Starting phenix.real_space_refine on Sat Jun 29 07:18:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wzb_37949/06_2024/8wzb_37949.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wzb_37949/06_2024/8wzb_37949.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wzb_37949/06_2024/8wzb_37949.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wzb_37949/06_2024/8wzb_37949.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wzb_37949/06_2024/8wzb_37949.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wzb_37949/06_2024/8wzb_37949.pdb" } resolution = 3.28 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= 0.011 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 67 5.16 5 C 11274 2.51 5 N 2975 2.21 5 O 3278 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 225": "NH1" <-> "NH2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B ASP 228": "OD1" <-> "OD2" Residue "F GLU 45": "OE1" <-> "OE2" Residue "F GLU 197": "OE1" <-> "OE2" Residue "G GLU 284": "OE1" <-> "OE2" Residue "G GLU 316": "OE1" <-> "OE2" Residue "G GLU 362": "OE1" <-> "OE2" Residue "G GLU 587": "OE1" <-> "OE2" Residue "G GLU 675": "OE1" <-> "OE2" Residue "G GLU 685": "OE1" <-> "OE2" Residue "G GLU 687": "OE1" <-> "OE2" Residue "S GLU 371": "OE1" <-> "OE2" Residue "S GLU 669": "OE1" <-> "OE2" Residue "c GLU 136": "OE1" <-> "OE2" Residue "c GLU 137": "OE1" <-> "OE2" Residue "I GLU 21": "OE1" <-> "OE2" Residue "I GLU 49": "OE1" <-> "OE2" Residue "I GLU 181": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 17594 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 369 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "B" Number of atoms: 1489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1489 Classifications: {'peptide': 181} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 164} Chain: "C" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 633 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 69} Chain breaks: 1 Chain: "D" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 387 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "E" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1612 Classifications: {'peptide': 201} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 182} Chain: "F" Number of atoms: 1514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1514 Classifications: {'peptide': 185} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 179} Chain: "G" Number of atoms: 3099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3099 Classifications: {'peptide': 387} Link IDs: {'CIS': 2, 'PTRANS': 31, 'TRANS': 353} Chain breaks: 5 Chain: "H" Number of atoms: 1912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1912 Classifications: {'peptide': 239} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 225} Chain breaks: 2 Chain: "S" Number of atoms: 3139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3139 Classifications: {'peptide': 392} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 360} Chain breaks: 5 Chain: "c" Number of atoms: 1926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1926 Classifications: {'peptide': 241} Modifications used: {'COO': 1} Link IDs: {'CIS': 5, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 223} Chain breaks: 2 Chain: "I" Number of atoms: 1514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1514 Classifications: {'peptide': 185} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 179} Time building chain proxies: 13.07, per 1000 atoms: 0.74 Number of scatterers: 17594 At special positions: 0 Unit cell: (130.662, 228.872, 133.224, 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 67 16.00 O 3278 8.00 N 2975 7.00 C 11274 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: 6.38 Conformation dependent library (CDL) restraints added in 2.7 seconds 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4030 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 23 sheets defined 29.3% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.77 Creating SS restraints... Processing helix chain 'A' and resid 1 through 10 removed outlier: 3.847A pdb=" N PHE A 10 " --> pdb=" O LEU A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 11 through 24 Processing helix chain 'A' and resid 28 through 46 removed outlier: 3.618A pdb=" N ALA A 46 " --> pdb=" O SER A 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 154 Processing helix chain 'B' and resid 238 through 242 removed outlier: 3.987A pdb=" N LEU B 242 " --> pdb=" O LEU B 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 238 through 242' Processing helix chain 'B' and resid 303 through 315 removed outlier: 3.663A pdb=" N LYS B 307 " --> pdb=" O THR B 303 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLN B 312 " --> pdb=" O GLN B 308 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU B 315 " --> pdb=" O ARG B 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 315 Processing helix chain 'D' and resid 286 through 290 Processing helix chain 'D' and resid 290 through 329 removed outlier: 3.520A pdb=" N TRP D 294 " --> pdb=" O GLY D 290 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU D 329 " --> pdb=" O ILE D 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 25 No H-bonds generated for 'chain 'E' and resid 23 through 25' Processing helix chain 'E' and resid 26 through 38 removed outlier: 3.810A pdb=" N ILE E 30 " --> pdb=" O LYS E 26 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY E 38 " --> pdb=" O ILE E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 58 removed outlier: 3.850A pdb=" N SER E 55 " --> pdb=" O PRO E 51 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ASN E 56 " --> pdb=" O GLU E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 75 removed outlier: 4.021A pdb=" N THR E 71 " --> pdb=" O PHE E 67 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER E 75 " --> pdb=" O THR E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 98 Processing helix chain 'E' and resid 101 through 109 removed outlier: 4.268A pdb=" N GLU E 107 " --> pdb=" O LEU E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 118 removed outlier: 3.794A pdb=" N ILE E 116 " --> pdb=" O SER E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 143 Processing helix chain 'E' and resid 154 through 165 removed outlier: 3.981A pdb=" N LYS E 158 " --> pdb=" O GLY E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 178 removed outlier: 3.570A pdb=" N GLU E 175 " --> pdb=" O GLN E 171 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N CYS E 177 " --> pdb=" O LEU E 173 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS E 178 " --> pdb=" O THR E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 195 removed outlier: 4.385A pdb=" N TRP E 187 " --> pdb=" O ASP E 183 " (cutoff:3.500A) Processing helix chain 'G' and resid 207 through 218 Processing helix chain 'G' and resid 227 through 241 removed outlier: 4.044A pdb=" N ASP G 241 " --> pdb=" O THR G 237 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 261 removed outlier: 3.502A pdb=" N SER G 255 " --> pdb=" O ILE G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 276 through 287 removed outlier: 3.758A pdb=" N TYR G 280 " --> pdb=" O MET G 276 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS G 287 " --> pdb=" O ALA G 283 " (cutoff:3.500A) Processing helix chain 'G' and resid 313 through 325 Processing helix chain 'G' and resid 329 through 347 Processing helix chain 'G' and resid 423 through 427 Processing helix chain 'G' and resid 478 through 495 removed outlier: 3.833A pdb=" N TYR G 482 " --> pdb=" O ASN G 478 " (cutoff:3.500A) Processing helix chain 'G' and resid 532 through 536 removed outlier: 3.668A pdb=" N VAL G 536 " --> pdb=" O ILE G 533 " (cutoff:3.500A) Processing helix chain 'G' and resid 617 through 621 removed outlier: 3.815A pdb=" N TYR G 620 " --> pdb=" O ILE G 617 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA G 621 " --> pdb=" O PRO G 618 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 617 through 621' Processing helix chain 'G' and resid 683 through 692 removed outlier: 3.602A pdb=" N MET G 692 " --> pdb=" O GLN G 688 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 9 Processing helix chain 'H' and resid 9 through 14 removed outlier: 4.028A pdb=" N ALA H 13 " --> pdb=" O SER H 9 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 39 Processing helix chain 'H' and resid 89 through 94 Processing helix chain 'H' and resid 95 through 99 removed outlier: 3.765A pdb=" N VAL H 98 " --> pdb=" O GLN H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 136 through 151 Processing helix chain 'H' and resid 216 through 220 removed outlier: 3.924A pdb=" N TYR H 219 " --> pdb=" O SER H 216 " (cutoff:3.500A) Processing helix chain 'H' and resid 271 through 276 Processing helix chain 'S' and resid 206 through 218 Processing helix chain 'S' and resid 227 through 242 Processing helix chain 'S' and resid 250 through 259 Processing helix chain 'S' and resid 277 through 286 removed outlier: 3.641A pdb=" N GLU S 281 " --> pdb=" O LEU S 277 " (cutoff:3.500A) Processing helix chain 'S' and resid 313 through 323 removed outlier: 3.770A pdb=" N SER S 317 " --> pdb=" O ASN S 313 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLN S 323 " --> pdb=" O TYR S 319 " (cutoff:3.500A) Processing helix chain 'S' and resid 330 through 347 Processing helix chain 'S' and resid 447 through 452 Processing helix chain 'S' and resid 453 through 457 removed outlier: 4.221A pdb=" N LYS S 456 " --> pdb=" O THR S 453 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE S 457 " --> pdb=" O ALA S 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 453 through 457' Processing helix chain 'S' and resid 478 through 495 removed outlier: 3.589A pdb=" N HIS S 495 " --> pdb=" O SER S 491 " (cutoff:3.500A) Processing helix chain 'S' and resid 531 through 538 removed outlier: 3.605A pdb=" N SER S 538 " --> pdb=" O ASP S 534 " (cutoff:3.500A) Processing helix chain 'S' and resid 595 through 599 removed outlier: 3.728A pdb=" N GLU S 598 " --> pdb=" O PRO S 595 " (cutoff:3.500A) Processing helix chain 'S' and resid 683 through 693 Processing helix chain 'c' and resid 2 through 6 removed outlier: 4.045A pdb=" N LEU c 6 " --> pdb=" O ALA c 3 " (cutoff:3.500A) Processing helix chain 'c' and resid 11 through 15 removed outlier: 4.024A pdb=" N GLY c 15 " --> pdb=" O LEU c 12 " (cutoff:3.500A) Processing helix chain 'c' and resid 21 through 39 removed outlier: 3.502A pdb=" N TYR c 39 " --> pdb=" O VAL c 35 " (cutoff:3.500A) Processing helix chain 'c' and resid 89 through 95 removed outlier: 3.843A pdb=" N GLN c 95 " --> pdb=" O GLU c 91 " (cutoff:3.500A) Processing helix chain 'c' and resid 96 through 99 removed outlier: 3.503A pdb=" N VAL c 99 " --> pdb=" O ILE c 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 96 through 99' Processing helix chain 'c' and resid 136 through 151 Processing helix chain 'c' and resid 177 through 181 removed outlier: 3.573A pdb=" N VAL c 181 " --> pdb=" O LEU c 178 " (cutoff:3.500A) Processing helix chain 'c' and resid 232 through 235 Processing helix chain 'c' and resid 271 