Starting phenix.real_space_refine on Sat Feb 17 02:24:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c26_7336/02_2024/6c26_7336_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c26_7336/02_2024/6c26_7336.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c26_7336/02_2024/6c26_7336.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c26_7336/02_2024/6c26_7336.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c26_7336/02_2024/6c26_7336_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c26_7336/02_2024/6c26_7336_neut_updated.pdb" } resolution = 3.5 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= 0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 55 5.16 5 C 11306 2.51 5 N 2684 2.21 5 O 3135 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 230": "NH1" <-> "NH2" Residue "A ARG 262": "NH1" <-> "NH2" Residue "A PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 497": "NH1" <-> "NH2" Residue "A ARG 592": "NH1" <-> "NH2" Residue "A ARG 605": "NH1" <-> "NH2" Residue "A ARG 615": "NH1" <-> "NH2" Residue "A ARG 651": "NH1" <-> "NH2" Residue "A TYR 665": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 700": "NH1" <-> "NH2" Residue "A ARG 717": "NH1" <-> "NH2" Residue "1 TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 270": "NH1" <-> "NH2" Residue "1 PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 424": "NH1" <-> "NH2" Residue "1 TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 241": "NH1" <-> "NH2" Residue "3 ARG 295": "NH1" <-> "NH2" Residue "3 PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 141": "NH1" <-> "NH2" Residue "B ARG 167": "NH1" <-> "NH2" Residue "B ASP 275": "OD1" <-> "OD2" Residue "B TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17188 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 5225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 648, 5225 Classifications: {'peptide': 648} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 23, 'TRANS': 624} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "1" Number of atoms: 3496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3496 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 23, 'TRANS': 408} Chain breaks: 2 Chain: "5" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 659 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "4" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 259 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "2" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 883 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 3, 'TRANS': 104} Chain: "3" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1028 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain breaks: 1 Chain: "C" Number of atoms: 1940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1940 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 234} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 3218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3218 Classifications: {'peptide': 397} Link IDs: {'PTRANS': 16, 'TRANS': 380} Chain: "D" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 5, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 129 Unusual residues: {'EGY': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "1" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'EGY': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'EGY': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'EGY': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'EGY': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 9.85, per 1000 atoms: 0.57 Number of scatterers: 17188 At special positions: 0 Unit cell: (140.352, 130.56, 154.496, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 55 16.00 P 8 15.00 O 3135 8.00 N 2684 7.00 C 11306 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 Links applied BETA1-2 " BMA D 3 " - " BMA D 4 " " BMA D 4 " - " BMA D 5 " " BMA D 5 " - " BMA D 6 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " BETA1-6 " BMA D 3 " - " BMA D 7 " NAG-ASN " NAG B 601 " - " ASN B 60 " " NAG D 1 " - " ASN A 539 " " NAG E 1 " - " ASN 1 336 " Time building additional restraints: 6.74 Conformation dependent library (CDL) restraints added in 3.0 seconds 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3946 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 58 helices and 19 sheets defined 36.3% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.10 Creating SS restraints... Processing helix chain 'A' and resid 6 through 24 Processing helix chain 'A' and resid 26 through 31 Processing helix chain 'A' and resid 34 through 37 No H-bonds generated for 'chain 'A' and resid 34 through 37' Processing helix chain 'A' and resid 47 through 54 removed outlier: 3.737A pdb=" N PHE A 50 " --> pdb=" O ASP A 47 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ASN A 51 " --> pdb=" O PRO A 48 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N TYR A 52 " --> pdb=" O TRP A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 67 No H-bonds generated for 'chain 'A' and resid 64 through 67' Processing helix chain 'A' and resid 92 through 103 removed outlier: 3.554A pdb=" N ASN A 103 " --> pdb=" O HIS A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 118 removed outlier: 3.533A pdb=" N PHE A 118 " --> pdb=" O VAL A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 137 removed outlier: 4.358A pdb=" N GLY A 124 " --> pdb=" O PRO A 120 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N VAL A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR A 126 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU A 136 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ILE A 137 " --> pdb=" O PHE A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 149 removed outlier: 4.265A pdb=" N LEU A 144 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 187 removed outlier: 4.023A pdb=" N THR A 173 " --> pdb=" O ALA A 169 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N MET A 176 