 Angle : 0.577 8.077 17152 Z= 0.292 Chirality : 0.044 0.175 1766 Planarity : 0.004 0.043 2248 Dihedral : 4.914 56.210 1694 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 3.98 % Allowed : 17.76 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.19), residues: 1492 helix: -1.13 (0.32), residues: 250 sheet: -2.58 (0.24), residues: 360 loop : -2.09 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 117 HIS 0.006 0.001 HIS a 31 PHE 0.015 0.001 PHE B 558 TYR 0.020 0.001 TYR B 365 ARG 0.005 0.000 ARG B 438 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 198 time to evaluate : 1.439 Fit side-chains revert: symmetry clash REVERT: b 363 MET cc_start: 0.7936 (ptp) cc_final: 0.7644 (ptp) REVERT: A 56 GLN cc_start: 0.7754 (mm110) cc_final: 0.7501 (mm-40) REVERT: a 37 ARG cc_start: 0.7541 (ttm110) cc_final: 0.6728 (mtm110) REVERT: a 38 LEU cc_start: 0.7433 (mm) cc_final: 0.6868 (mp) REVERT: a 109 ASN cc_start: 0.8212 (p0) cc_final: 0.7921 (p0) REVERT: C 32 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.7439 (mt) REVERT: C 188 PHE cc_start: 0.7218 (m-10) cc_final: 0.7000 (m-10) REVERT: c 29 LEU cc_start: 0.8436 (mm) cc_final: 0.8205 (mm) REVERT: c 94 MET cc_start: 0.6779 (ptp) cc_final: 0.6246 (mtm) REVERT: c 148 ASP cc_start: 0.7766 (m-30) cc_final: 0.7505 (m-30) REVERT: c 149 LYS cc_start: 0.7411 (mmmt) cc_final: 0.7151 (mmtm) REVERT: c 230 MET cc_start: 0.7200 (mmm) cc_final: 0.6904 (mmt) REVERT: c 250 TYR cc_start: 0.6798 (p90) cc_final: 0.6071 (p90) outliers start: 52 outliers final: 39 residues processed: 228 average time/residue: 0.2730 time to fit residues: 87.4920 Evaluate side-chains 223 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 183 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain b residue 370 VAL Chi-restraints excluded: chain b residue 447 THR Chi-restraints excluded: chain b residue 469 VAL Chi-restraints excluded: chain b residue 491 SER Chi-restraints excluded: chain b residue 501 PHE Chi-restraints excluded: chain b residue 519 ASP Chi-restraints excluded: chain b residue 544 HIS Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain a residue 31 HIS Chi-restraints excluded: chain a residue 40 ASN Chi-restraints excluded: chain a residue 70 ASP Chi-restraints excluded: chain a residue 74 ASN Chi-restraints excluded: chain a residue 110 ASN Chi-restraints excluded: chain a residue 114 THR Chi-restraints excluded: chain a residue 185 GLU Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain c residue 45 LEU Chi-restraints excluded: chain c residue 51 LEU Chi-restraints excluded: chain c residue 83 SER Chi-restraints excluded: chain c residue 84 LEU Chi-restraints excluded: chain c residue 89 THR Chi-restraints excluded: chain c residue 95 GLN Chi-restraints excluded: chain c residue 130 VAL Chi-restraints excluded: chain c residue 153 ILE Chi-restraints excluded: chain c residue 214 LEU Chi-restraints excluded: chain c residue 221 ILE Chi-restraints excluded: chain c residue 255 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 3.9990 chunk 82 optimal weight: 0.0670 chunk 2 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 100 optimal weight: 0.0870 chunk 0 optimal weight: 3.9990 chunk 74 optimal weight: 0.0770 chunk 130 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 overall best weight: 0.3254 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 544 HIS ** b 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 31 HIS a 110 ASN ** a 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12646 Z= 0.191 Angle : 0.562 8.490 17152 Z= 0.284 Chirality : 0.043 0.169 1766 Planarity : 0.004 0.043 2248 Dihedral : 4.434 21.551 1692 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 