through 276 removed outlier: 3.533A pdb=" N MET c 275 " --> pdb=" O ASP c 271 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 140 through 146 removed outlier: 10.124A pdb=" N ILE B 140 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N ILE B 214 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ARG B 142 " --> pdb=" O ILE B 214 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LYS B 216 " --> pdb=" O ARG B 142 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N LEU B 144 " --> pdb=" O LYS B 216 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP B 210 " --> pdb=" O PHE B 196 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ILE B 194 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR B 195 " --> pdb=" O LYS E 201 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS E 201 " --> pdb=" O THR B 195 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 223 through 226 Processing sheet with id=AA3, first strand: chain 'B' and resid 247 through 250 Processing sheet with id=AA4, first strand: chain 'C' and resid 231 through 237 removed outlier: 6.470A pdb=" N PHE C 232 " --> pdb=" O PHE C 293 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ASP C 295 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N TYR C 234 " --> pdb=" O ASP C 295 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N GLN C 297 " --> pdb=" O TYR C 234 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ILE C 236 " --> pdb=" O GLN C 297 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU C 290 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL C 273 " --> pdb=" O LEU C 290 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ILE C 292 " --> pdb=" O LYS C 271 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS C 271 " --> pdb=" O ILE C 292 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 40 through 47 removed outlier: 6.360A pdb=" N ILE E 41 " --> pdb=" O ALA E 85 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ALA E 85 " --> pdb=" O ILE E 41 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLN E 43 " --> pdb=" O ILE E 83 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE E 83 " --> pdb=" O GLN E 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 19 through 21 removed outlier: 4.022A pdb=" N LYS F 35 " --> pdb=" O GLU F 21 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP F 70 " --> pdb=" O GLN F 79 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N GLN F 79 " --> pdb=" O ASP F 70 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N GLN F 102 " --> pdb=" O GLU F 93 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA F 95 " --> pdb=" O HIS F 100 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N HIS F 100 " --> pdb=" O ALA F 95 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY F 139 " --> pdb=" O GLY F 126 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ALA F 149 " --> pdb=" O THR F 140 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LYS F 162 " --> pdb=" O PRO F 171 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N CYS F 180 " --> pdb=" O PHE F 176 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 32 through 33 Processing sheet with id=AA8, first strand: chain 'G' and resid 441 through 442 removed outlier: 6.728A pdb=" N TYR G 365 " --> pdb=" O LYS G 357 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LYS G 357 " --> pdb=" O TYR G 365 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL G 367 " --> pdb=" O TRP G 355 " (cutoff:3.500A) removed outlier: 9.435A pdb=" N ASN G 644 " --> pdb=" O ARG G 353 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N TRP G 355 " --> pdb=" O ASN G 644 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR G 646 " --> pdb=" O TRP G 355 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY G 648 " --> pdb=" O LYS G 357 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 496 through 498 Processing sheet with id=AB1, first strand: chain 'G' and resid 502 through 503 removed outlier: 3.836A pdb=" N GLU G 522 " --> pdb=" O GLN G 503 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 609 through 613 removed outlier: 3.703A pdb=" N SER G 613 " --> pdb=" O ILE G 622 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE G 622 " --> pdb=" O SER G 613 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 83 through 84 removed outlier: 3.533A pdb=" N GLY H 62 " --> pdb=" O LYS H 72 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N GLN H 61 " --> pdb=" O PHE H 46 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N PHE H 46 " --> pdb=" O GLN H 61 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N LEU H 63 " --> pdb=" O VAL H 44 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N VAL H 44 " --> pdb=" O LEU H 63 " (cutoff:3.500A) removed outlier: 14.131A pdb=" N TYR H 258 " --> pdb=" O ARG H 43 " (cutoff:3.500A) removed outlier: 9.858A pdb=" N LEU H 45 " --> pdb=" O TYR H 258 " (cutoff:3.500A) removed outlier: 9.076A pdb=" N TYR H 260 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N TRP H 47 " --> pdb=" O TYR H 260 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY H 264 " --> pdb=" O ARG H 49 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N ASN H 257 " --> pdb=" O ALA H 252 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY H 259 " --> pdb=" O TYR H 250 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR H 250 " --> pdb=" O GLY H 259 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N LEU H 247 " --> pdb=" O SER H 241 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 110 through 111 removed outlier: 3.574A pdb=" N ILE H 134 " --> pdb=" O TYR H 111 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 154 through 155 Processing sheet with id=AB6, first strand: chain 'H' and resid 159 through 161 Processing sheet with id=AB7, first strand: chain 'S' and resid 441 through 442 removed outlier: 7.055A pdb=" N TYR S 365 " --> pdb=" O GLY S 356 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N GLY S 356 " --> pdb=" O TYR S 365 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N VAL S 367 " --> pdb=" O PHE S 354 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N PHE S 354 " --> pdb=" O VAL S 367 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLU S 369 " --> pdb=" O CYS S 352 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N CYS S 352 " --> pdb=" O GLU S 369 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLU S 371 " --> pdb=" O GLN S 350 " (cutoff:3.500A) removed outlier: 15.844A pdb=" N PHE S 642 " --> pdb=" O ARG S 351 " (cutoff:3.500A) removed outlier: 11.067A pdb=" N ARG S 353 " --> pdb=" O PHE S 642 " (cutoff:3.500A) removed outlier: 9.566A pdb=" N ASN S 644 " --> pdb=" O ARG S 353 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N TRP S 355 " --> pdb=" O ASN S 644 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR S 646 " --> pdb=" O TRP S 355 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY S 648 " --> pdb=" O LYS S 357 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ALA S 633 " --> pdb=" O SER S 627 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER S 637 " --> pdb=" O ALA S 623 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'S' and resid 496 through 498 Processing sheet with id=AB9, first strand: chain 'c' and resid 83 through 84 removed outlier: 3.564A pdb=" N SER c 83 " --> pdb=" O TYR c 75 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS c 72 " --> pdb=" O GLY c 62 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY c 62 " --> pdb=" O LYS c 72 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N GLN c 61 " --> pdb=" O PHE c 46 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N PHE c 46 " --> pdb=" O GLN c 61 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N LEU c 63 " --> pdb=" O VAL c 44 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N VAL c 44 " --> pdb=" O LEU c 63 " (cutoff:3.500A) removed outlier: 12.628A pdb=" N TYR c 260 " --> pdb=" O ARG c 43 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N LEU c 45 " --> pdb=" O TYR c 260 " (cutoff:3.500A) removed outlier: 9.703A pdb=" N TYR c 262 " --> pdb=" O LEU c 45 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N TRP c 47 " --> pdb=" O TYR c 262 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N GLY c 264 " --> pdb=" O TRP c 47 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ARG c 49 " --> pdb=" O GLY c 264 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'c' and resid 110 through 112 Processing sheet with id=AC2, first strand: chain 'c' and resid 153 through 155 Processing sheet with id=AC3, first strand: chain 'c' and resid 159 through 160 removed outlier: 4.026A pdb=" N PHE c 160 " --> pdb=" O HIS c 168 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N HIS c 168 " --> pdb=" O PHE c 160 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'c' and resid 226 through 231 Processing sheet with id=AC5, first strand: chain 'I' and resid 19 through 24 removed outlier: 3.714A pdb=" N GLU I 19 " --> pdb=" O ARG I 37 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS I 35 " --> pdb=" O GLU I 21 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N GLU I 23 " --> pdb=" O HIS I 33 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N HIS I 33 " --> pdb=" O GLU I 23 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER I 47 " --> pdb=" O GLN I 56 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLN I 56 " --> pdb=" O SER I 47 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N GLU I 49 " --> pdb=" O HIS I 54 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N HIS I 54 " --> pdb=" O GLU I 49 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N GLN I 79 " --> pdb=" O ASP I 70 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N GLN I 102 " --> pdb=" O GLU I 93 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N GLN I 125 " --> pdb=" O GLU I 116 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR I 140 " --> pdb=" O ALA I 149 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ALA I 149 " --> pdb=" O THR I 140 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY I 161 " --> pdb=" O ALA I 150 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS I 162 " --> pdb=" O PRO I 171 " (cutoff:3.500A) 633 hydrogen bonds defined for protein. 1761 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.61 Time building geometry restraints manager: 6.