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA A 185 " --> pdb=" O PHE A 181 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LYS A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 205 Processing helix chain 'A' and resid 212 through 227 removed outlier: 4.015A pdb=" N ILE A 218 " --> pdb=" O ILE A 214 " (cutoff:3.500A) Proline residue: A 219 - end of helix removed outlier: 3.671A pdb=" N LEU A 227 " --> pdb=" O PHE A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 252 removed outlier: 3.984A pdb=" N THR A 240 " --> pdb=" O TYR A 236 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N THR A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N TRP A 242 " --> pdb=" O ALA A 238 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN A 252 " --> pdb=" O VAL A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 262 No H-bonds generated for 'chain 'A' and resid 259 through 262' Processing helix chain 'A' and resid 267 through 281 removed outlier: 3.888A pdb=" N PHE A 281 " --> pdb=" O GLN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 287 No H-bonds generated for 'chain 'A' and resid 285 through 287' Processing helix chain 'A' and resid 293 through 296 No H-bonds generated for 'chain 'A' and resid 293 through 296' Processing helix chain 'A' and resid 357 through 362 Processing helix chain 'A' and resid 366 through 378 Proline residue: A 371 - end of helix removed outlier: 3.630A pdb=" N VAL A 374 " --> pdb=" O PHE A 370 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N PHE A 375 " --> pdb=" O PRO A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 400 removed outlier: 3.704A pdb=" N VAL A 393 " --> pdb=" O ILE A 389 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU A 394 " --> pdb=" O ALA A 390 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY A 400 " --> pdb=" O SER A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 416 removed outlier: 4.082A pdb=" N VAL A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 428 removed outlier: 4.320A pdb=" N ILE A 427 " --> pdb=" O LYS A 423 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR A 428 " --> pdb=" O ILE A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 472 removed outlier: 3.713A pdb=" N TYR A 458 " --> pdb=" O SER A 454 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ARG A 471 " --> pdb=" O THR A 467 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR A 472 " --> pdb=" O TRP A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 505 removed outlier: 4.243A pdb=" N LEU A 503 " --> pdb=" O ALA A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 526 removed outlier: 3.839A pdb=" N GLY A 520 " --> pdb=" O TRP A 517 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N TYR A 521 " --> pdb=" O ASP A 518 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN A 522 " --> pdb=" O TYR A 519 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE A 523 " --> pdb=" O GLY A 520 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY A 524 " --> pdb=" O TYR A 521 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N MET A 526 " --> pdb=" O ILE A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 549 Processing helix chain 'A' and resid 554 through 562 removed outlier: 4.558A pdb=" N GLU A 559 " --> pdb=" O GLU A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 595 removed outlier: 4.267A pdb=" N LEU A 588 " --> pdb=" O ASN A 585 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TRP A 589 " --> pdb=" O LYS A 586 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N MET A 590 " --> pdb=" O PHE A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 644 No H-bonds generated for 'chain 'A' and resid 642 through 644' Processing helix chain 'A' and resid 692 through 700 removed outlier: 3.744A pdb=" N GLY A 696 " --> pdb=" O LEU A 692 " (cutoff:3.500A) Processing helix chain '1' and resid 192 through 194 No H-bonds generated for 'chain '1' and resid 192 through 194' Processing helix chain '1' and resid 270 through 278 Processing helix chain '1' and resid 345 through 347 No H-bonds generated for 'chain '1' and resid 345 through 347' Processing helix chain '1' and resid 443 through 468 removed outlier: 4.012A pdb=" N PHE 1 447 " --> pdb=" O LYS 1 443 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS 1 448 " --> pdb=" O SER 1 444 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N LYS 1 449 " --> pdb=" O SER 1 445 " (cutoff:3.500A) Proline residue: 1 450 - end of helix removed outlier: 3.746A pdb=" N MET 1 462 " --> pdb=" O PHE 1 458 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLY 1 463 " --> pdb=" O THR 1 459 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL 1 464 " --> pdb=" O ALA 1 460 " (cutoff:3.500A) Processing helix chain '5' and resid 3 through 10 Processing helix chain '5' and resid 25 through 47 removed outlier: 4.138A pdb=" N ILE 5 30 " --> pdb=" O PRO 5 26 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE 5 34 " --> pdb=" O ILE 5 30 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N VAL 5 35 " --> pdb=" O CYS 5 31 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU 5 37 " --> pdb=" O LEU 5 33 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA 5 46 " --> pdb=" O SER 5 42 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL 5 47 " --> pdb=" O ALA 5 43 " (cutoff:3.500A) Processing helix chain '5' and resid 53 through 79 removed outlier: 4.256A pdb=" N LEU 5 73 " --> pdb=" O LEU 5 69 " (cutoff:3.500A) Processing helix chain '4' and resid 4 through 31 removed outlier: 3.889A pdb=" N LEU 4 21 " --> pdb=" O VAL 4 17 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ILE 4 22 " --> pdb=" O MET 4 18 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL 4 23 " --> pdb=" O MET 4 19 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE 4 24 " --> pdb=" O THR 4 20 " (cutoff:3.500A) Processing helix chain '2' and resid 23 through 40 removed outlier: 3.848A pdb=" N GLN 2 37 " --> pdb=" O ALA 2 33 " (cutoff:3.500A) Processing