4.06 % Allowed : 18.30 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.20), residues: 1492 helix: -0.90 (0.33), residues: 250 sheet: -2.46 (0.24), residues: 360 loop : -1.97 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 117 HIS 0.006 0.001 HIS a 31 PHE 0.016 0.001 PHE B 558 TYR 0.020 0.001 TYR B 365 ARG 0.006 0.000 ARG B 438 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 192 time to evaluate : 1.432 Fit side-chains revert: symmetry clash REVERT: B 366 ILE cc_start: 0.8701 (OUTLIER) cc_final: 0.8274 (mp) REVERT: b 363 MET cc_start: 0.7873 (ptp) cc_final: 0.7288 (ptp) REVERT: b 434 ASN cc_start: 0.7970 (m-40) cc_final: 0.7508 (m-40) REVERT: A 155 LEU cc_start: 0.8125 (mp) cc_final: 0.7761 (mp) REVERT: a 37 ARG cc_start: 0.7486 (ttm110) cc_final: 0.6803 (mtm110) REVERT: a 38 LEU cc_start: 0.7393 (OUTLIER) cc_final: 0.6837 (mp) REVERT: C 32 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7484 (mt) REVERT: c 92 MET cc_start: 0.7520 (ptm) cc_final: 0.7234 (ttp) REVERT: c 94 MET cc_start: 0.6786 (ptp) cc_final: 0.6240 (mtm) REVERT: c 148 ASP cc_start: 0.7723 (m-30) cc_final: 0.7498 (m-30) REVERT: c 149 LYS cc_start: 0.7471 (mmmt) cc_final: 0.7229 (mmtm) REVERT: c 230 MET cc_start: 0.7155 (mmm) cc_final: 0.6901 (mmt) REVERT: c 250 TYR cc_start: 0.6806 (p90) cc_final: 0.6059 (p90) REVERT: c 262 TYR cc_start: 0.8720 (t80) cc_final: 0.8358 (t80) REVERT: c 270 MET cc_start: 0.6470 (mmm) cc_final: 0.6159 (mmm) outliers start: 53 outliers final: 40 residues processed: 225 average time/residue: 0.2499 time to fit residues: 80.4858 Evaluate side-chains 227 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 184 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 642 PHE Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain b residue 370 VAL Chi-restraints excluded: chain b residue 447 THR Chi-restraints excluded: chain b residue 469 VAL Chi-restraints excluded: chain b residue 491 SER Chi-restraints excluded: chain b residue 501 PHE Chi-restraints excluded: chain b residue 519 ASP Chi-restraints excluded: chain b residue 544 HIS Chi-restraints excluded: chain A residue 40 ASN Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain a residue 31 HIS Chi-restraints excluded: chain a residue 38 LEU Chi-restraints excluded: chain a residue 40 ASN Chi-restraints excluded: chain a residue 70 ASP Chi-restraints excluded: chain a residue 74 ASN Chi-restraints excluded: chain a residue 114 THR Chi-restraints excluded: chain a residue 185 GLU Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain c residue 51 LEU Chi-restraints excluded: chain c residue 83 SER Chi-restraints excluded: chain c residue 84 LEU Chi-restraints excluded: chain c residue 89 THR Chi-restraints excluded: chain c residue 130 VAL Chi-restraints excluded: chain c residue 214 LEU Chi-restraints excluded: chain c residue 221 ILE Chi-restraints excluded: chain c residue 255 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 0.1980 chunk 130 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 85 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 145 optimal weight: 0.9990 chunk 120 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 139 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 544 HIS ** b 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 31 HIS ** a 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.4254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12646 Z= 0.286 Angle : 0.605 8.258 17152 Z= 0.306 Chirality : 0.044 0.168 1766 Planarity : 0.004 0.044 2248 Dihedral : 4.609 22.019 1692 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 4.36 % Allowed : 18.76 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.20), residues: 1492 