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5446 1.34 - 1.46: 4398 1.46 - 1.59: 8092 1.59 - 1.71: 2 1.71 - 1.83: 113 Bond restraints: 18051 Sorted by residual: bond pdb=" CG PRO G 448 " pdb=" CD PRO G 448 " ideal model delta sigma weight residual 1.503 1.272 0.231 3.40e-02 8.65e+02 4.63e+01 bond pdb=" C ASP H 106 " pdb=" N PRO H 107 " ideal model delta sigma weight residual 1.334 1.403 -0.069 2.34e-02 1.83e+03 8.73e+00 bond pdb=" C LEU C 302 " pdb=" N THR C 303 " ideal model delta sigma weight residual 1.331 1.388 -0.057 2.07e-02 2.33e+03 7.68e+00 bond pdb=" CB PRO G 606 " pdb=" CG PRO G 606 " ideal model delta sigma weight residual 1.492 1.624 -0.132 5.00e-02 4.00e+02 6.98e+00 bond pdb=" CA ARG B 225 " pdb=" C ARG B 225 " ideal model delta sigma weight residual 1.528 1.493 0.035 1.37e-02 5.33e+03 6.35e+00 ... (remaining 18046 not shown) Histogram of bond angle deviations from ideal: 84.11 - 97.60: 3 97.60 - 111.09: 6565 111.09 - 124.58: 17447 124.58 - 138.08: 448 138.08 - 151.57: 6 Bond angle restraints: 24469 Sorted by residual: angle pdb=" CA PRO G 448 " pdb=" N PRO G 448 " pdb=" CD PRO G 448 " ideal model delta sigma weight residual 112.00 84.11 27.89 1.40e+00 5.10e-01 3.97e+02 angle pdb=" C THR c 255 " pdb=" N LYS c 256 " pdb=" CA LYS c 256 " ideal model delta sigma weight residual 121.70 151.57 -29.87 1.80e+00 3.09e-01 2.75e+02 angle pdb=" C HIS c 251 " pdb=" N ALA c 252 " pdb=" CA ALA c 252 " ideal model delta sigma weight residual 121.70 150.29 -28.59 1.80e+00 3.09e-01 2.52e+02 angle pdb=" C SER G 637 " pdb=" N ASN G 638 " pdb=" CA ASN G 638 " ideal model delta sigma weight residual 121.70 148.46 -26.76 1.80e+00 3.09e-01 2.21e+02 angle pdb=" C LYS H 183 " pdb=" N LEU H 184 " pdb=" CA LEU H 184 " ideal model delta sigma weight residual 121.70 142.09 -20.39 1.80e+00 3.09e-01 1.28e+02 ... (remaining 24464 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.11: 9122 18.11 - 36.22: 1203 36.22 - 54.32: 335 54.32 - 72.43: 52 72.43 - 90.54: 25 Dihedral angle restraints: 10737 sinusoidal: 4430 harmonic: 6307 Sorted by residual: dihedral pdb=" CA LYS c 256 " pdb=" C LYS c 256 " pdb=" N ASN c 257 " pdb=" CA ASN c 257 " ideal model delta harmonic sigma weight residual 180.00 152.16 27.84 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" CA PHE B 213 " pdb=" C PHE B 213 " pdb=" N ILE B 214 " pdb=" CA ILE B 214 " ideal model delta harmonic sigma weight residual 180.00 154.73 25.27 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA TYR G 472 " pdb=" C TYR G 472 " pdb=" N PRO G 473 " pdb=" CA PRO G 473 " ideal model delta harmonic sigma weight residual 180.00 155.83 24.17 0 5.00e+00 4.00e-02 2.34e+01 ... (remaining 10734 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 2202 0.072 - 0.145: 341 0.145 - 0.217: 35 0.217 - 0.290: 5 0.290 - 0.362: 2 Chirality restraints: 2585 Sorted by residual: chirality pdb=" CG LEU c 29 " pdb=" CB LEU c 29 " pdb=" CD1 LEU c 29 " pdb=" CD2 LEU c 29 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.27e+00 chirality pdb=" CB ILE G 676 " pdb=" CA ILE G 676 " pdb=" CG1 ILE G 676 " pdb=" CG2 ILE G 676 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" CA PRO G 606 " pdb=" N PRO G 606 " pdb=" C PRO G 606 " pdb=" CB PRO G 606 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 1.94e+00 ... (remaining 2582 not shown) Planarity restraints: 3186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR G 447 " 0.161 5.00e-02 4.00e+02 2.08e-01 6.91e+01 pdb=" N PRO G 448 " -0.357 5.00e-02 4.00e+02 pdb=" CA PRO G 448 " 0.108 5.00e-02 4.00e+02 pdb=" CD PRO G 448 " 0.088 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 283 " 0.092 5.00e-02 4.00e+02 1.37e-01 2.99e+01 pdb=" N PRO B 284 " -0.236 5.00e-02 4.00e+02 pdb=" CA PRO B 284 " 0.073 5.00e-02 4.00e+02 pdb=" CD PRO B 284 " 0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 166 " -0.069 5.00e-02 4.00e+02 1.03e-01 1.69e+01 pdb=" N PRO E 167 " 0.178 5.00e-02 4.00e+02 pdb=" CA PRO E 167 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO E 167 " -0.057 5.00e-02 4.00e+02 ... (remaining 3183 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 4779 2.81 - 3.33: 14187 3.33 - 3.86: 30074 3.86 - 4.38: 33436 4.38 - 4.90: 58224 Nonbonded interactions: 140700 Sorted by model distance: nonbonded pdb=" OG1 THR B 246 " pdb=" OE2 GLU H 81 " model vdw 2.290 2.440 nonbonded pdb=" OH TYR F 44 " pdb=" O SER F 47 " model vdw 2.293 2.440 nonbonded pdb=" O ALA G 449 " pdb=" OG1 THR G 453 " model vdw 2.300 2.440 nonbonded pdb=" O ASP G 241 " pdb=" OH TYR S 216 " model vdw 2.317 2.440 nonbonded pdb=" OG SER G 683 " pdb=" OE1 GLU G 685 " model vdw 2.320 2.440 ... (remaining 140695 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 'F' selection = chain 'I' } ncs_group { reference = chain 'G' selection = (chain 'S' and (resid 206 through 261 or resid 273 through 377 or resid 413 thro \ ugh 693)) } ncs_group { reference = chain 'H' selection = (chain 'c' and (resid 1 through 113 or resid 133 through 276)) } 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: 21.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 30.600 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 50.090 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.110 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.231 18051 Z= 0.323 Angle : 1.119 29.869 24469 Z= 0.595 Chirality : 0.054 0.362 2585 Planarity : 0.010 0.208 3186 Dihedral : 17.825 90.538 6707 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.23 % Favored : 95.73 % Rotamer: Outliers : 0.74 % Allowed : 28.51 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.59 % 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: -2.34 (0.16), residues: 2129 helix: -2.11 (0.17), residues: 526 sheet: -1.22 (0.26), residues: 380 loop : -1.37 (0.16), residues: 1223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 36 HIS 0.019 0.001 HIS F 77 PHE 0.035 0.002 PHE c 213 TYR 0.045 0.002 TYR F 44 ARG 0.024 0.001 ARG c 37 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 1894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 498 time to evaluate : 1.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.7571 (ttt180) cc_final: 0.7354 (ttt180) REVERT: E 97 MET cc_start: 0.6297 (tpp) cc_final: 0.5870 (ttm) REVERT: G 256 GLN cc_start: 0.8195 (mp10) cc_final: 0.7942 (mp-120) REVERT: G 341 LYS cc_start: 0.8343 (tttp) cc_final: 0.7684 (tttp) REVERT: G 675 GLU cc_start: 0.7317 (tm-30) cc_final: 0.7052 (tp30) REVERT: S 211 GLN cc_start: 0.8466 (mt0) cc_final: 0.8218 (mt0) REVERT: S 212 ASN cc_start: 0.8338 (m-40) cc_final: 0.8136 (m-40) REVERT: S 345 ASP cc_start: 0.7873 (m-30) cc_final: 0.7525 (m-30) REVERT: S 466 ASP cc_start: 0.7466 (t0) cc_final: 0.7123 (t0) REVERT: I 66 ARG cc_start: 0.7253 (ttm170) cc_final: 0.7002 (ttm-80) REVERT: I 75 LYS cc_start: 0.8197 (mtmm) cc_final: 0.7894 (mtmm) outliers start: 14 outliers final: 11 residues processed: 503 average time/residue: 0.3521 time to fit residues: 250.2463 Evaluate side-chains 490 residues out of total 1894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 479 time to evaluate : 1.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 225 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain G residue 470 ILE Chi-restraints excluded: chain H residue 271 ASP Chi-restraints excluded: chain c residue 23 ASP Chi-restraints excluded: chain c residue 214 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 179 optimal weight: 0.0570 chunk 161 optimal weight: 0.0070 chunk 89 optimal weight: 0.0070 chunk 55 optimal weight: 0.9980 chunk 108 optimal weight: 0.3980 chunk 86 optimal weight: 0.4980 chunk 166 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 124 optimal weight: 0.0030 chunk 193 optimal weight: 0.9990 overall best weight: 0.0944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 297 GLN E 87 HIS F 77 HIS F 119 ASN G 347 HIS H 257 ASN S 211 GLN S 481 ASN c 61 GLN c 67 GLN c 109 HIS I 145 GLN I 165 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.1039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 18051 Z= 0.156 Angle : 0.620 14.374 24469 Z= 0.320 Chirality : 0.042 0.193 2585 Planarity : 0.006 0.113 3186 Dihedral : 5.567 51.194 2423 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.48 % Favored : 96.43 % Rotamer: Outliers : 4.12 % Allowed : 26.29 % Favored : 69.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.59 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.17), residues: 2129 helix: -0.48 (0.21), residues: 537 sheet: -1.02 (0.26), residues: 384 loop : -1.08 (0.17), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 36 HIS 0.005 0.000 HIS c 109 PHE 0.010 0.001 PHE c 213 TYR 0.020 0.001 TYR B 234 ARG 0.008 0.000 ARG B 224 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 1894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 494 time to evaluate : 1.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 38 LEU cc_start: 0.8464 (mm) cc_final: 0.8245 (mt) REVERT: F 44 TYR cc_start: 0.7939 (t80) cc_final: 0.7298 (t80) REVERT: F 147 GLU cc_start: 0.6914 (tt0) cc_final: 0.6710 (tt0) REVERT: F 193 ARG cc_start: 0.7469 (ttt180) cc_final: 0.7168 (ttt180) REVERT: G 252 GLU cc_start: 0.7053 (tp30) cc_final: 0.6488 (tp30) REVERT: G 256 GLN cc_start: 0.8149 (OUTLIER) cc_final: 0.7764 (mm-40) REVERT: H 24 ARG cc_start: 0.8088 (mmt-90) cc_final: 0.7857 (mmt90) REVERT: H 51 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7809 (mt) REVERT: S 284 GLU cc_start: 0.7282 (mm-30) cc_final: 0.7016 (mm-30) REVERT: S 345 ASP cc_start: 0.7902 (m-30) cc_final: 0.7616 (m-30) REVERT: S 453 THR cc_start: 0.8214 (m) cc_final: 0.7994 (t) REVERT: S 466 ASP cc_start: 0.7481 (t0) cc_final: 0.7140 (t0) REVERT: S 667 TYR cc_start: 0.8250 (m-10) cc_final: 0.7919 (m-10) REVERT: S 687 GLU cc_start: 0.7517 (mt-10) cc_final: 0.7259 (mt-10) REVERT: c 59 ILE cc_start: 0.8907 (mm) cc_final: 0.8660 (mm) REVERT: I 75 LYS cc_start: 0.8200 (mtmm) cc_final: 0.7899 (mtmm) outliers start: 78 outliers final: 52 residues processed: 527 average time/residue: 0.3588 time to fit residues: 270.6252 Evaluate side-chains 534 residues out of total 1894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 480 time to evaluate : 1.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain E residue 5 MET Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 197 GLU Chi-restraints excluded: chain F residue 199 GLU Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 256 GLN Chi-restraints excluded: chain G residue 257 ASP Chi-restraints excluded: chain G residue 290 PHE Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 357 LYS Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain G residue 638 ASN Chi-restraints excluded: chain G residue 655 VAL Chi-restraints excluded: chain G residue 683 SER Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 79 CYS Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 185 SER Chi-restraints excluded: chain H residue 220 ASP Chi-restraints excluded: chain H residue 261 ILE Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain H residue 271 ASP Chi-restraints excluded: chain S residue 205 MET Chi-restraints excluded: chain S residue 251 ILE Chi-restraints excluded: chain S residue 470 ILE Chi-restraints excluded: chain S residue 692 MET Chi-restraints excluded: chain c residue 23 ASP Chi-restraints excluded: chain c residue 45 LEU Chi-restraints excluded: chain c residue 94 MET Chi-restraints excluded: chain c residue 178 LEU Chi-restraints excluded: chain c residue 214 LEU Chi-restraints excluded: chain c residue 220 ASP Chi-restraints excluded: chain c residue 261 ILE Chi-restraints excluded: chain c residue 267 GLU Chi-restraints excluded: chain c residue 271 ASP Chi-restraints excluded: chain I residue 62 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 107 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 160 optimal weight: 0.1980 chunk 131 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 193 optimal weight: 0.8980 chunk 209 optimal weight: 1.9990 chunk 172 optimal weight: 0.9980 chunk 192 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 155 optimal weight: 0.1980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 98 GLN G 256 GLN G 286 GLN H 61 GLN H 133 GLN H 229 GLN S 211 GLN S 350 GLN S 531 GLN S 651 HIS c 18 GLN c 269 ASN ** I 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 18051 Z= 0.333 Angle : 0.678 14.143 24469 Z= 0.348 Chirality : 0.045 0.202 2585 Planarity : 0.006 0.081 3186 Dihedral : 5.138 54.579 2407 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.90 % Favored : 96.01 % Rotamer: Outliers : 4.91 % Allowed : 25.13 % Favored : 69.