helix chain '2' and resid 44 through 67 removed outlier: 3.909A pdb=" N PHE 2 53 " --> pdb=" O THR 2 49 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLY 2 58 " --> pdb=" O LEU 2 54 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ILE 2 65 " --> pdb=" O GLN 2 61 " (cutoff:3.500A) Processing helix chain '2' and resid 74 through 99 removed outlier: 4.177A pdb=" N GLY 2 80 " --> pdb=" O ALA 2 76 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE 2 81 " --> pdb=" O PHE 2 77 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU 2 91 " --> pdb=" O GLN 2 87 " (cutoff:3.500A) Processing helix chain '2' and resid 109 through 124 removed outlier: 4.031A pdb=" N LEU 2 121 " --> pdb=" O ALA 2 117 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N HIS 2 122 " --> pdb=" O SER 2 118 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N PHE 2 123 " --> pdb=" O LEU 2 119 " (cutoff:3.500A) Processing helix chain '3' and resid 210 through 215 Processing helix chain '3' and resid 218 through 232 Processing helix chain '3' and resid 235 through 240 Processing helix chain '3' and resid 269 through 288 Processing helix chain '3' and resid 292 through 296 Processing helix chain '3' and resid 306 through 334 Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 196 through 216 removed outlier: 3.936A pdb=" N LEU C 208 " --> pdb=" O PHE C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 253 removed outlier: 3.688A pdb=" N ALA C 239 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N THR C 240 " --> pdb=" O GLY C 236 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE C 241 " --> pdb=" O PHE C 237 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE C 247 " --> pdb=" O GLY C 243 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N PHE C 248 " --> pdb=" O PHE C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 282 Proline residue: C 270 - end of helix Processing helix chain 'B' and resid 38 through 47 removed outlier: 3.733A pdb=" N SER B 41 " --> pdb=" O GLU B 38 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N VAL B 42 " --> pdb=" O GLU B 39 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N TYR B 43 " --> pdb=" O TYR B 40 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LYS B 45 " --> pdb=" O VAL B 42 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ASP B 46 " --> pdb=" O TYR B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 93 Processing helix chain 'B' and resid 96 through 105 removed outlier: 4.111A pdb=" N ASN B 105 " --> pdb=" O LYS B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 129 Processing helix chain 'B' and resid 247 through 256 removed outlier: 3.599A pdb=" N LYS B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 411 removed outlier: 3.855A pdb=" N GLY B 401 " --> pdb=" O SER B 397 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N VAL B 402 " --> pdb=" O ALA B 398 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 568 through 572 removed outlier: 3.572A pdb=" N PHE A 670 " --> pdb=" O ILE A 679 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLN A 681 " --> pdb=" O GLU A 668 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLU A 668 " --> pdb=" O GLN A 681 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 645 through 647 Processing sheet with id= C, first strand: chain '1' and resid 174 through 178 removed outlier: 4.044A pdb=" N ARG 1 38 " --> pdb=" O SER 1 174 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS 1 37 " --> pdb=" O GLU 1 52 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR 1 50 " --> pdb=" O THR 1 39 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '1' and resid 66 through 70 removed outlier: 3.556A pdb=" N GLN 1 95 " --> pdb=" O ILE 1 116 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain '1' and resid 154 through 158 removed outlier: 3.721A pdb=" N GLN 1 154 " --> pdb=" O HIS 1 226 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain '1' and resid 197 through 199 Processing sheet with id= G, first strand: chain '1' and resid 231 through 233 Processing sheet with id= H, first strand: chain '1' and resid 303 through 305 removed outlier: 3.541A pdb=" N GLY 1 340 " --> pdb=" O TYR 1 303 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N THR 1 338 " --> pdb=" O THR 1 305 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ASN 1 376 " --> pdb=" O LEU 1 236 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N ARG 1 238 " --> pdb=" O ASN 1 376 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLU 1 378 " --> pdb=" O ARG 1 238 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N ILE 1 240 " --> pdb=" O GLU 1 378 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N SER 1 380 " --> pdb=" O ILE 1 240 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N LEU 1 242 " --> pdb=" O SER 1 380 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N PHE 1 382 " --> pdb=" O LEU 1 242 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL 1 417 " --> pdb=" O LEU 1 383 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain '1' and resid 290 through 294 removed outlier: 3.785A pdb=" N MET 1 293 " --> pdb=" O PHE 1 321 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE 1 321 " --> pdb=" O MET 1 293 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE 1 322 " --> pdb=" O HIS 1 315 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N HIS 1 315 " --> pdb=" O PHE 1 322 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain '1' and resid 349 through 351 removed outlier: 3.860A pdb=" N ASP 1 391 " --> pdb=" O LYS 1 438 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ASP 1 440 " --> pdb=" O ILE 1 389 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ILE 1 389 " --> pdb=" O ASP 1 440 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 25 through 27 Processing sheet with id= L, first strand: chain 'C' and resid 92 through 96 removed outlier: 4.245A pdb=" N ALA C 135 " --> pdb=" O LEU C 155 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU C 155 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU C 137 " --> pdb=" O GLU C 153 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N GLU C 153 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N LEU C 139 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N PHE C 151 " --> pdb=" O LEU C 139 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 78 through 80 removed outlier: 6.282A pdb=" N ASN B 108 " --> pdb=" O ILE B 79 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL B 218 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N GLY B 220 " --> pdb=" O PRO B 190 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 131 through 133 Processing sheet with id= O, first strand: chain 'B' and resid 139 through 142 removed outlier: 3.531A pdb=" N ARG B 141 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE B 199 " --> pdb=" O ARG B 141 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 151 through 154 removed outlier: 3.580A pdb=" N LEU B 151 " --> pdb=" O PHE B 174 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 263 through 267 removed outlier: 4.329A pdb=" N VAL B 263 " --> pdb=" O TRP B 299 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TRP B 299 " --> pdb=" O VAL B 263 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLY B 295 " --> pdb=" O VAL B 267 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 270 through 273 removed outlier: 3.764A pdb=" N SER B 272 " --> pdb=" O ILE B 291 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 372 through 375 removed outlier: 3.706A pdb=" N TYR B 323 " --> pdb=" O LEU B 316 " (cutoff:3.500A) 557 hydrogen bonds defined for protein. 1593 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.50 Time building geometry restraints manager: 7.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2642 1.30 - 1.43: 5072 1.43 - 1.56: 9788 1.56 - 1.69: 33 1.69 - 1.82: 92 Bond restraints: 17627 Sorted by residual: bond pdb=" C2 BMA D 4 " pdb=" O2 BMA D 4 " ideal model delta sigma weight residual 1.402 1.566 -0.164 2.00e-02 2.50e+03 6.69e+01 bond pdb=" C1 BMA D 4 " pdb=" C2 BMA D 4 " ideal model delta sigma weight residual 1.519 1.634 -0.115 2.00e-02 2.50e+03 3.29e+01 bond pdb=" C1 BMA D 3 " pdb=" C2 BMA D 3 " ideal model delta sigma weight residual 1.519 1.632 -0.113 2.00e-02 2.50e+03 3.19e+01 bond pdb=" C2 BMA D 5 " pdb=" O2 BMA D 5 " ideal model delta sigma weight residual 1.402 1.509 -0.107 2.00e-02 2.50e+03 2.85e+01 bond pdb=" C21 EGY C 301 " pdb=" O21 EGY C 301 " ideal model delta sigma weight residual 1.330 1.430 -0.100 2.00e-02 2.50e+03 2.50e+01 ... (remaining 17622 not shown) Histogram of bond angle deviations from ideal: 96.41 - 106.41: 499 106.41 - 116.41: 11246 116.41 - 126.41: 11854 126.41 - 136.41: 284 136.41 - 146.41: 2 Bond angle restraints: 23885 Sorted by residual: angle pdb=" C TYR A 76 " pdb=" N PRO A 77 " pdb=" CA PRO A 77 " ideal model delta sigma weight residual 119.56 103.90 15.66 1.01e+00 9.80e-01 2.41e+02 angle pdb=" N GLU 1 209 " pdb=" CA GLU 1 209 " pdb=" C GLU 1 209 " ideal model delta sigma weight residual 111.28 120.85 -9.57 1.09e+00 8.42e-01 7.71e+01 angle pdb=" C LEU B 346 " pdb=" N PRO B 347 " pdb=" CA PRO B 347 " ideal model delta sigma weight residual 119.92 129.02 -9.10 1.07e+00 8.73e-01 7.24e+01 angle pdb=" N ILE A 278 " pdb=" CA ILE A 278 " pdb=" C ILE A 278 " ideal model delta sigma weight residual 110.62 118.99 -8.37 1.02e+00 9.61e-01 6.74e+01 angle pdb=" N TYR A 76 " pdb=" CA TYR A 76 " pdb=" C TYR A 76 " ideal model delta sigma weight residual 113.45 123.89 -10.44 1.39e+00 5.18e-01 5.64e+01 ... (remaining 23880 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.72: 10097 31.72 - 63.45: 296 63.45 - 95.17: 97 95.17 - 126.90: 34 126.90 - 158.62: 5 Dihedral angle restraints: 10529 sinusoidal: 4429 harmonic: 6100 Sorted by residual: dihedral pdb=" CA TYR 1 84 " pdb=" C TYR 1 84 " pdb=" N PHE 1 85 " pdb=" CA PHE 1 85 " ideal model delta harmonic sigma weight residual 180.00 151.64 28.36 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CA ASN A 60 " pdb=" C ASN A 60 " pdb=" N ASN A 61 " pdb=" CA ASN A 61 " ideal model delta harmonic sigma weight residual 180.00 151.86 28.14 0 5.00e+00 4.00e-02 3.17e+01 dihedral pdb=" CA ASN B 225 " pdb=" C ASN B 225 " pdb=" N ASN B 226 " pdb=" CA ASN B 226 " ideal model delta harmonic sigma weight residual -180.00 -152.61 -27.39 0 5.00e+00 4.00e-02 3.00e+01 ... (remaining 10526 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 2214 0.086 - 0.173: 389 0.173 - 0.259: 63 0.259 - 0.345: 17 0.345 - 0.431: 5 Chirality restraints: 2688 Sorted by residual: chirality pdb=" CA TYR A 76 " pdb=" N TYR A 76 " pdb=" C TYR A 76 " pdb=" CB TYR A 76 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.65e+00 chirality pdb=" C2 BMA D 3 " pdb=" C1 BMA D 3 " pdb=" C3 BMA D 3 " pdb=" O2 BMA D 3 " both_signs ideal model delta sigma weight residual False 2.47 2.90 -0.43 2.00e-01 2.50e+01 4.63e+00 chirality pdb=" C2 NAG E 1 " pdb=" C1 NAG E 1 " pdb=" C3 NAG E 1 " pdb=" N2 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.07 -0.43 2.00e-01 2.50e+01 4.52e+00 ... (remaining 2685 not shown) Planarity restraints: 2931 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA 3 234 " 0.014 2.00e-02 2.50e+03 2.94e-02 8.62e+00 pdb=" C ALA 3 234 " -0.051 2.00e-02 2.50e+03 pdb=" O ALA 3 234 " 0.020 2.00e-02 2.50e+03 pdb=" N TYR 3 235 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 597 " -0.015 2.00e-02 2.50e+03 2.93e-02 8.59e+00 pdb=" C ILE A 597 " 0.051 2.00e-02 2.50e+03 pdb=" O ILE A 597 " -0.019 2.00e-02 2.50e+03 pdb=" N TRP A 598 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE 1 398 " 0.016 2.00e-02 2.50e+03 2.14e-02 8.01e+00 pdb=" CG PHE 1 398 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE 1 398 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE 1 398 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 PHE 1 398 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE 1 398 