helix: -0.87 (0.33), residues: 250 sheet: -2.45 (0.24), residues: 360 loop : -1.91 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 117 HIS 0.019 0.001 HIS a 31 PHE 0.017 0.002 PHE C 188 TYR 0.018 0.002 TYR B 365 ARG 0.008 0.001 ARG a 30 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 189 time to evaluate : 1.315 Fit side-chains revert: symmetry clash REVERT: B 366 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8297 (mp) REVERT: A 155 LEU cc_start: 0.8109 (mp) cc_final: 0.7838 (mp) REVERT: a 37 ARG cc_start: 0.7445 (ttm110) cc_final: 0.7032 (ttp-110) REVERT: a 38 LEU cc_start: 0.7238 (OUTLIER) cc_final: 0.6837 (mp) REVERT: a 109 ASN cc_start: 0.8327 (p0) cc_final: 0.7913 (p0) REVERT: C 188 PHE cc_start: 0.7554 (m-10) cc_final: 0.7335 (m-10) REVERT: c 29 LEU cc_start: 0.8355 (mm) cc_final: 0.8060 (mm) REVERT: c 94 MET cc_start: 0.6751 (ptp) cc_final: 0.6216 (mtm) REVERT: c 148 ASP cc_start: 0.7801 (m-30) cc_final: 0.7587 (m-30) REVERT: c 149 LYS cc_start: 0.7612 (mmmt) cc_final: 0.7373 (mmtm) REVERT: c 230 MET cc_start: 0.7323 (mmm) cc_final: 0.7069 (mmt) REVERT: c 270 MET cc_start: 0.6579 (mmm) cc_final: 0.6307 (mmm) outliers start: 57 outliers final: 42 residues processed: 226 average time/residue: 0.2525 time to fit residues: 81.3845 Evaluate side-chains 225 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 181 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain b residue 316 GLU Chi-restraints excluded: chain b residue 370 VAL Chi-restraints excluded: chain b residue 447 THR Chi-restraints excluded: chain b residue 469 VAL Chi-restraints excluded: chain b residue 491 SER Chi-restraints excluded: chain b residue 501 PHE Chi-restraints excluded: chain b residue 519 ASP Chi-restraints excluded: chain b residue 544 HIS Chi-restraints excluded: chain b residue 588 VAL Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 40 ASN Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain a residue 31 HIS Chi-restraints excluded: chain a residue 38 LEU Chi-restraints excluded: chain a residue 40 ASN Chi-restraints excluded: chain a residue 70 ASP Chi-restraints excluded: chain a residue 74 ASN Chi-restraints excluded: chain a residue 185 GLU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain c residue 51 LEU Chi-restraints excluded: chain c residue 83 SER Chi-restraints excluded: chain c residue 84 LEU Chi-restraints excluded: chain c residue 89 THR Chi-restraints excluded: chain c residue 130 VAL Chi-restraints excluded: chain c residue 153 ILE Chi-restraints excluded: chain c residue 214 LEU Chi-restraints excluded: chain c residue 221 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 0.5980 chunk 82 optimal weight: 0.9980 chunk 105 optimal weight: 0.7980 chunk 122 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 144 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 66 optimal weight: 0.0670 chunk 89 optimal weight: 0.9990 chunk 57 optimal weight: 0.0970 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 GLN ** b 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 544 HIS ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 31 HIS ** a 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.4415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12646 Z= 0.232 Angle : 0.594 7.886 17152 Z= 0.301 Chirality : 0.044 0.175 1766 Planarity : 0.004 0.043 2248 Dihedral : 4.614 21.981 1692 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 4.44 % Allowed : 19.30 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.20), residues: 1492 helix: -0.80 (0.33), residues: 250 sheet: -2.40 (0.24), residues: 360 loop : -1.85 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 117 HIS 0.008 0.001 HIS a 31 PHE 0.026 0.002 PHE C 160 TYR 0.034 0.002 TYR C 258 ARG 0.007 0.000 ARG B 438 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 190 time to evaluate : 1.