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.54 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.18), residues: 2129 helix: 0.02 (0.21), residues: 552 sheet: -1.24 (0.24), residues: 443 loop : -0.84 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 36 HIS 0.010 0.001 HIS F 154 PHE 0.034 0.002 PHE F 82 TYR 0.018 0.002 TYR H 260 ARG 0.009 0.001 ARG G 442 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 1894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 508 time to evaluate : 1.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 262 ASN cc_start: 0.8446 (m-40) cc_final: 0.8115 (m110) REVERT: E 47 LEU cc_start: 0.7858 (tp) cc_final: 0.7595 (tp) REVERT: E 163 LEU cc_start: 0.7705 (mm) cc_final: 0.7484 (mm) REVERT: E 188 LEU cc_start: 0.7935 (tp) cc_final: 0.7732 (tp) REVERT: F 91 GLU cc_start: 0.7396 (mp0) cc_final: 0.6874 (mp0) REVERT: F 106 TYR cc_start: 0.8525 (m-80) cc_final: 0.7817 (m-80) REVERT: F 147 GLU cc_start: 0.7378 (tt0) cc_final: 0.7127 (tt0) REVERT: F 158 ARG cc_start: 0.8072 (ptp-170) cc_final: 0.7728 (ptp90) REVERT: F 193 ARG cc_start: 0.7527 (ttt180) cc_final: 0.7181 (ttt180) REVERT: G 281 GLU cc_start: 0.7363 (mt-10) cc_final: 0.7120 (mt-10) REVERT: G 314 VAL cc_start: 0.8031 (OUTLIER) cc_final: 0.7624 (t) REVERT: G 335 ARG cc_start: 0.8687 (tpp80) cc_final: 0.8314 (ttm-80) REVERT: G 451 ILE cc_start: 0.5397 (OUTLIER) cc_final: 0.5061 (mt) REVERT: G 626 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.7806 (mtm-85) REVERT: G 688 GLN cc_start: 0.7786 (pp30) cc_final: 0.7450 (pp30) REVERT: H 6 LEU cc_start: 0.7820 (mt) cc_final: 0.7555 (mp) REVERT: H 43 ARG cc_start: 0.8213 (ttp80) cc_final: 0.7925 (ttp80) REVERT: H 216 SER cc_start: 0.8546 (t) cc_final: 0.8129 (p) REVERT: S 280 TYR cc_start: 0.7912 (m-10) cc_final: 0.7570 (m-10) REVERT: S 284 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7473 (mm-30) REVERT: S 345 ASP cc_start: 0.7952 (m-30) cc_final: 0.7653 (m-30) REVERT: S 466 ASP cc_start: 0.7487 (t0) cc_final: 0.7171 (t0) REVERT: S 479 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7556 (tt0) REVERT: S 622 ILE cc_start: 0.8164 (mm) cc_final: 0.7682 (pt) REVERT: S 640 LYS cc_start: 0.7991 (mttm) cc_final: 0.7581 (mttm) REVERT: S 667 TYR cc_start: 0.8498 (m-10) cc_final: 0.7844 (m-80) REVERT: S 687 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7321 (mt-10) REVERT: I 75 LYS cc_start: 0.8361 (mtmm) cc_final: 0.8084 (mtmm) REVERT: I 183 HIS cc_start: 0.8571 (m-70) cc_final: 0.8369 (m90) outliers start: 93 outliers final: 59 residues processed: 545 average time/residue: 0.3403 time to fit residues: 264.1685 Evaluate side-chains 548 residues out of total 1894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 486 time to evaluate : 2.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 297 GLN Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 309 MET Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 246 ASP Chi-restraints excluded: chain G residue 286 GLN Chi-restraints excluded: chain G residue 290 PHE Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 357 LYS Chi-restraints excluded: chain G residue 432 VAL Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain G residue 451 ILE Chi-restraints excluded: chain G residue 523 GLU Chi-restraints excluded: chain G residue 546 VAL Chi-restraints excluded: chain G residue 592 LEU Chi-restraints excluded: chain G residue 626 ARG Chi-restraints excluded: chain G residue 638 ASN Chi-restraints excluded: chain G residue 655 VAL Chi-restraints excluded: chain G residue 683 SER Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain H residue 271 ASP Chi-restraints excluded: chain H residue 276 LEU Chi-restraints excluded: chain S residue 205 MET Chi-restraints excluded: chain S residue 251 ILE Chi-restraints excluded: chain S residue 277 LEU Chi-restraints excluded: chain S residue 427 LYS Chi-restraints excluded: chain S residue 526 ASP Chi-restraints excluded: chain S residue 610 THR Chi-restraints excluded: chain S residue 692 MET Chi-restraints excluded: chain c residue 23 ASP Chi-restraints excluded: chain c residue 143 ILE Chi-restraints excluded: chain c residue 178 LEU Chi-restraints excluded: chain c residue 214 LEU Chi-restraints excluded: chain c residue 220 ASP Chi-restraints excluded: chain c residue 261 ILE Chi-restraints excluded: chain c residue 267 GLU Chi-restraints excluded: chain c residue 271 ASP Chi-restraints excluded: chain I residue 49 GLU Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain I residue 136 LYS Chi-restraints excluded: chain I residue 180 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 191 optimal weight: 0.4980 chunk 145 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 92 optimal weight: 0.3980 chunk 130 optimal weight: 0.9980 chunk 194 optimal weight: 0.0970 chunk 205 optimal weight: 0.3980 chunk 101 optimal weight: 1.9990 chunk 184 optimal weight: 0.0980 chunk 55 optimal weight: 1.9990 overall best weight: 0.2978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 286 GLN H 61 GLN H 67 GLN H 229 GLN S 211 GLN S 651 HIS c 109 HIS ** I 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18051 Z= 0.205 Angle : 0.610 13.655 24469 Z= 0.310 Chirality : 0.043 0.168 2585 Planarity : 0.005 0.069 3186 Dihedral : 5.014 54.454 2407 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.80 % Favored : 96.15 % Rotamer: Outliers : 4.75 % Allowed : 25.87 % Favored : 69.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.54 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.18), residues: 2129 helix: 0.37 (0.22), residues: 554 sheet: -1.22 (0.24), residues: 433 loop : -0.68 (0.18), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 36 HIS 0.004 0.001 HIS F 154 PHE 0.019 0.001 PHE c 213 TYR 0.027 0.001 TYR F 20 ARG 0.010 0.001 ARG F 66 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 1894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 503 time to evaluate : 2.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 271 LYS cc_start: 0.8153 (ptmm) cc_final: 0.7881 (ttmm) REVERT: B 287 LYS cc_start: 0.8536 (mtmm) cc_final: 0.8130 (mtmp) REVERT: E 163 LEU cc_start: 0.7743 (mm) cc_final: 0.7500 (mm) REVERT: F 20 TYR cc_start: 0.7970 (t80) cc_final: 0.7616 (t80) REVERT: F 60 LYS cc_start: 0.8261 (mttm) cc_final: 0.8011 (mttt) REVERT: F 147 GLU cc_start: 0.7359 (tt0) cc_final: 0.7085 (tt0) REVERT: F 158 ARG cc_start: 0.8053 (ptp-170) cc_final: 0.7679 (ptp90) REVERT: F 193 ARG cc_start: 0.7504 (ttt180) cc_final: 0.7126 (ttt180) REVERT: G 252 GLU cc_start: 0.7380 (tp30) cc_final: 0.6660 (tp30) REVERT: G 281 GLU cc_start: 0.7417 (mt-10) cc_final: 0.7095 (mt-10) REVERT: G 320 TYR cc_start: 0.8217 (m-10) cc_final: 0.7563 (m-10) REVERT: G 326 VAL cc_start: 0.8113 (OUTLIER) cc_final: 0.7799 (p) REVERT: G 335 ARG cc_start: 0.8697 (tpp80) cc_final: 0.8365 (ttm-80) REVERT: G 626 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.7637 (mtm-85) REVERT: G 688 GLN cc_start: 0.7800 (pp30) cc_final: 0.7491 (tm-30) REVERT: H 6 LEU cc_start: 0.7849 (mt) cc_final: 0.7513 (mp) REVERT: H 216 SER cc_start: 0.8541 (t) cc_final: 0.8083 (p) REVERT: S 281 GLU cc_start: 0.7313 (mm-30) cc_final: 0.7093 (mm-30) REVERT: S 284 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7383 (mm-30) REVERT: S 330 THR cc_start: 0.8032 (p) cc_final: 0.7665 (m) REVERT: S 345 ASP cc_start: 0.7980 (m-30) cc_final: 0.7688 (m-30) REVERT: S 466 ASP cc_start: 0.7453 (t0) cc_final: 0.7141 (t0) REVERT: S 622 ILE cc_start: 0.8169 (mm) cc_final: 0.7712 (pt) REVERT: S 640 LYS cc_start: 0.7959 (mttm) cc_final: 0.7547 (mttm) REVERT: S 667 TYR cc_start: 0.8510 (m-10) cc_final: 0.7948 (m-80) REVERT: S 687 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7261 (mt-10) REVERT: c 24 ARG cc_start: 0.8288 (mmp80) cc_final: 0.8079 (mpt180) REVERT: c 29 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.8034 (mm) REVERT: c 43 ARG cc_start: 0.8388 (ptt-90) cc_final: 0.8125 (ptt-90) REVERT: I 75 LYS cc_start: 0.8337 (mtmm) cc_final: 0.8056 (mtmm) REVERT: I 183 HIS cc_start: 0.8586 (m-70) cc_final: 0.8368 (m90) outliers start: 90 outliers final: 68 residues processed: 546 average time/residue: 0.3462 time to fit residues: 268.2159 Evaluate side-chains 580 residues out of total 1894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 509 time to evaluate : 1.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 297 GLN Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 309 MET Chi-restraints excluded: chain D residue 303 MET Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 199 GLU Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 257 ASP Chi-restraints excluded: chain G residue 286 GLN Chi-restraints excluded: chain G residue 290 PHE Chi-restraints excluded: chain G residue 326 VAL Chi-restraints excluded: chain G residue 357 LYS Chi-restraints excluded: chain G residue 433 CYS Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain G residue 592 LEU Chi-restraints excluded: chain G residue 626 ARG Chi-restraints excluded: chain G residue 638 ASN Chi-restraints excluded: chain G residue 655 VAL Chi-restraints excluded: chain G residue 683 SER Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 261 ILE Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain H residue 271 ASP Chi-restraints excluded: chain H residue 276 LEU Chi-restraints excluded: chain S residue 205 MET Chi-restraints excluded: chain S residue 251 ILE Chi-restraints excluded: chain S residue 277 LEU Chi-restraints excluded: chain S residue 432 VAL Chi-restraints excluded: chain S residue 447 THR Chi-restraints excluded: chain S residue 526 ASP Chi-restraints excluded: chain S residue 610 THR Chi-restraints excluded: chain S residue 692 MET Chi-restraints excluded: chain c residue 23 ASP Chi-restraints excluded: chain c residue 29 LEU Chi-restraints excluded: chain c residue 68 LEU Chi-restraints excluded: chain c residue 94 MET Chi-restraints excluded: chain c residue 99 VAL Chi-restraints excluded: chain c residue 143 ILE Chi-restraints excluded: chain c residue 178 LEU Chi-restraints excluded: chain c residue 181 VAL Chi-restraints excluded: chain c residue 214 LEU Chi-restraints excluded: chain c residue 220 ASP Chi-restraints excluded: chain c residue 229 GLN Chi-restraints excluded: chain c residue 251 HIS Chi-restraints excluded: chain c residue 261 ILE Chi-restraints excluded: chain c residue 265 THR Chi-restraints excluded: chain c residue 267 GLU Chi-restraints excluded: chain c residue 271 ASP Chi-restraints excluded: chain I residue 49 GLU Chi-restraints excluded: chain I residue 136 LYS Chi-restraints excluded: chain I residue 180 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 171 optimal weight: 0.9990 chunk 116 optimal weight: 0.6980 chunk 2 optimal weight: 0.0000 chunk 153 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 175 optimal weight: 0.5980 chunk 142 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 184 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 162 ASN F 77 HIS ** G 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 GLN H 229 GLN S 651 HIS ** c 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 113 HIS ** I 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 18051 Z= 0.296 Angle : 0.646 13.796 24469 Z= 0.328 Chirality : 0.044 0.174 2585 Planarity : 0.005 0.070 3186 Dihedral : 5.093 55.584 2407 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.09 % Favored : 95.82 % Rotamer: Outliers : 6.07 % Allowed : 25.03 % Favored : 68.