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE 1 398 " 0.001 2.00e-02 2.50e+03 ... (remaining 2928 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.45: 49 2.45 - 3.06: 10236 3.06 - 3.67: 23628 3.67 - 4.29: 32969 4.29 - 4.90: 56385 Nonbonded interactions: 123267 Sorted by model distance: nonbonded pdb=" NZ LYS C 77 " pdb=" OG1 THR C 143 " model vdw 1.833 2.520 nonbonded pdb=" OH TYR B 69 " pdb=" ND2 ASN B 105 " model vdw 1.955 2.520 nonbonded pdb=" O LYS 1 171 " pdb=" O GLU 1 209 " model vdw 2.001 3.040 nonbonded pdb=" O PRO B 321 " pdb=" O4 BMA D 4 " model vdw 2.131 2.440 nonbonded pdb=" CG2 ILE B 291 " pdb=" O GLY B 342 " model vdw 2.139 3.460 ... (remaining 123262 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.500 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: 4.170 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 46.430 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 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 : 0.011 0.164 17627 Z= 0.739 Angle : 1.407 22.899 23885 Z= 0.704 Chirality : 0.073 0.431 2688 Planarity : 0.008 0.067 2928 Dihedral : 18.345 158.619 6583 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.79 % Favored : 90.16 % Rotamer: Outliers : 2.07 % Allowed : 7.15 % Favored : 90.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.59 (0.14), residues: 2043 helix: -2.90 (0.13), residues: 779 sheet: -2.07 (0.27), residues: 353 loop : -3.55 (0.15), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.004 TRP A 675 HIS 0.011 0.002 HIS A 193 PHE 0.049 0.004 PHE 1 398 TYR 0.034 0.003 TYR 3 277 ARG 0.016 0.002 ARG A 690 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 378 time to evaluate : 1.894 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 LYS cc_start: 0.8039 (ttpp) cc_final: 0.7839 (ttmt) REVERT: A 286 LYS cc_start: 0.7810 (ttmm) cc_final: 0.7537 (ttpt) REVERT: A 383 ASP cc_start: 0.7551 (t0) cc_final: 0.7325 (t0) REVERT: A 402 MET cc_start: 0.7752 (mpt) cc_final: 0.7371 (mpt) REVERT: A 481 LEU cc_start: 0.8375 (mm) cc_final: 0.7697 (tt) REVERT: A 565 ASP cc_start: 0.8409 (t0) cc_final: 0.8025 (t70) REVERT: A 583 ASP cc_start: 0.8796 (t70) cc_final: 0.8526 (m-30) REVERT: 1 84 TYR cc_start: 0.7664 (m-80) cc_final: 0.7427 (m-10) REVERT: 1 95 GLN cc_start: 0.7840 (pm20) cc_final: 0.7552 (pt0) REVERT: 1 203 PHE cc_start: 0.8106 (OUTLIER) cc_final: 0.7514 (m-10) REVERT: 1 424 ARG cc_start: 0.7704 (ttm-80) cc_final: 0.7493 (mtp85) REVERT: 5 7 TYR cc_start: 0.8736 (t80) cc_final: 0.8449 (t80) REVERT: 2 67 LEU cc_start: 0.8501 (tp) cc_final: 0.8273 (tt) REVERT: 3 255 MET cc_start: 0.5789 (tpp) cc_final: 0.5467 (tpt) REVERT: C 275 SER cc_start: 0.8715 (m) cc_final: 0.8408 (p) REVERT: B 106 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7883 (mp0) REVERT: B 159 LEU cc_start: 0.8906 (mm) cc_final: 0.8660 (mp) REVERT: B 325 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8674 (pp) REVERT: B 348 ASP cc_start: 0.7990 (t0) cc_final: 0.7675 (t0) REVERT: B 415 THR cc_start: 0.9553 (m) cc_final: 0.9059 (p) outliers start: 38 outliers final: 18 residues processed: 408 average time/residue: 0.3115 time to fit residues: 184.8851 Evaluate side-chains 228 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 208 time to evaluate : 1.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain 1 residue 194 LEU Chi-restraints excluded: chain 1 residue 203 PHE Chi-restraints excluded: chain 1 residue 209 GLU Chi-restraints excluded: chain 1 residue 377 VAL Chi-restraints excluded: chain 1 residue 427 ILE Chi-restraints excluded: chain 5 residue 84 VAL Chi-restraints excluded: chain 2 residue 95 ARG Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 71 LYS Chi-restraints excluded: chain B residue 325 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 171 optimal weight: 3.9990 chunk 153 optimal weight: 9.9990 chunk 85 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 159 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 184 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN A 193 HIS ** A 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 ASN A 540 ASN A 674 ASN 1 343 ASN ** 1 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 GLN B 222 GLN B 259 ASN B 307 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17627 Z= 0.245 Angle : 0.744 14.342 23885 Z= 0.365 Chirality : 0.048 0.415 2688 Planarity : 0.005 0.054 2928 Dihedral : 18.654 157.406 2781 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 4.69 % Allowed : 11.84 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (0.16), residues: 2043 helix: -1.15 (0.17), residues: 776 sheet: -1.89 (0.27), residues: 351 loop : -3.33 (0.16), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 208 HIS 0.004 0.001 HIS A 266 PHE 0.042 0.001 PHE 1 398 TYR 0.020 0.001 TYR 3 235 ARG 0.008 0.001 ARG A 262 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 230 time to evaluate : 2.099 Fit side-chains revert: symmetry clash REVERT: A 25 PHE cc_start: 0.7899 (t80) cc_final: 0.7623 (t80) REVERT: A 65 LYS cc_start: 0.8592 (mttp) cc_final: 0.8327 (mtpt) REVERT: A 122 PHE cc_start: 0.8256 (OUTLIER) cc_final: 0.7703 (m-80) REVERT: A 135 LYS cc_start: 0.8152 (ttpp) cc_final: 0.7931 (ttmt) REVERT: A 286 LYS cc_start: 0.7753 (ttmm) cc_final: 0.7473 (ttpt) REVERT: A 412 VAL cc_start: 0.8471 (OUTLIER) cc_final: 0.8130 (p) REVERT: A 481 LEU cc_start: 0.8367 (mm) cc_final: 0.7575 (tt) REVERT: A 495 ASP cc_start: 0.8513 (p0) cc_final: 0.8227 (p0) REVERT: A 565 ASP cc_start: 0.8236 (t0) cc_final: 0.7774 (t70) REVERT: A 624 MET cc_start: 0.8979 (tpt) cc_final: 0.8572 (tpt) REVERT: A 663 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7109 (pp) REVERT: A 676 MET cc_start: 0.7822 (ttm) cc_final: 0.7375 (ttm) REVERT: 1 84 TYR cc_start: 0.7614 (m-80) cc_final: 0.7342 (m-10) REVERT: 1 197 LYS cc_start: 0.7481 (mttt) cc_final: 0.6951 (ptmt) REVERT: 1 203 PHE cc_start: 0.8132 (OUTLIER) cc_final: 0.7605 (m-10) REVERT: 1 209 GLU cc_start: 0.8994 (OUTLIER) cc_final: 0.8325 (mp0) REVERT: 1 242 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8450 (tt) REVERT: 5 7 TYR cc_start: 0.8717 (t80) cc_final: 0.8434 (t80) REVERT: 2 98 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.7966 (tp) REVERT: C 275 SER cc_start: 0.8870 (m) cc_final: 0.8456 (p) REVERT: B 112 MET cc_start: 0.8184 (ptp) cc_final: 0.7959 (ptp) REVERT: B 299 TRP cc_start: 0.8209 (t60) cc_final: 0.7760 (t-100) REVERT: B 325 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8422 (pp) REVERT: B 348 ASP cc_start: 0.8295 (t0) cc_final: 0.7998 (t0) outliers start: 86 outliers final: 44 residues processed: 305 average time/residue: 0.2732 time to fit residues: 128.2032 Evaluate side-chains 249 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 197 time to evaluate : 1.