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 366 ILE cc_start: 0.8722 (OUTLIER) cc_final: 0.8273 (mp) REVERT: B 619 GLN cc_start: 0.5696 (mt0) cc_final: 0.5382 (tt0) REVERT: b 363 MET cc_start: 0.7718 (ptp) cc_final: 0.7435 (ptp) REVERT: A 155 LEU cc_start: 0.8091 (mp) cc_final: 0.7793 (mp) REVERT: a 37 ARG cc_start: 0.7436 (ttm110) cc_final: 0.7053 (ttp-110) REVERT: a 38 LEU cc_start: 0.7201 (OUTLIER) cc_final: 0.6759 (mp) REVERT: a 109 ASN cc_start: 0.8359 (p0) cc_final: 0.7946 (p0) REVERT: C 18 GLN cc_start: 0.7542 (OUTLIER) cc_final: 0.7320 (pm20) REVERT: C 188 PHE cc_start: 0.7647 (m-10) cc_final: 0.7423 (m-10) REVERT: c 29 LEU cc_start: 0.8343 (mm) cc_final: 0.8065 (mm) REVERT: c 94 MET cc_start: 0.6713 (ptp) cc_final: 0.6169 (mtm) REVERT: c 149 LYS cc_start: 0.7571 (mmmt) cc_final: 0.7348 (mmtm) REVERT: c 230 MET cc_start: 0.7326 (mmm) cc_final: 0.7065 (mmt) REVERT: c 262 TYR cc_start: 0.8767 (t80) cc_final: 0.8311 (t80) REVERT: c 270 MET cc_start: 0.6630 (mmm) cc_final: 0.6421 (mmm) outliers start: 58 outliers final: 44 residues processed: 230 average time/residue: 0.2577 time to fit residues: 84.5660 Evaluate side-chains 231 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 184 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 642 PHE Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain b residue 370 VAL Chi-restraints excluded: chain b residue 447 THR Chi-restraints excluded: chain b residue 469 VAL Chi-restraints excluded: chain b residue 491 SER Chi-restraints excluded: chain b residue 501 PHE Chi-restraints excluded: chain b residue 519 ASP Chi-restraints excluded: chain b residue 544 HIS Chi-restraints excluded: chain b residue 588 VAL Chi-restraints excluded: chain b residue 598 GLU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 40 ASN Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain a residue 38 LEU Chi-restraints excluded: chain a residue 68 THR Chi-restraints excluded: chain a residue 70 ASP Chi-restraints excluded: chain a residue 74 ASN Chi-restraints excluded: chain a residue 104 VAL Chi-restraints excluded: chain a residue 185 GLU Chi-restraints excluded: chain C residue 18 GLN Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain c residue 51 LEU Chi-restraints excluded: chain c residue 78 ASN Chi-restraints excluded: chain c residue 83 SER Chi-restraints excluded: chain c residue 84 LEU Chi-restraints excluded: chain c residue 89 THR Chi-restraints excluded: chain c residue 130 VAL Chi-restraints excluded: chain c residue 214 LEU Chi-restraints excluded: chain c residue 221 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 113 optimal weight: 0.7980 chunk 131 optimal weight: 0.0980 chunk 138 optimal weight: 0.4980 chunk 126 optimal weight: 4.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 544 HIS ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 110 ASN ** a 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.4650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12646 Z= 0.274 Angle : 0.613 8.368 17152 Z= 0.310 Chirality : 0.044 0.230 1766 Planarity : 0.004 0.058 2248 Dihedral : 4.697 22.428 1692 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 4.44 % Allowed : 19.98 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.20), residues: 1492 helix: -0.82 (0.33), residues: 250 sheet: -2.39 (0.23), residues: 398 loop : -1.78 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP c 82 HIS 0.014 0.001 HIS b 544 PHE 0.021 0.002 PHE C 160 TYR 0.030 0.002 TYR C 258 ARG 0.011 0.001 ARG c 171 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 191 time to evaluate : 1.