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.54 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.18), residues: 2129 helix: 0.51 (0.22), residues: 560 sheet: -1.21 (0.25), residues: 427 loop : -0.68 (0.18), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 36 HIS 0.005 0.001 HIS F 77 PHE 0.018 0.001 PHE c 213 TYR 0.019 0.002 TYR F 20 ARG 0.011 0.001 ARG F 66 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 1894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 524 time to evaluate : 1.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 242 LEU cc_start: 0.6299 (mt) cc_final: 0.5994 (mt) REVERT: B 271 LYS cc_start: 0.8453 (ptmm) cc_final: 0.8237 (ttmm) REVERT: B 287 LYS cc_start: 0.8637 (mtmm) cc_final: 0.8331 (mttp) REVERT: C 311 ARG cc_start: 0.6742 (OUTLIER) cc_final: 0.5694 (mtt90) REVERT: D 300 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7467 (mt-10) REVERT: E 163 LEU cc_start: 0.7877 (mm) cc_final: 0.7616 (mm) REVERT: F 20 TYR cc_start: 0.8020 (t80) cc_final: 0.7655 (t80) REVERT: F 38 LEU cc_start: 0.8891 (mm) cc_final: 0.8685 (mt) REVERT: F 60 LYS cc_start: 0.8451 (mttm) cc_final: 0.8043 (mttt) REVERT: F 66 ARG cc_start: 0.8381 (mtp-110) cc_final: 0.8180 (ttm110) REVERT: F 97 ASP cc_start: 0.7211 (OUTLIER) cc_final: 0.6847 (t70) REVERT: F 147 GLU cc_start: 0.7460 (tt0) cc_final: 0.7222 (tt0) REVERT: G 252 GLU cc_start: 0.7475 (tp30) cc_final: 0.6799 (tp30) REVERT: G 281 GLU cc_start: 0.7425 (mt-10) cc_final: 0.7121 (mt-10) REVERT: G 320 TYR cc_start: 0.8341 (m-10) cc_final: 0.7699 (m-10) REVERT: G 326 VAL cc_start: 0.8268 (t) cc_final: 0.8048 (p) REVERT: G 617 ILE cc_start: 0.8694 (mt) cc_final: 0.8122 (tp) REVERT: G 626 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.7769 (mtm-85) REVERT: G 688 GLN cc_start: 0.7843 (pp30) cc_final: 0.7466 (pp30) REVERT: H 6 LEU cc_start: 0.7938 (mt) cc_final: 0.7565 (mp) REVERT: S 242 GLU cc_start: 0.6770 (pp20) cc_final: 0.6522 (pp20) REVERT: S 282 ILE cc_start: 0.8056 (pt) cc_final: 0.7848 (pt) REVERT: S 284 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7367 (mm-30) REVERT: S 330 THR cc_start: 0.8144 (p) cc_final: 0.7821 (m) REVERT: S 470 ILE cc_start: 0.7787 (OUTLIER) cc_final: 0.7566 (mm) REVERT: S 479 GLU cc_start: 0.7950 (tt0) cc_final: 0.7386 (tt0) REVERT: S 484 ARG cc_start: 0.9010 (OUTLIER) cc_final: 0.7976 (mmm160) REVERT: S 587 GLU cc_start: 0.7937 (pt0) cc_final: 0.7602 (pt0) REVERT: S 622 ILE cc_start: 0.8215 (mm) cc_final: 0.7851 (pt) REVERT: S 640 LYS cc_start: 0.8038 (mttm) cc_final: 0.7593 (mttm) REVERT: S 667 TYR cc_start: 0.8533 (m-10) cc_final: 0.8267 (m-80) REVERT: c 29 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8122 (mm) REVERT: c 136 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.7100 (tp30) REVERT: I 45 GLU cc_start: 0.6832 (tt0) cc_final: 0.6530 (mt-10) REVERT: I 75 LYS cc_start: 0.8373 (mtmm) cc_final: 0.8105 (mtmm) REVERT: I 183 HIS cc_start: 0.8668 (m-70) cc_final: 0.8446 (m90) outliers start: 115 outliers final: 75 residues processed: 577 average time/residue: 0.3544 time to fit residues: 290.4683 Evaluate side-chains 598 residues out of total 1894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 515 time to evaluate : 1.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 297 GLN Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain C residue 309 MET Chi-restraints excluded: chain C residue 311 ARG Chi-restraints excluded: chain D residue 300 GLU Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 199 GLU Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 246 ASP Chi-restraints excluded: chain G residue 257 ASP Chi-restraints excluded: chain G residue 286 GLN Chi-restraints excluded: chain G residue 290 PHE Chi-restraints excluded: chain G residue 357 LYS Chi-restraints excluded: chain G residue 371 GLU Chi-restraints excluded: chain G residue 432 VAL Chi-restraints excluded: chain G residue 433 CYS Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain G residue 592 LEU Chi-restraints excluded: chain G residue 626 ARG Chi-restraints excluded: chain G residue 638 ASN Chi-restraints excluded: chain G residue 655 VAL Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 261 ILE Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain H residue 271 ASP Chi-restraints excluded: chain H residue 276 LEU Chi-restraints excluded: chain S residue 205 MET Chi-restraints excluded: chain S residue 251 ILE Chi-restraints excluded: chain S residue 277 LEU Chi-restraints excluded: chain S residue 362 GLU Chi-restraints excluded: chain S residue 432 VAL Chi-restraints excluded: chain S residue 447 THR Chi-restraints excluded: chain S residue 457 ILE Chi-restraints excluded: chain S residue 470 ILE Chi-restraints excluded: chain S residue 484 ARG Chi-restraints excluded: chain S residue 556 ASN Chi-restraints excluded: chain S residue 610 THR Chi-restraints excluded: chain S residue 692 MET Chi-restraints excluded: chain c residue 23 ASP Chi-restraints excluded: chain c residue 29 LEU Chi-restraints excluded: chain c residue 94 MET Chi-restraints excluded: chain c residue 99 VAL Chi-restraints excluded: chain c residue 136 GLU Chi-restraints excluded: chain c residue 178 LEU Chi-restraints excluded: chain c residue 181 VAL Chi-restraints excluded: chain c residue 214 LEU Chi-restraints excluded: chain c residue 220 ASP Chi-restraints excluded: chain c residue 229 GLN Chi-restraints excluded: chain c residue 251 HIS Chi-restraints excluded: chain c residue 257 ASN Chi-restraints excluded: chain c residue 261 ILE Chi-restraints excluded: chain c residue 267 GLU Chi-restraints excluded: chain c residue 271 ASP Chi-restraints excluded: chain I residue 29 GLU Chi-restraints excluded: chain I residue 49 GLU Chi-restraints excluded: chain I residue 120 HIS Chi-restraints excluded: chain I residue 136 LYS Chi-restraints excluded: chain I residue 180 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 69 optimal weight: 0.8980 chunk 185 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 120 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 206 optimal weight: 0.0770 chunk 171 optimal weight: 0.6980 chunk 95 optimal weight: 0.7980 chunk 17 optimal weight: 0.2980 chunk 68 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 48 HIS F 77 HIS F 143 HIS ** G 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 229 GLN S 651 HIS c 109 HIS ** I 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18051 Z= 0.283 Angle : 0.648 13.693 24469 Z= 0.328 Chirality : 0.044 0.185 2585 Planarity : 0.005 0.070 3186 Dihedral : 5.142 58.897 2406 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.23 % Favored : 95.68 % Rotamer: Outliers : 5.54 % Allowed : 26.35 % Favored : 68.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.54 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.18), residues: 2129 helix: 0.52 (0.22), residues: 562 sheet: -1.28 (0.25), residues: 422 loop : -0.63 (0.18), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 36 HIS 0.006 0.001 HIS c 109 PHE 0.021 0.001 PHE c 213 TYR 0.021 0.002 TYR B 234 ARG 0.008 0.001 ARG F 66 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 1894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 527 time to evaluate : 1.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 210 ASP cc_start: 0.8185 (t0) cc_final: 0.7867 (t0) REVERT: B 214 ILE cc_start: 0.7528 (mm) cc_final: 0.7117 (tp) REVERT: B 234 TYR cc_start: 0.8176 (t80) cc_final: 0.7824 (t80) REVERT: C 311 ARG cc_start: 0.6680 (OUTLIER) cc_final: 0.5698 (ttt90) REVERT: E 95 GLU cc_start: 0.7233 (mt-10) cc_final: 0.6979 (mt-10) REVERT: E 163 LEU cc_start: 0.7965 (mm) cc_final: 0.7704 (mm) REVERT: F 20 TYR cc_start: 0.8043 (t80) cc_final: 0.7617 (t80) REVERT: F 60 LYS cc_start: 0.8543 (mttm) cc_final: 0.8260 (mttt) REVERT: F 97 ASP cc_start: 0.7215 (OUTLIER) cc_final: 0.6870 (t70) REVERT: F 147 GLU cc_start: 0.7458 (tt0) cc_final: 0.7250 (tt0) REVERT: G 281 GLU cc_start: 0.7411 (mt-10) cc_final: 0.7115 (mt-10) REVERT: G 284 GLU cc_start: 0.7595 (mm-30) cc_final: 0.7346 (mm-30) REVERT: G 320 TYR cc_start: 0.8403 (m-10) cc_final: 0.7758 (m-10) REVERT: G 362 GLU cc_start: 0.7547 (pm20) cc_final: 0.7293 (pm20) REVERT: G 466 ASP cc_start: 0.7720 (t0) cc_final: 0.7391 (t0) REVERT: G 503 GLN cc_start: 0.8078 (mt0) cc_final: 0.7733 (mp10) REVERT: G 617 ILE cc_start: 0.8713 (mt) cc_final: 0.7816 (tp) REVERT: G 619 GLN cc_start: 0.8341 (pm20) cc_final: 0.7839 (pm20) REVERT: G 626 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.7743 (mtm-85) REVERT: G 688 GLN cc_start: 0.7873 (pp30) cc_final: 0.7536 (tm-30) REVERT: H 6 LEU cc_start: 0.7958 (mt) cc_final: 0.7665 (mp) REVERT: H 25 ARG cc_start: 0.7817 (mtt90) cc_final: 0.7614 (mtt90) REVERT: H 57 TYR cc_start: 0.8247 (m-80) cc_final: 0.8036 (m-80) REVERT: S 238 LYS cc_start: 0.7972 (mtpp) cc_final: 0.7700 (ttpp) REVERT: S 242 GLU cc_start: 0.6785 (pp20) cc_final: 0.6529 (pp20) REVERT: S 282 ILE cc_start: 0.8117 (pt) cc_final: 0.7891 (pt) REVERT: S 284 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7387 (mm-30) REVERT: S 330 THR cc_start: 0.8192 (p) cc_final: 0.7926 (m) REVERT: S 470 ILE cc_start: 0.7925 (OUTLIER) cc_final: 0.7707 (mm) REVERT: S 479 GLU cc_start: 0.7994 (tt0) cc_final: 0.7496 (tt0) REVERT: S 484 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.7917 (mmm160) REVERT: S 587 GLU cc_start: 0.8037 (pt0) cc_final: 0.7724 (pt0) REVERT: S 622 ILE cc_start: 0.8202 (mm) cc_final: 0.7889 (pt) REVERT: S 641 LYS cc_start: 0.8527 (pttt) cc_final: 0.8147 (ptmm) REVERT: S 667 TYR cc_start: 0.8554 (m-10) cc_final: 0.8276 (m-80) REVERT: S 678 GLU cc_start: 0.7765 (mp0) cc_final: 0.7180 (mt-10) REVERT: c 24 ARG cc_start: 0.8290 (mmp80) cc_final: 0.8071 (mpt180) REVERT: c 29 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8173 (mm) REVERT: c 37 ARG cc_start: 0.8314 (ttp80) cc_final: 0.7943 (tmm-80) REVERT: c 136 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.7094 (tp30) REVERT: I 45 GLU cc_start: 0.6843 (tt0) cc_final: 