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 508 ASP Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain 1 residue 50 THR Chi-restraints excluded: chain 1 residue 194 LEU Chi-restraints excluded: chain 1 residue 203 PHE Chi-restraints excluded: chain 1 residue 209 GLU Chi-restraints excluded: chain 1 residue 230 LEU Chi-restraints excluded: chain 1 residue 233 VAL Chi-restraints excluded: chain 1 residue 242 LEU Chi-restraints excluded: chain 1 residue 293 MET Chi-restraints excluded: chain 1 residue 308 VAL Chi-restraints excluded: chain 1 residue 313 THR Chi-restraints excluded: chain 1 residue 377 VAL Chi-restraints excluded: chain 1 residue 427 ILE Chi-restraints excluded: chain 1 residue 430 VAL Chi-restraints excluded: chain 1 residue 466 VAL Chi-restraints excluded: chain 5 residue 69 LEU Chi-restraints excluded: chain 5 residue 84 VAL Chi-restraints excluded: chain 4 residue 30 SER Chi-restraints excluded: chain 2 residue 55 VAL Chi-restraints excluded: chain 2 residue 60 ILE Chi-restraints excluded: chain 2 residue 66 ILE Chi-restraints excluded: chain 2 residue 98 LEU Chi-restraints excluded: chain C residue 185 HIS Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 387 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 102 optimal weight: 0.9980 chunk 57 optimal weight: 6.9990 chunk 153 optimal weight: 0.6980 chunk 125 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 184 optimal weight: 3.9990 chunk 199 optimal weight: 3.9990 chunk 164 optimal weight: 5.9990 chunk 183 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 148 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 HIS A 103 ASN A 216 ASN ** A 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 118 GLN ** 1 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 17 GLN 2 61 GLN C 160 ASN B 32 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17627 Z= 0.184 Angle : 0.679 13.775 23885 Z= 0.325 Chirality : 0.046 0.394 2688 Planarity : 0.004 0.062 2928 Dihedral : 16.197 159.125 2766 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 4.20 % Allowed : 14.18 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.17), residues: 2043 helix: -0.23 (0.18), residues: 784 sheet: -1.63 (0.28), residues: 340 loop : -3.09 (0.16), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 49 HIS 0.003 0.001 HIS 1 416 PHE 0.047 0.001 PHE 1 398 TYR 0.015 0.001 TYR 2 41 ARG 0.019 0.000 ARG C 37 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 231 time to evaluate : 1.830 Fit side-chains revert: symmetry clash REVERT: A 25 PHE cc_start: 0.7873 (t80) cc_final: 0.6673 (m-10) REVERT: A 65 LYS cc_start: 0.8558 (mttp) cc_final: 0.8276 (mtpp) REVERT: A 122 PHE cc_start: 0.8110 (OUTLIER) cc_final: 0.7337 (m-80) REVERT: A 135 LYS cc_start: 0.8185 (ttpp) cc_final: 0.7953 (ttmt) REVERT: A 286 LYS cc_start: 0.7758 (ttmm) cc_final: 0.7484 (ttpt) REVERT: A 402 MET cc_start: 0.7799 (mpt) cc_final: 0.7307 (mpt) REVERT: A 412 VAL cc_start: 0.8524 (OUTLIER) cc_final: 0.8146 (p) REVERT: A 481 LEU cc_start: 0.8410 (mm) cc_final: 0.7761 (tp) REVERT: A 495 ASP cc_start: 0.8532 (p0) cc_final: 0.8072 (m-30) REVERT: A 565 ASP cc_start: 0.8194 (t0) cc_final: 0.7712 (t70) REVERT: A 624 MET cc_start: 0.8910 (tpt) cc_final: 0.8609 (tpt) REVERT: A 628 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8918 (tm) REVERT: A 663 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.6957 (pp) REVERT: 1 84 TYR cc_start: 0.7481 (m-80) cc_final: 0.7127 (m-10) REVERT: 1 165 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8584 (tt) REVERT: 1 197 LYS cc_start: 0.7537 (mttt) cc_final: 0.6972 (ptmt) REVERT: 1 203 PHE cc_start: 0.8101 (OUTLIER) cc_final: 0.7606 (m-10) REVERT: 1 242 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8415 (tt) REVERT: 5 7 TYR cc_start: 0.8678 (t80) cc_final: 0.8446 (t80) REVERT: 4 14 PHE cc_start: 0.8621 (OUTLIER) cc_final: 0.8022 (m-80) REVERT: 2 98 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7816 (tp) REVERT: C 69 ASN cc_start: 0.7926 (t0) cc_final: 0.7663 (t0) REVERT: C 154 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8611 (pt) REVERT: C 275 SER cc_start: 0.8827 (m) cc_final: 0.8489 (p) REVERT: B 112 MET cc_start: 0.8151 (ptp) cc_final: 0.7905 (ptm) REVERT: B 299 TRP cc_start: 0.8135 (t60) cc_final: 0.7682 (t-100) REVERT: B 325 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8313 (pp) REVERT: B 348 ASP cc_start: 0.8291 (t0) cc_final: 0.7975 (t0) outliers start: 77 outliers final: 46 residues processed: 295 average time/residue: 0.3032 time to fit residues: 138.1377 Evaluate side-chains 259 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 202 time to evaluate : 1.