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 366 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8271 (mp) REVERT: B 619 GLN cc_start: 0.5790 (mt0) cc_final: 0.5509 (tt0) REVERT: b 363 MET cc_start: 0.7763 (ptp) cc_final: 0.7435 (ptp) REVERT: A 111 ASP cc_start: 0.7774 (m-30) cc_final: 0.7538 (m-30) REVERT: A 155 LEU cc_start: 0.8131 (mp) cc_final: 0.7830 (mp) REVERT: a 37 ARG cc_start: 0.7532 (ttm110) cc_final: 0.7083 (ttp-110) REVERT: a 38 LEU cc_start: 0.7209 (OUTLIER) cc_final: 0.6778 (mp) REVERT: a 109 ASN cc_start: 0.8364 (p0) cc_final: 0.7949 (p0) REVERT: C 188 PHE cc_start: 0.7676 (m-10) cc_final: 0.7452 (m-10) REVERT: c 29 LEU cc_start: 0.8365 (mm) cc_final: 0.8059 (mm) REVERT: c 94 MET cc_start: 0.6728 (ptp) cc_final: 0.6194 (mtm) REVERT: c 149 LYS cc_start: 0.7695 (mmmt) cc_final: 0.7459 (mmtm) REVERT: c 230 MET cc_start: 0.7336 (mmm) cc_final: 0.7071 (mmt) outliers start: 58 outliers final: 49 residues processed: 228 average time/residue: 0.2590 time to fit residues: 84.2640 Evaluate side-chains 231 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 180 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 642 PHE Chi-restraints excluded: chain b residue 316 GLU Chi-restraints excluded: chain b residue 370 VAL Chi-restraints excluded: chain b residue 447 THR Chi-restraints excluded: chain b residue 469 VAL Chi-restraints excluded: chain b residue 491 SER Chi-restraints excluded: chain b residue 501 PHE Chi-restraints excluded: chain b residue 519 ASP Chi-restraints excluded: chain b residue 544 HIS Chi-restraints excluded: chain b residue 588 VAL Chi-restraints excluded: chain b residue 598 GLU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 40 ASN Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain a residue 31 HIS Chi-restraints excluded: chain a residue 38 LEU Chi-restraints excluded: chain a residue 40 ASN Chi-restraints excluded: chain a residue 68 THR Chi-restraints excluded: chain a residue 70 ASP Chi-restraints excluded: chain a residue 74 ASN Chi-restraints excluded: chain a residue 185 GLU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain c residue 51 LEU Chi-restraints excluded: chain c residue 83 SER Chi-restraints excluded: chain c residue 84 LEU Chi-restraints excluded: chain c residue 89 THR Chi-restraints excluded: chain c residue 130 VAL Chi-restraints excluded: chain c residue 132 VAL Chi-restraints excluded: chain c residue 153 ILE Chi-restraints excluded: chain c residue 214 LEU Chi-restraints excluded: chain c residue 221 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 0.0060 chunk 138 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 105 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 121 optimal weight: 0.8980 chunk 127 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 142 optimal weight: 0.0170 chunk 86 optimal weight: 0.9990 overall best weight: 0.4434 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 544 HIS ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 110 ASN ** a 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.4710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12646 Z= 0.230 Angle : 0.605 8.480 17152 Z= 0.305 Chirality : 0.044 0.230 1766 Planarity : 0.004 0.043 2248 Dihedral : 4.673 22.136 1692 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 4.13 % Allowed : 20.83 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.64 (0.20), residues: 1492 helix: -0.78 (0.33), residues: 250 sheet: -2.35 (0.23), residues: 398 loop : -1.73 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP c 82 HIS 0.008 0.001 HIS b 544 PHE 0.020 0.002 PHE C 160 TYR 0.032 0.002 TYR C 258 ARG 