0.6568 (mt-10) REVERT: I 75 LYS cc_start: 0.8372 (mtmm) cc_final: 0.8111 (mtmm) REVERT: I 76 LYS cc_start: 0.8740 (mttp) cc_final: 0.8321 (mttp) REVERT: I 167 ASN cc_start: 0.8081 (p0) cc_final: 0.7810 (p0) REVERT: I 183 HIS cc_start: 0.8697 (m-70) cc_final: 0.8487 (m90) REVERT: I 191 THR cc_start: 0.8856 (m) cc_final: 0.8384 (p) outliers start: 105 outliers final: 76 residues processed: 573 average time/residue: 0.3557 time to fit residues: 285.2887 Evaluate side-chains 597 residues out of total 1894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 514 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 250 LYS Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 297 GLN Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain C residue 309 MET Chi-restraints excluded: chain C residue 311 ARG Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 199 GLU Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 246 ASP Chi-restraints excluded: chain G residue 257 ASP Chi-restraints excluded: chain G residue 286 GLN Chi-restraints excluded: chain G residue 290 PHE Chi-restraints excluded: chain G residue 357 LYS Chi-restraints excluded: chain G residue 432 VAL Chi-restraints excluded: chain G residue 433 CYS Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain G residue 455 ARG Chi-restraints excluded: chain G residue 519 ASP Chi-restraints excluded: chain G residue 626 ARG Chi-restraints excluded: chain G residue 638 ASN Chi-restraints excluded: chain G residue 655 VAL Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 92 MET Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 243 LEU Chi-restraints excluded: chain H residue 261 ILE Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain H residue 271 ASP Chi-restraints excluded: chain H residue 276 LEU Chi-restraints excluded: chain S residue 205 MET Chi-restraints excluded: chain S residue 251 ILE Chi-restraints excluded: chain S residue 277 LEU Chi-restraints excluded: chain S residue 362 GLU Chi-restraints excluded: chain S residue 432 VAL Chi-restraints excluded: chain S residue 447 THR Chi-restraints excluded: chain S residue 470 ILE Chi-restraints excluded: chain S residue 484 ARG Chi-restraints excluded: chain S residue 556 ASN Chi-restraints excluded: chain S residue 610 THR Chi-restraints excluded: chain S residue 692 MET Chi-restraints excluded: chain c residue 23 ASP Chi-restraints excluded: chain c residue 29 LEU Chi-restraints excluded: chain c residue 54 VAL Chi-restraints excluded: chain c residue 94 MET Chi-restraints excluded: chain c residue 99 VAL Chi-restraints excluded: chain c residue 136 GLU Chi-restraints excluded: chain c residue 138 THR Chi-restraints excluded: chain c residue 178 LEU Chi-restraints excluded: chain c residue 181 VAL Chi-restraints excluded: chain c residue 214 LEU Chi-restraints excluded: chain c residue 220 ASP Chi-restraints excluded: chain c residue 251 HIS Chi-restraints excluded: chain c residue 257 ASN Chi-restraints excluded: chain c residue 261 ILE Chi-restraints excluded: chain c residue 267 GLU Chi-restraints excluded: chain I residue 29 GLU Chi-restraints excluded: chain I residue 120 HIS Chi-restraints excluded: chain I residue 136 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 198 optimal weight: 0.9990 chunk 23 optimal weight: 0.0370 chunk 117 optimal weight: 0.3980 chunk 150 optimal weight: 0.9980 chunk 116 optimal weight: 0.7980 chunk 173 optimal weight: 0.5980 chunk 115 optimal weight: 0.9980 chunk 205 optimal weight: 0.7980 chunk 128 optimal weight: 1.9990 chunk 125 optimal weight: 0.5980 chunk 94 optimal weight: 0.9980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 48 HIS F 77 HIS ** G 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 229 GLN S 651 HIS c 18 GLN c 109 HIS I 56 GLN ** I 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 18051 Z= 0.292 Angle : 0.664 13.869 24469 Z= 0.335 Chirality : 0.044 0.222 2585 Planarity : 0.005 0.069 3186 Dihedral : 5.133 58.022 2406 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.46 % Favored : 95.44 % Rotamer: Outliers : 5.49 % Allowed : 26.45 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.54 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.18), residues: 2129 helix: 0.51 (0.22), residues: 563 sheet: -1.34 (0.25), residues: 423 loop : -0.64 (0.18), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 36 HIS 0.006 0.001 HIS c 109 PHE 0.020 0.001 PHE c 213 TYR 0.019 0.002 TYR B 234 ARG 0.010 0.001 ARG F 66 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 1894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 532 time to evaluate : 1.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 214 ILE cc_start: 0.7618 (mm) cc_final: 0.7198 (tp) REVERT: B 224 ARG cc_start: 0.7434 (tmm-80) cc_final: 0.7169 (tmm-80) REVERT: B 242 LEU cc_start: 0.6304 (mt) cc_final: 0.6020 (mt) REVERT: C 311 ARG cc_start: 0.6732 (OUTLIER) cc_final: 0.5764 (mtt90) REVERT: D 296 MET cc_start: 0.8701 (mmm) cc_final: 0.8303 (mmm) REVERT: E 95 GLU cc_start: 0.7261 (mt-10) cc_final: 0.7009 (mt-10) REVERT: E 163 LEU cc_start: 0.8005 (mm) cc_final: 0.7751 (mm) REVERT: F 20 TYR cc_start: 0.8069 (t80) cc_final: 0.7650 (t80) REVERT: F 60 LYS cc_start: 0.8600 (mttm) cc_final: 0.8282 (mttt) REVERT: G 281 GLU cc_start: 0.7390 (mt-10) cc_final: 0.7104 (mt-10) REVERT: G 284 GLU cc_start: 0.7612 (mm-30) cc_final: 0.7335 (mm-30) REVERT: G 320 TYR cc_start: 0.8459 (m-10) cc_final: 0.7792 (m-10) REVERT: G 438 ARG cc_start: 0.8108 (mmt90) cc_final: 0.7893 (mtt90) REVERT: G 466 ASP cc_start: 0.7755 (t0) cc_final: 0.7405 (t0) REVERT: G 617 ILE cc_start: 0.8673 (mt) cc_final: 0.8098 (tp) REVERT: G 626 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.7843 (mtm-85) REVERT: G 688 GLN cc_start: 0.7868 (pp30) cc_final: 0.7611 (pp30) REVERT: H 6 LEU cc_start: 0.7979 (mt) cc_final: 0.7635 (mp) REVERT: H 23 ASP cc_start: 0.7232 (OUTLIER) cc_final: 0.6992 (m-30) REVERT: S 238 LYS cc_start: 0.7970 (mtpp) cc_final: 0.7702 (ttpp) REVERT: S 282 ILE cc_start: 0.8158 (pt) cc_final: 0.7945 (pt) REVERT: S 284 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7368 (mm-30) REVERT: S 330 THR cc_start: 0.8221 (p) cc_final: 0.7958 (m) REVERT: S 470 ILE cc_start: 0.8020 (OUTLIER) cc_final: 0.7793 (mm) REVERT: S 479 GLU cc_start: 0.8004 (tt0) cc_final: 0.7522 (tt0) REVERT: S 484 ARG cc_start: 0.8992 (OUTLIER) cc_final: 0.7845 (mmm160) REVERT: S 587 GLU cc_start: 0.8085 (pt0) cc_final: 0.7798 (pt0) REVERT: S 622 ILE cc_start: 0.8200 (mm) cc_final: 0.7901 (pt) REVERT: S 641 LYS cc_start: 0.8534 (pttt) cc_final: 0.8162 (ptmm) REVERT: S 667 TYR cc_start: 0.8554 (m-10) cc_final: 0.8252 (m-80) REVERT: S 678 GLU cc_start: 0.7831 (mp0) cc_final: 0.7282 (mt-10) REVERT: c 24 ARG cc_start: 0.8271 (mmp80) cc_final: 0.8056 (mpt180) REVERT: c 29 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8201 (mm) REVERT: c 37 ARG cc_start: 0.8348 (ttp80) cc_final: 0.7972 (tmm-80) REVERT: c 136 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.7099 (tp30) REVERT: I 45 GLU cc_start: 0.6872 (tt0) cc_final: 0.6554 (mt-10) REVERT: I 76 LYS cc_start: 0.8769 (mttp) cc_final: 0.8365 (mttp) REVERT: I 167 ASN cc_start: 0.8057 (p0) cc_final: 0.7763 (p0) REVERT: I 183 HIS cc_start: 0.8722 (m-70) cc_final: 0.8492 (m90) REVERT: I 191 THR cc_start: 0.8864 (m) cc_final: 0.8340 (p) outliers start: 104 outliers final: 78 residues processed: 577 average time/residue: 0.3580 time to fit residues: 291.2790 Evaluate side-chains 601 residues out of total 1894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 516 time to evaluate : 2.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 250 LYS Chi-restraints excluded: chain B residue 263 ASP Chi-restraints excluded: chain B residue 297 GLN Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain C residue 309 MET Chi-restraints excluded: chain C residue 311 ARG Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 199 GLU Chi-restraints excluded: chain G residue 234 LYS Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 246 ASP Chi-restraints excluded: chain G residue 286 GLN Chi-restraints excluded: chain G residue 290 PHE Chi-restraints excluded: chain G residue 357 LYS Chi-restraints excluded: chain G residue 432 VAL Chi-restraints excluded: chain G residue 433 CYS Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain G residue 455 ARG Chi-restraints excluded: chain G residue 519 ASP Chi-restraints excluded: chain G residue 626 ARG Chi-restraints excluded: chain G residue 638 ASN Chi-restraints excluded: chain G residue 655 VAL Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 167 THR Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 261 ILE Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain H residue 271 ASP Chi-restraints excluded: chain H residue 276 LEU Chi-restraints excluded: chain S residue 277 LEU Chi-restraints excluded: chain S residue 432 VAL Chi-restraints excluded: chain S residue 447 THR Chi-restraints excluded: chain S residue 470 ILE Chi-restraints excluded: chain S residue 484 ARG Chi-restraints excluded: chain S residue 533 ILE Chi-restraints excluded: chain S residue 556 ASN Chi-restraints excluded: chain S residue 610 THR Chi-restraints excluded: chain S residue 692 MET Chi-restraints excluded: chain c residue 23 ASP Chi-restraints excluded: chain c residue 29 LEU Chi-restraints excluded: chain c residue 54 VAL Chi-restraints excluded: chain c residue 94 MET Chi-restraints excluded: chain c residue 99 VAL Chi-restraints excluded: chain c residue 136 GLU Chi-restraints excluded: chain c residue 138 THR Chi-restraints excluded: chain c residue 143 ILE Chi-restraints excluded: chain c residue 178 LEU Chi-restraints excluded: chain c residue 181 VAL Chi-restraints excluded: chain c residue 214 LEU Chi-restraints excluded: chain c residue 223 ARG Chi-restraints excluded: chain c residue 251 HIS Chi-restraints excluded: chain c residue 257 ASN Chi-restraints excluded: chain c residue 261 ILE Chi-restraints excluded: chain c residue 263 VAL Chi-restraints excluded: chain c residue 267 GLU Chi-restraints excluded: chain I residue 29 GLU Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain I residue 120 HIS Chi-restraints excluded: chain I residue 136 LYS Chi-restraints excluded: chain I residue 180 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 127 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 122 optimal weight: 0.3980 chunk 61 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 130 optimal weight: 0.1980 chunk 139 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 161 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 48 HIS F 77 HIS ** G 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 229 GLN S 651 HIS c 109 HIS ** I 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 18051 Z= 0.300 Angle : 0.673 14.395 24469 Z= 0.340 Chirality : 0.045 0.206 2585 Planarity : 0.005 0.068 3186 Dihedral : 5.194 59.616 2406 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.56 % Favored : 95.35 % Rotamer: Outliers : 5.39 % Allowed : 26.87 % Favored : 67.