0.009 0.001 ARG c 171 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 186 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 366 ILE cc_start: 0.8642 (OUTLIER) cc_final: 0.8207 (mp) REVERT: B 619 GLN cc_start: 0.5837 (mt0) cc_final: 0.5590 (tt0) REVERT: b 363 MET cc_start: 0.7705 (ptp) cc_final: 0.7409 (ptp) REVERT: A 111 ASP cc_start: 0.7827 (m-30) cc_final: 0.7605 (m-30) REVERT: A 155 LEU cc_start: 0.8155 (mp) cc_final: 0.7853 (mp) REVERT: a 37 ARG cc_start: 0.7454 (ttm110) cc_final: 0.7020 (ttp-110) REVERT: a 38 LEU cc_start: 0.7234 (OUTLIER) cc_final: 0.6862 (mp) REVERT: a 109 ASN cc_start: 0.8369 (p0) cc_final: 0.7940 (p0) REVERT: c 29 LEU cc_start: 0.8360 (mm) cc_final: 0.8074 (mm) REVERT: c 94 MET cc_start: 0.6829 (ptp) cc_final: 0.6231 (mtm) REVERT: c 149 LYS cc_start: 0.7583 (mmmt) cc_final: 0.7363 (mmtm) REVERT: c 230 MET cc_start: 0.7337 (mmm) cc_final: 0.7084 (mmt) REVERT: c 262 TYR cc_start: 0.8734 (t80) cc_final: 0.8283 (t80) outliers start: 54 outliers final: 50 residues processed: 222 average time/residue: 0.2504 time to fit residues: 79.5483 Evaluate side-chains 233 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 181 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 642 PHE Chi-restraints excluded: chain b residue 316 GLU Chi-restraints excluded: chain b residue 370 VAL Chi-restraints excluded: chain b residue 447 THR Chi-restraints excluded: chain b residue 469 VAL Chi-restraints excluded: chain b residue 491 SER Chi-restraints excluded: chain b residue 501 PHE Chi-restraints excluded: chain b residue 519 ASP Chi-restraints excluded: chain b residue 544 HIS Chi-restraints excluded: chain b residue 588 VAL Chi-restraints excluded: chain b residue 598 GLU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 40 ASN Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain a residue 31 HIS Chi-restraints excluded: chain a residue 38 LEU Chi-restraints excluded: chain a residue 40 ASN Chi-restraints excluded: chain a residue 68 THR Chi-restraints excluded: chain a residue 70 ASP Chi-restraints excluded: chain a residue 74 ASN Chi-restraints excluded: chain a residue 110 ASN Chi-restraints excluded: chain a residue 185 GLU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain c residue 51 LEU Chi-restraints excluded: chain c residue 83 SER Chi-restraints excluded: chain c residue 84 LEU Chi-restraints excluded: chain c residue 89 THR Chi-restraints excluded: chain c residue 130 VAL Chi-restraints excluded: chain c residue 132 VAL Chi-restraints excluded: chain c residue 214 LEU Chi-restraints excluded: chain c residue 221 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 149 optimal weight: 0.4980 chunk 137 optimal weight: 4.9990 chunk 118 optimal weight: 0.2980 chunk 12 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 126 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 544 HIS ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 110 ASN ** a 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.4902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12646 Z= 0.296 Angle : 0.636 9.500 17152 Z= 0.320 Chirality : 0.045 0.234 1766 Planarity : 0.004 0.045 2248 Dihedral : 4.768 22.815 1692 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 4.21 % Allowed : 21.29 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.20), residues: 1492 helix: -0.83 (0.32), residues: 250 sheet: -2.29 (0.24), residues: 380 loop : -1.73 (0.20), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP c 82 HIS 0.005 0.001 HIS a 120 PHE 0.020 0.002 PHE C 160 TYR 0.031 0.002 TYR C 258 ARG 0.008 0.001 ARG c 171 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 178 time to evaluate : 1.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 366 ILE cc_start: 0.8676 (OUTLIER) cc_final: 0.8214 (mp) REVERT: B 619 GLN cc_start: 0.6083 (mt0) cc_final: 0.5848 (tt0) REVERT: b 363 MET cc_start: 0.7752 (ptp) cc_final: 0.7417 (ptp) REVERT: A 111 ASP cc_start: 0.7854 (m-30) cc_final: 0.7643 (m-30) REVERT: A 155 LEU cc_start: 0.8185 (mp) cc_final: 0.7888 (mp) REVERT: a 37 ARG cc_start: 0.7485 (ttm110) cc_final: 0.7025 (ttp-110) REVERT: a 38 LEU cc_start: 0.7435 (OUTLIER) cc_final: 0.6989 (mp) REVERT: a 109 ASN cc_start: 0.8394 (p0) cc_final: 0.7958 (p0) REVERT: a 187 ARG cc_start: 0.7562 (mmt90) cc_final: 0.7360 (mpt-90) REVERT: c 29 LEU cc_start: 0.8363 (mm) cc_final: 0.8045 (mm) REVERT: c 94 MET cc_start: 0.6840 (ptp) cc_final: 0.6266 (mtm) REVERT: c 230 MET cc_start: 0.7358 (mmm) cc_final: 0.7094 (mmt) outliers start: 55 outliers final: 49 residues processed: 216 average time/residue: 0.2569 time to fit residues: 79.1071 Evaluate side-chains 223 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 172 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 642 PHE Chi-restraints excluded: chain b residue 316 GLU Chi-restraints excluded: chain b residue 370 VAL Chi-restraints excluded: chain b residue 447 THR Chi-restraints excluded: chain b residue 469 VAL Chi-restraints excluded: chain b residue 491 SER Chi-restraints excluded: chain b residue 501 PHE Chi-restraints excluded: chain b residue 519 ASP Chi-restraints excluded: chain b residue 544 HIS Chi-restraints excluded: chain b residue 588 VAL Chi-restraints excluded: chain b residue 598 GLU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 40 ASN Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain a residue 31 HIS Chi-restraints excluded: chain a residue 38 LEU Chi-restraints excluded: chain a residue 68 THR Chi-restraints excluded: chain a residue 70 ASP Chi-restraints excluded: chain a residue 74 ASN Chi-restraints excluded: chain a residue 185 GLU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain c residue 51 LEU Chi-restraints excluded: chain c residue 83 SER Chi-restraints excluded: chain c residue 84 LEU Chi-restraints excluded: chain c residue 89 THR Chi-restraints excluded: chain c residue 130 VAL Chi-restraints excluded: chain c residue 132 VAL Chi-restraints excluded: chain c residue 153 ILE Chi-restraints excluded: chain c residue 214 LEU Chi-restraints excluded: chain c residue 221 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 122 optimal weight: 0.5980 chunk 15 optimal weight: 0.0980 chunk 21 optimal weight: 0.0020 chunk 104 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 86 optimal weight: 4.9990 overall best weight: 0.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 544 HIS ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.133350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.103308 restraints weight = 18724.046| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.67 r_work: 0.3398 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.4900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12646 Z= 0.225 Angle : 0.611 9.489 17152 Z= 0.307 Chirality : 0.044 0.237 1766 Planarity : 0.004 0.042 2248 Dihedral : 4.690 22.264 1692 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 3.98 % Allowed : 21.52 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.20), residues: 1492 helix: -0.78 (0.33), residues: 250 sheet: -2.23 (0.24), residues: 380 loop : -1.71 (0.20), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP c 82 HIS 0.004 0.001 HIS b 544 PHE 0.015 0.002 PHE B 558 TYR 0.031 0.002 TYR C 258 ARG 0.008 0.001 ARG c 171 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3440.60 seconds wall clock time: 62 minutes 33.74 seconds (3753.74 seconds total)