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.50 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.18), residues: 2129 helix: 0.54 (0.22), residues: 561 sheet: -1.31 (0.25), residues: 418 loop : -0.65 (0.18), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 36 HIS 0.007 0.001 HIS c 109 PHE 0.023 0.001 PHE c 213 TYR 0.018 0.002 TYR I 48 ARG 0.011 0.001 ARG H 40 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 1894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 518 time to evaluate : 1.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 214 ILE cc_start: 0.7700 (mm) cc_final: 0.7258 (tp) REVERT: B 224 ARG cc_start: 0.7458 (tmm-80) cc_final: 0.7187 (tmm-80) REVERT: B 242 LEU cc_start: 0.6295 (mt) cc_final: 0.5998 (mt) REVERT: B 265 VAL cc_start: 0.8910 (t) cc_final: 0.8600 (m) REVERT: C 311 ARG cc_start: 0.6719 (OUTLIER) cc_final: 0.5821 (ttt90) REVERT: E 95 GLU cc_start: 0.7240 (mt-10) cc_final: 0.6984 (mt-10) REVERT: E 136 GLU cc_start: 0.7746 (tt0) cc_final: 0.7434 (tt0) REVERT: E 161 ILE cc_start: 0.8242 (mt) cc_final: 0.7975 (mm) REVERT: E 163 LEU cc_start: 0.8075 (mm) cc_final: 0.7824 (mm) REVERT: F 20 TYR cc_start: 0.8077 (t80) cc_final: 0.7657 (t80) REVERT: F 60 LYS cc_start: 0.8626 (mttm) cc_final: 0.8285 (mttt) REVERT: F 97 ASP cc_start: 0.7234 (OUTLIER) cc_final: 0.6886 (t70) REVERT: F 147 GLU cc_start: 0.7406 (tt0) cc_final: 0.7151 (tt0) REVERT: G 281 GLU cc_start: 0.7303 (mt-10) cc_final: 0.7066 (mt-10) REVERT: G 284 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7374 (mm-30) REVERT: G 335 ARG cc_start: 0.8616 (tpp80) cc_final: 0.8380 (ttm-80) REVERT: G 451 ILE cc_start: 0.5987 (OUTLIER) cc_final: 0.5655 (mt) REVERT: G 466 ASP cc_start: 0.7787 (t0) cc_final: 0.7447 (t0) REVERT: G 479 GLU cc_start: 0.8064 (tt0) cc_final: 0.7864 (tt0) REVERT: G 617 ILE cc_start: 0.8676 (mt) cc_final: 0.8103 (tp) REVERT: G 626 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.7868 (mtm-85) REVERT: G 669 GLU cc_start: 0.7695 (pm20) cc_final: 0.7464 (mp0) REVERT: G 688 GLN cc_start: 0.7885 (pp30) cc_final: 0.7667 (pp30) REVERT: H 6 LEU cc_start: 0.8031 (mt) cc_final: 0.7544 (mp) REVERT: H 23 ASP cc_start: 0.7297 (OUTLIER) cc_final: 0.6997 (m-30) REVERT: H 66 ASP cc_start: 0.8394 (t0) cc_final: 0.8135 (t0) REVERT: H 91 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7504 (mp0) REVERT: H 156 ARG cc_start: 0.7999 (mmm-85) cc_final: 0.7793 (mmm160) REVERT: S 238 LYS cc_start: 0.7929 (mtpp) cc_final: 0.7656 (ttpp) REVERT: S 282 ILE cc_start: 0.8169 (pt) cc_final: 0.7959 (pt) REVERT: S 284 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7377 (mm-30) REVERT: S 330 THR cc_start: 0.8206 (p) cc_final: 0.7979 (m) REVERT: S 470 ILE cc_start: 0.8060 (OUTLIER) cc_final: 0.7850 (mm) REVERT: S 479 GLU cc_start: 0.8010 (tt0) cc_final: 0.7545 (tt0) REVERT: S 587 GLU cc_start: 0.8143 (pt0) cc_final: 0.7858 (pt0) REVERT: S 622 ILE cc_start: 0.8232 (mm) cc_final: 0.7974 (pt) REVERT: S 641 LYS cc_start: 0.8549 (pttt) cc_final: 0.8155 (ptmm) REVERT: S 667 TYR cc_start: 0.8555 (m-10) cc_final: 0.8246 (m-80) REVERT: S 678 GLU cc_start: 0.7743 (mp0) cc_final: 0.7487 (mp0) REVERT: c 29 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8156 (mm) REVERT: c 37 ARG cc_start: 0.8376 (ttp80) cc_final: 0.8024 (tmm-80) REVERT: c 110 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.7020 (mp0) REVERT: c 136 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.7109 (tp30) REVERT: I 45 GLU cc_start: 0.6844 (tt0) cc_final: 0.6556 (mt-10) REVERT: I 167 ASN cc_start: 0.8069 (p0) cc_final: 0.7742 (p0) REVERT: I 183 HIS cc_start: 0.8737 (m-70) cc_final: 0.8498 (m90) REVERT: I 191 THR cc_start: 0.8815 (m) cc_final: 0.8378 (p) outliers start: 102 outliers final: 80 residues processed: 566 average time/residue: 0.3494 time to fit residues: 279.1151 Evaluate side-chains 591 residues out of total 1894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 502 time to evaluate : 1.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 250 LYS Chi-restraints excluded: chain B residue 297 GLN Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain C residue 309 MET Chi-restraints excluded: chain C residue 311 ARG Chi-restraints excluded: chain D residue 303 MET Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 199 GLU Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 246 ASP Chi-restraints excluded: chain G residue 249 ASP Chi-restraints excluded: chain G residue 257 ASP Chi-restraints excluded: chain G residue 286 GLN Chi-restraints excluded: chain G residue 290 PHE Chi-restraints excluded: chain G residue 357 LYS Chi-restraints excluded: chain G residue 432 VAL Chi-restraints excluded: chain G residue 433 CYS Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain G residue 451 ILE Chi-restraints excluded: chain G residue 455 ARG Chi-restraints excluded: chain G residue 519 ASP Chi-restraints excluded: chain G residue 626 ARG Chi-restraints excluded: chain G residue 638 ASN Chi-restraints excluded: chain G residue 655 VAL Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 261 ILE Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain H residue 271 ASP Chi-restraints excluded: chain H residue 276 LEU Chi-restraints excluded: chain S residue 277 LEU Chi-restraints excluded: chain S residue 432 VAL Chi-restraints excluded: chain S residue 447 THR Chi-restraints excluded: chain S residue 470 ILE Chi-restraints excluded: chain S residue 484 ARG Chi-restraints excluded: chain S residue 533 ILE Chi-restraints excluded: chain S residue 556 ASN Chi-restraints excluded: chain S residue 610 THR Chi-restraints excluded: chain S residue 692 MET Chi-restraints excluded: chain c residue 23 ASP Chi-restraints excluded: chain c residue 29 LEU Chi-restraints excluded: chain c residue 54 VAL Chi-restraints excluded: chain c residue 99 VAL Chi-restraints excluded: chain c residue 110 GLU Chi-restraints excluded: chain c residue 136 GLU Chi-restraints excluded: chain c residue 138 THR Chi-restraints excluded: chain c residue 143 ILE Chi-restraints excluded: chain c residue 178 LEU Chi-restraints excluded: chain c residue 181 VAL Chi-restraints excluded: chain c residue 214 LEU Chi-restraints excluded: chain c residue 215 ASP Chi-restraints excluded: chain c residue 251 HIS Chi-restraints excluded: chain c residue 255 THR Chi-restraints excluded: chain c residue 261 ILE Chi-restraints excluded: chain c residue 263 VAL Chi-restraints excluded: chain c residue 267 GLU Chi-restraints excluded: chain I residue 29 GLU Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain I residue 120 HIS Chi-restraints excluded: chain I residue 136 LYS Chi-restraints excluded: chain I residue 180 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 186 optimal weight: 0.2980 chunk 196 optimal weight: 2.9990 chunk 179 optimal weight: 0.7980 chunk 191 optimal weight: 0.0770 chunk 115 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 150 optimal weight: 0.0770 chunk 58 optimal weight: 0.5980 chunk 172 optimal weight: 0.8980 chunk 180 optimal weight: 0.9980 chunk 190 optimal weight: 0.1980 overall best weight: 0.2496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 48 HIS F 77 HIS ** G 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 229 GLN S 350 GLN S 651 HIS c 109 HIS c 229 GLN I 40 ASN ** I 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18051 Z= 0.208 Angle : 0.656 13.623 24469 Z= 0.329 Chirality : 0.044 0.244 2585 Planarity : 0.005 0.067 3186 Dihedral : 5.081 57.413 2406 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.27 % Favored : 95.63 % Rotamer: Outliers : 4.54 % Allowed : 27.82 % Favored : 67.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.54 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.18), residues: 2129 helix: 0.62 (0.22), residues: 565 sheet: -1.38 (0.25), residues: 427 loop : -0.62 (0.19), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 36 HIS 0.009 0.001 HIS c 109 PHE 0.019 0.001 PHE B 213 TYR 0.018 0.001 TYR I 48 ARG 0.011 0.001 ARG H 40 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 1894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 510 time to evaluate : 2.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 210 ASP cc_start: 0.8128 (t0) cc_final: 0.7875 (t0) REVERT: B 224 ARG cc_start: 0.7482 (tmm-80) cc_final: 0.7269 (tmm-80) REVERT: B 234 TYR cc_start: 0.8088 (t80) cc_final: 0.7456 (t80) REVERT: B 242 LEU cc_start: 0.6155 (mt) cc_final: 0.5765 (mt) REVERT: B 265 VAL cc_start: 0.8858 (t) cc_final: 0.8518 (m) REVERT: C 311 ARG cc_start: 0.6528 (OUTLIER) cc_final: 0.5785 (ttt180) REVERT: E 95 GLU cc_start: 0.7194 (mt-10) cc_final: 0.6928 (mt-10) REVERT: E 136 GLU cc_start: 0.7776 (tt0) cc_final: 0.7477 (tt0) REVERT: E 161 ILE cc_start: 0.8166 (mt) cc_final: 0.7877 (mm) REVERT: E 163 LEU cc_start: 0.8045 (mm) cc_final: 0.7821 (mm) REVERT: F 20 TYR cc_start: 0.8073 (t80) cc_final: 0.7654 (t80) REVERT: F 35 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.8086 (mttm) REVERT: F 60 LYS cc_start: 0.8574 (mttm) cc_final: 0.8144 (mttt) REVERT: F 97 ASP cc_start: 0.7113 (OUTLIER) cc_final: 0.6762 (t70) REVERT: G 252 GLU cc_start: 0.7464 (tp30) cc_final: 0.7213 (tp30) REVERT: G 281 GLU cc_start: 0.7317 (mt-10) cc_final: 0.7084 (mt-10) REVERT: G 284 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7238 (mm-30) REVERT: G 466 ASP cc_start: 0.7759 (t0) cc_final: 0.7423 (t0) REVERT: G 479 GLU cc_start: 0.8039 (tt0) cc_final: 0.7823 (tt0) REVERT: G 617 ILE cc_start: 0.8617 (mt) cc_final: 0.8029 (tp) REVERT: G 626 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.7825 (mtm-85) REVERT: H 6 LEU cc_start: 0.7900 (mt) cc_final: 0.7569 (mp) REVERT: H 23 ASP cc_start: 0.7226 (OUTLIER) cc_final: 0.6893 (m-30) REVERT: H 43 ARG cc_start: 0.8224 (mtm110) cc_final: 0.7865 (ttp80) REVERT: H 66 ASP cc_start: 0.8402 (t0) cc_final: 0.8121 (t0) REVERT: H 136 GLU cc_start: 0.8518 (tp30) cc_final: 0.8216 (tp30) REVERT: S 238 LYS cc_start: 0.7833 (mtpp) cc_final: 0.7598 (ttpp) REVERT: S 243 ARG cc_start: 0.7453 (ttm-80) cc_final: 0.6957 (ptm160) REVERT: S 282 ILE cc_start: 0.8170 (pt) cc_final: 0.7937 (pt) REVERT: S 284 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7345 (mm-30) REVERT: S 330 THR cc_start: 0.8198 (p) cc_final: 0.7975 (m) REVERT: S 470 ILE cc_start: 0.8010 (OUTLIER) cc_final: 0.7798 (mm) REVERT: S 479 GLU cc_start: 0.7938 (tt0) cc_final: 0.7471 (tt0) REVERT: S 587 GLU cc_start: 0.8128 (pt0) cc_final: 0.7879 (pt0) REVERT: S 622 ILE cc_start: 0.8205 (mm) cc_final: 0.7942 (pt) REVERT: S 641 LYS cc_start: 0.8548 (pttt) cc_final: 0.8152 (ptmm) REVERT: S 667 TYR cc_start: 0.8555 (m-10) cc_final: 0.8287 (m-80) REVERT: c 29 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8200 (mm) REVERT: c 37 ARG cc_start: 0.8247 (ttp80) cc_final: 0.7790 (tmm-80) REVERT: c 77 LEU cc_start: 0.8768 (mm) cc_final: 0.8546 (mt) REVERT: I 45 GLU cc_start: 0.6835 (tt0) cc_final: 0.6568 (mt-10) REVERT: I 76 LYS cc_start: 0.8752 (mttp) cc_final: 0.8442 (mttp) REVERT: I 167 ASN cc_start: 0.8101 (p0) cc_final: 0.7766 (p0) REVERT: I 191 THR cc_start: 0.8785 (m) cc_final: 0.8341 (p) outliers start: 86 outliers final: 70 residues processed: 549 average time/residue: 0.3458 time to fit residues: 268.1201 Evaluate side-chains 574 residues out of total 1894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 497 time to evaluate : 1.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 250 LYS Chi-restraints excluded: chain B residue 297 GLN Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain C residue 309 MET Chi-restraints excluded: chain C residue 311 ARG Chi-restraints excluded: chain D residue 303 MET Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 199 GLU Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 246 ASP Chi-restraints excluded: chain G residue 286 GLN Chi-restraints excluded: chain G residue 290 PHE Chi-restraints excluded: chain G residue 316 GLU Chi-restraints excluded: chain G residue 357 LYS Chi-restraints excluded: chain G residue 432 VAL Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain G residue 455 ARG Chi-restraints excluded: chain G residue 519 ASP Chi-restraints excluded: chain G residue 626 ARG Chi-restraints excluded: chain G residue 638 ASN Chi-restraints excluded: chain G residue 655 VAL Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 261 ILE Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain H residue 271 ASP Chi-restraints excluded: chain H residue 276 LEU Chi-restraints excluded: chain S residue 277 LEU Chi-restraints excluded: chain S residue 432 VAL Chi-restraints excluded: chain S residue 447 THR Chi-restraints excluded: chain S residue 470 ILE Chi-restraints excluded: chain S residue 610 THR Chi-restraints excluded: chain S residue 692 MET Chi-restraints excluded: chain c residue 23 ASP Chi-restraints excluded: chain c residue 29 LEU Chi-restraints excluded: chain c residue 99 VAL Chi-restraints excluded: chain c residue 138 THR Chi-restraints excluded: chain c residue 143 ILE Chi-restraints excluded: chain c residue 178 LEU Chi-restraints excluded: chain c residue 181 VAL Chi-restraints excluded: chain c residue 214 LEU Chi-restraints excluded: chain c residue 215 ASP Chi-restraints excluded: chain c residue 251 HIS Chi-restraints excluded: chain c residue 261 ILE Chi-restraints excluded: chain c residue 263 VAL Chi-restraints excluded: chain c residue 267 GLU Chi-restraints excluded: chain I residue 29 GLU Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain I residue 120 HIS Chi-restraints excluded: chain I residue 136 LYS Chi-restraints excluded: chain I residue 197 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 125 optimal weight: 0.9990 chunk 202 optimal weight: 0.0980 chunk 123 optimal weight: 0.6980 chunk 95 optimal weight: 0.6980 chunk 140 optimal weight: 0.8980 chunk 212 optimal weight: 0.6980 chunk 195 optimal weight: 0.9980 chunk 168 optimal weight: 0.0050 chunk 17 optimal weight: 0.4980 chunk 130 optimal weight: 0.4980 chunk 103 optimal weight: 0.6980 overall best weight: 0.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 48 HIS F 77 HIS G 256 GLN ** G 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 229 GLN S 651 HIS c 109 HIS ** I 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 18051 Z= 0.253 Angle : 0.686 13.464 24469 Z= 0.342 Chirality : 0.045 0.243 2585 Planarity : 0.005 0.067 3186 Dihedral : 5.121 58.930 2406 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.37 % Favored : 95.54 % Rotamer: Outliers : 4.59 % Allowed : 27.72 % Favored : 67.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.54 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.18), residues: 2129 helix: 0.66 (0.22), residues: 564 sheet: -1.30 (0.25), residues: 426 loop : -0.59 (0.19), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 36 HIS 0.011 0.001 HIS c 109 PHE 0.028 0.001 PHE B 213 TYR 0.019 0.001 TYR S 229 ARG 0.015 0.001 ARG F 66 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 1894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 510 time to evaluate : 2.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 210 ASP cc_start: 0.8083 (t0) cc_final: 0.7846 (t0) REVERT: B 224 ARG cc_start: 0.7479 (tmm-80) cc_final: 0.7237 (tmm-80) REVERT: B 242 LEU cc_start: 0.6042 (mt) cc_final: 0.5704 (mt) REVERT: B 265 VAL cc_start: 0.8884 (t) cc_final: 0.8559 (m) REVERT: C 311 ARG cc_start: 0.6659 (OUTLIER) cc_final: 0.5887 (ttt180) REVERT: E 27 GLU cc_start: 0.7777 (tt0) cc_final: 0.7486 (tt0) REVERT: E 95 GLU cc_start: 0.7201 (mt-10) cc_final: 0.6928 (mt-10) REVERT: E 136 GLU cc_start: 0.7782 (tt0) cc_final: 0.7487 (tt0) REVERT: E 161 ILE cc_start: 0.8155 (mt) cc_final: 0.7873 (mm) REVERT: E 163 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7846 (mm) REVERT: F 20 TYR cc_start: 0.8062 (t80) cc_final: 0.7698 (t80) REVERT: F 35 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8108 (mttm) REVERT: F 97 ASP cc_start: 0.7168 (OUTLIER) cc_final: 0.6818 (t70) REVERT: G 281 GLU cc_start: 0.7321 (mt-10) cc_final: 0.7081 (mt-10) REVERT: G 284 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7116 (mm-30) REVERT: G 351 ARG cc_start: 0.6996 (mtt-85) cc_final: 0.6731 (mtt-85) REVERT: G 451 ILE cc_start: 0.6009 (OUTLIER) cc_final: 0.5689 (mt) REVERT: G 466 ASP cc_start: 0.7777 (t0) cc_final: 0.7439 (t0) REVERT: G 479 GLU cc_start: 0.8046 (tt0) cc_final: 0.7834 (tt0) REVERT: G 617 ILE cc_start: 0.8625 (mt) cc_final: 0.8051 (tp) REVERT: G 626 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.7866 (mtm-85) REVERT: H 6 LEU cc_start: 0.7898 (mt) cc_final: 0.7594 (mp) REVERT: H 23 ASP cc_start: 0.7217 (OUTLIER) cc_final: 0.6889 (m-30) REVERT: H 24 ARG cc_start: 0.8034 (mmt90) cc_final: 0.7758 (mmt90) REVERT: H 43 ARG cc_start: 0.8240 (mtm110) cc_final: 0.7875 (ttp80) REVERT: H 66 ASP cc_start: 0.8419 (t0) cc_final: 0.8146 (t0) REVERT: H 91 GLU cc_start: 0.7664 (mp0) cc_final: 0.7455 (mp0) REVERT: H 136 GLU cc_start: 0.8531 (tp30) cc_final: 0.8230 (tp30) REVERT: S 238 LYS cc_start: 0.7843 (mtpp) cc_final: 0.7596 (ttpp) REVERT: S 284 GLU cc_start: 0.7692 (mm-30) cc_final: 0.7415 (mm-30) REVERT: S 287 LYS cc_start: 0.8299 (mptt) cc_final: 0.8069 (mptt) REVERT: S 330 THR cc_start: 0.8185 (p) cc_final: 0.7984 (m) REVERT: S 470 ILE cc_start: 0.8037 (OUTLIER) cc_final: 0.7815 (mm) REVERT: S 479 GLU cc_start: 0.7971 (tt0) cc_final: 0.7501 (tt0) REVERT: S 622 ILE cc_start: 0.8226 (mm) cc_final: 0.7974 (pt) REVERT: S 641 LYS cc_start: 0.8564 (pttt) cc_final: 0.8156 (ptmm) REVERT: S 667 TYR cc_start: 0.8557 (m-10) cc_final: 0.8286 (m-80) REVERT: S 679 MET cc_start: 0.7318 (pmm) cc_final: 0.6965 (pmm) REVERT: c 29 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8196 (mm) REVERT: c 37 ARG cc_start: 0.8231 (ttp80) cc_final: 0.7576 (ttp-170) REVERT: c 77 LEU cc_start: 0.8769 (mm) cc_final: 0.8556 (mt) REVERT: I 45 GLU cc_start: 0.6842 (tt0) cc_final: 0.6573 (mt-10) REVERT: I 76 LYS cc_start: 0.8755 (mttp) cc_final: 0.8413 (mttp) REVERT: I 167 ASN cc_start: 0.8104 (p0) cc_final: 0.7761 (p0) REVERT: I 191 THR cc_start: 0.8797 (m) cc_final: 0.8356 (p) REVERT: I 193 ARG cc_start: 0.7321 (ttt-90) cc_final: 0.7022 (mtt-85) outliers start: 87 outliers final: 71 residues processed: 548 average time/residue: 0.3496 time to fit residues: 271.2594 Evaluate side-chains 583 residues out of total 1894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 503 time to evaluate : 1.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 250 LYS Chi-restraints excluded: chain B residue 297 GLN Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain C residue 309 MET Chi-restraints excluded: chain C residue 311 ARG Chi-restraints excluded: chain D residue 303 MET Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain E residue 5 MET Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 199 GLU Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 246 ASP Chi-restraints excluded: chain G residue 286 GLN Chi-restraints excluded: chain G residue 290 PHE Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain G residue 357 LYS Chi-restraints excluded: chain G residue 432 VAL Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain G residue 451 ILE Chi-restraints excluded: chain G residue 455 ARG Chi-restraints excluded: chain G residue 519 ASP Chi-restraints excluded: chain G residue 626 ARG Chi-restraints excluded: chain G residue 638 ASN Chi-restraints excluded: chain G residue 655 VAL Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 261 ILE Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain H residue 271 ASP Chi-restraints excluded: chain H residue 276 LEU Chi-restraints excluded: chain S residue 277 LEU Chi-restraints excluded: chain S residue 432 VAL Chi-restraints excluded: chain S residue 447 THR Chi-restraints excluded: chain S residue 470 ILE Chi-restraints excluded: chain S residue 610 THR Chi-restraints excluded: chain S residue 692 MET Chi-restraints excluded: chain c residue 23 ASP Chi-restraints excluded: chain c residue 29 LEU Chi-restraints excluded: chain c residue 54 VAL Chi-restraints excluded: chain c residue 138 THR Chi-restraints excluded: chain c residue 143 ILE Chi-restraints excluded: chain c residue 178 LEU Chi-restraints excluded: chain c residue 181 VAL Chi-restraints excluded: chain c residue 214 LEU Chi-restraints excluded: chain c residue 215 ASP Chi-restraints excluded: chain c residue 239 LEU Chi-restraints excluded: chain c residue 251 HIS Chi-restraints excluded: chain c residue 261 ILE Chi-restraints excluded: chain c residue 263 VAL Chi-restraints excluded: chain c residue 267 GLU Chi-restraints excluded: chain I residue 29 GLU Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain I residue 120 HIS Chi-restraints excluded: chain I residue 136 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 134 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 51 optimal weight: 0.2980 chunk 155 optimal weight: 0.8980 chunk 24 optimal weight: 0.0980 chunk 46 optimal weight: 0.5980 chunk 169 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 173 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 48 HIS F 77 HIS ** G 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 229 GLN S 651 HIS c 109 HIS ** I 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.129260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.110703 restraints weight = 31251.371| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.45 r_work: 0.3337 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 18051 Z= 0.300 Angle : 0.699 14.535 24469 Z= 0.351 Chirality : 0.045 0.245 2585 Planarity : 0.005 0.079 3186 Dihedral : 5.189 59.830 2406 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.79 % Favored : 95.12 % Rotamer: Outliers : 4.54 % Allowed : 28.04 % Favored : 67.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.54 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.18), residues: 2129 helix: 0.61 (0.22), residues: 566 sheet: -1.36 (0.24), residues: 441 loop : -0.57 (0.19), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 36 HIS 0.009 0.001 HIS c 109 PHE 0.030 0.001 PHE B 213 TYR 0.019 0.002 TYR I 48 ARG 0.011 0.001 ARG H 40 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5613.53 seconds wall clock time: 99 minutes 46.49 seconds (5986.49 seconds total)