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 496 PHE Chi-restraints excluded: chain A residue 508 ASP Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain 1 residue 50 THR Chi-restraints excluded: chain 1 residue 79 SER Chi-restraints excluded: chain 1 residue 165 LEU Chi-restraints excluded: chain 1 residue 194 LEU Chi-restraints excluded: chain 1 residue 203 PHE Chi-restraints excluded: chain 1 residue 242 LEU Chi-restraints excluded: chain 1 residue 293 MET Chi-restraints excluded: chain 1 residue 308 VAL Chi-restraints excluded: chain 1 residue 313 THR Chi-restraints excluded: chain 1 residue 377 VAL Chi-restraints excluded: chain 1 residue 420 THR Chi-restraints excluded: chain 1 residue 427 ILE Chi-restraints excluded: chain 1 residue 430 VAL Chi-restraints excluded: chain 1 residue 466 VAL Chi-restraints excluded: chain 5 residue 84 VAL Chi-restraints excluded: chain 4 residue 14 PHE Chi-restraints excluded: chain 4 residue 30 SER Chi-restraints excluded: chain 2 residue 60 ILE Chi-restraints excluded: chain 2 residue 66 ILE Chi-restraints excluded: chain 2 residue 96 LEU Chi-restraints excluded: chain 2 residue 98 LEU Chi-restraints excluded: chain 3 residue 332 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 185 HIS Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 387 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 182 optimal weight: 0.0020 chunk 138 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 185 optimal weight: 5.9990 chunk 196 optimal weight: 0.0570 chunk 96 optimal weight: 0.9990 chunk 175 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.4112 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 425 ASN 1 429 GLN 5 17 GLN 2 61 GLN C 80 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17627 Z= 0.233 Angle : 0.665 11.591 23885 Z= 0.320 Chirality : 0.046 0.395 2688 Planarity : 0.004 0.051 2928 Dihedral : 14.790 159.242 2761 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 5.56 % Allowed : 14.24 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.18), residues: 2043 helix: 0.33 (0.19), residues: 783 sheet: -1.55 (0.28), residues: 335 loop : -3.01 (0.17), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 98 HIS 0.003 0.001 HIS 1 416 PHE 0.022 0.001 PHE 1 398 TYR 0.017 0.001 TYR 2 41 ARG 0.004 0.000 ARG A 497 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 201 time to evaluate : 1.902 Fit side-chains REVERT: A 122 PHE cc_start: 0.8171 (OUTLIER) cc_final: 0.7595 (m-80) REVERT: A 286 LYS cc_start: 0.7791 (ttmm) cc_final: 0.7502 (ttpt) REVERT: A 378 PHE cc_start: 0.8074 (OUTLIER) cc_final: 0.7777 (t80) REVERT: A 402 MET cc_start: 0.7815 (mpt) cc_final: 0.7293 (mpt) REVERT: A 412 VAL cc_start: 0.8530 (OUTLIER) cc_final: 0.8151 (p) REVERT: A 481 LEU cc_start: 0.8433 (mm) cc_final: 0.7786 (tp) REVERT: A 565 ASP cc_start: 0.8204 (t0) cc_final: 0.7717 (t70) REVERT: A 663 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7080 (pp) REVERT: 1 84 TYR cc_start: 0.7447 (m-80) cc_final: 0.7082 (m-10) REVERT: 1 165 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8640 (tt) REVERT: 1 197 LYS cc_start: 0.7461 (mttt) cc_final: 0.6895 (ptmt) REVERT: 1 203 PHE cc_start: 0.8097 (OUTLIER) cc_final: 0.7708 (m-10) REVERT: 1 242 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8459 (tt) REVERT: 5 7 TYR cc_start: 0.8725 (t80) cc_final: 0.8482 (t80) REVERT: 4 14 PHE cc_start: 0.8626 (OUTLIER) cc_final: 0.7946 (m-80) REVERT: 2 98 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7889 (tp) REVERT: C 69 ASN cc_start: 0.8211 (t0) cc_final: 0.7877 (t0) REVERT: C 275 SER cc_start: 0.8863 (m) cc_final: 0.8568 (p) REVERT: B 325 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8315 (pp) REVERT: B 348 ASP cc_start: 0.8286 (t0) cc_final: 0.8066 (t0) outliers start: 102 outliers final: 62 residues processed: 285 average time/residue: 0.2837 time to fit residues: 123.8705 Evaluate side-chains 253 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 181 time to evaluate : 1.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 496 PHE Chi-restraints excluded: chain A residue 508 ASP Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain 1 residue 50 THR Chi-restraints excluded: chain 1 residue 79 SER Chi-restraints excluded: chain 1 residue 85 PHE Chi-restraints excluded: chain 1 residue 86 THR Chi-restraints excluded: chain 1 residue 160 THR Chi-restraints excluded: chain 1 residue 165 LEU Chi-restraints excluded: chain 1 residue 194 LEU Chi-restraints excluded: chain 1 residue 203 PHE Chi-restraints excluded: chain 1 residue 233 VAL Chi-restraints excluded: chain 1 residue 242 LEU Chi-restraints excluded: chain 1 residue 250 GLN Chi-restraints excluded: chain 1 residue 288 VAL Chi-restraints excluded: chain 1 residue 293 MET Chi-restraints excluded: chain 1 residue 308 VAL Chi-restraints excluded: chain 1 residue 313 THR Chi-restraints excluded: chain 1 residue 377 VAL Chi-restraints excluded: chain 1 residue 420 THR Chi-restraints excluded: chain 1 residue 466 VAL Chi-restraints excluded: chain 5 residue 69 LEU Chi-restraints excluded: chain 5 residue 84 VAL Chi-restraints excluded: chain 4 residue 14 PHE Chi-restraints excluded: chain 4 residue 30 SER Chi-restraints excluded: chain 2 residue 28 LYS Chi-restraints excluded: chain 2 residue 55 VAL Chi-restraints excluded: chain 2 residue 60 ILE Chi-restraints excluded: chain 2 residue 61 GLN Chi-restraints excluded: chain 2 residue 83 ILE Chi-restraints excluded: chain 2 residue 96 LEU Chi-restraints excluded: chain 2 residue 98 LEU Chi-restraints excluded: chain 3 residue 329 THR Chi-restraints excluded: chain 3 residue 332 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 185 HIS Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 387 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 163 optimal weight: 8.9990 chunk 111 optimal weight: 0.4980 chunk 2 optimal weight: 2.9990 chunk 146 optimal weight: 8.9990 chunk 80 optimal weight: 0.7980 chunk 167 optimal weight: 8.9990 chunk 135 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 176 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 61 GLN B 138 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 17627 Z= 0.381 Angle : 0.723 11.497 23885 Z= 0.352 Chirality : 0.049 0.385 2688 Planarity : 0.005 0.068 2928 Dihedral : 14.539 157.937 2757 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 6.49 % Allowed : 14.89 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.18), residues: 2043 helix: 0.44 (0.19), residues: 780 sheet: -1.53 (0.28), residues: 343 loop : -2.95 (0.17), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 98 HIS 0.005 0.001 HIS C 182 PHE 0.029 0.002 PHE 3 293 TYR 0.022 0.002 TYR 2 41 ARG 0.006 0.001 ARG A 497 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 192 time to evaluate : 2.031 Fit side-chains REVERT: A 122 PHE cc_start: 0.8193 (OUTLIER) cc_final: 0.7915 (m-80) REVERT: A 286 LYS cc_start: 0.7782 (ttmm) cc_final: 0.7489 (ttpt) REVERT: A 378 PHE cc_start: 0.7943 (OUTLIER) cc_final: 0.7692 (t80) REVERT: A 402 MET cc_start: 0.7833 (mpt) cc_final: 0.7356 (mpt) REVERT: A 412 VAL cc_start: 0.8490 (OUTLIER) cc_final: 0.8055 (p) REVERT: A 481 LEU cc_start: 0.8400 (mm) cc_final: 0.7659 (tp) REVERT: A 565 ASP cc_start: 0.8203 (t0) cc_final: 0.7690 (t70) REVERT: A 663 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7145 (pp) REVERT: 1 84 TYR cc_start: 0.7561 (m-80) cc_final: 0.7259 (m-10) REVERT: 1 165 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8633 (tt) REVERT: 1 197 LYS cc_start: 0.7394 (mttt) cc_final: 0.6810 (ptmt) REVERT: 1 203 PHE cc_start: 0.8175 (OUTLIER) cc_final: 0.7740 (m-10) REVERT: 1 242 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8535 (tt) REVERT: 1 244 HIS cc_start: 0.8912 (OUTLIER) cc_final: 0.8391 (t-90) REVERT: 1 376 ASN cc_start: 0.8483 (OUTLIER) cc_final: 0.8271 (p0) REVERT: 1 418 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8166 (ttmm) REVERT: 1 448 LYS cc_start: 0.7329 (OUTLIER) cc_final: 0.6939 (tptt) REVERT: 5 7 TYR cc_start: 0.8732 (t80) cc_final: 0.8479 (t80) REVERT: 4 14 PHE cc_start: 0.8646 (OUTLIER) cc_final: 0.7955 (m-80) REVERT: 2 98 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8102 (tp) REVERT: C 69 ASN cc_start: 0.8269 (t0) cc_final: 0.7974 (t0) REVERT: C 275 SER cc_start: 0.8920 (m) cc_final: 0.8601 (p) REVERT: B 299 TRP cc_start: 0.8383 (t60) cc_final: 0.8156 (t-100) REVERT: B 325 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8441 (pp) outliers start: 119 outliers final: 80 residues processed: 287 average time/residue: 0.2614 time to fit residues: 117.0723 Evaluate side-chains 276 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 182 time to evaluate : 1.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 496 PHE Chi-restraints excluded: chain A residue 508 ASP Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain 1 residue 50 THR Chi-restraints excluded: chain 1 residue 79 SER Chi-restraints excluded: chain 1 residue 85 PHE Chi-restraints excluded: chain 1 residue 86 THR Chi-restraints excluded: chain 1 residue 132 VAL Chi-restraints excluded: chain 1 residue 160 THR Chi-restraints excluded: chain 1 residue 165 LEU Chi-restraints excluded: chain 1 residue 180 SER Chi-restraints excluded: chain 1 residue 194 LEU Chi-restraints excluded: chain 1 residue 203 PHE Chi-restraints excluded: chain 1 residue 220 LEU Chi-restraints excluded: chain 1 residue 230 LEU Chi-restraints excluded: chain 1 residue 233 VAL Chi-restraints excluded: chain 1 residue 242 LEU Chi-restraints excluded: chain 1 residue 244 HIS Chi-restraints excluded: chain 1 residue 250 GLN Chi-restraints excluded: chain 1 residue 288 VAL Chi-restraints excluded: chain 1 residue 293 MET Chi-restraints excluded: chain 1 residue 308 VAL Chi-restraints excluded: chain 1 residue 313 THR Chi-restraints excluded: chain 1 residue 342 THR Chi-restraints excluded: chain 1 residue 376 ASN Chi-restraints excluded: chain 1 residue 377 VAL Chi-restraints excluded: chain 1 residue 418 LYS Chi-restraints excluded: chain 1 residue 420 THR Chi-restraints excluded: chain 1 residue 448 LYS Chi-restraints excluded: chain 1 residue 455 CYS Chi-restraints excluded: chain 1 residue 466 VAL Chi-restraints excluded: chain 5 residue 69 LEU Chi-restraints excluded: chain 5 residue 84 VAL Chi-restraints excluded: chain 4 residue 14 PHE Chi-restraints excluded: chain 4 residue 30 SER Chi-restraints excluded: chain 2 residue 28 LYS Chi-restraints excluded: chain 2 residue 60 ILE Chi-restraints excluded: chain 2 residue 83 ILE Chi-restraints excluded: chain 2 residue 96 LEU Chi-restraints excluded: chain 2 residue 98 LEU Chi-restraints excluded: chain 2 residue 124 VAL Chi-restraints excluded: chain 3 residue 208 LYS Chi-restraints excluded: chain 3 residue 283 LEU Chi-restraints excluded: chain 3 residue 328 THR Chi-restraints excluded: chain 3 residue 329 THR Chi-restraints excluded: chain 3 residue 332 THR Chi-restraints excluded: chain C residue 94 MET Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 185 HIS Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 310 ASP Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 387 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 66 optimal weight: 6.9990 chunk 176 optimal weight: 7.9990 chunk 38 optimal weight: 8.9990 chunk 115 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 196 optimal weight: 2.9990 chunk 163 optimal weight: 8.9990 chunk 90 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 280 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17627 Z= 0.240 Angle : 0.657 11.412 23885 Z= 0.316 Chirality : 0.046 0.371 2688 Planarity : 0.004 0.066 2928 Dihedral : 13.960 158.629 2756 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 5.40 % Allowed : 16.42 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.18), residues: 2043 helix: 0.73 (0.19), residues: 775 sheet: -1.31 (0.29), residues: 322 loop : -2.83 (0.17), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 98 HIS 0.003 0.001 HIS A 542 PHE 0.023 0.001 PHE 3 293 TYR 0.023 0.001 TYR 2 41 ARG 0.004 0.000 ARG A 497 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 191 time to evaluate : 1.890 Fit side-chains REVERT: A 286 LYS cc_start: 0.7749 (ttmm) cc_final: 0.7467 (ttpt) REVERT: A 402 MET cc_start: 0.7838 (mpt) cc_final: 0.7370 (mpt) REVERT: A 412 VAL cc_start: 0.8511 (OUTLIER) cc_final: 0.8024 (p) REVERT: A 481 LEU cc_start: 0.8382 (mm) cc_final: 0.7625 (tp) REVERT: A 510 ASP cc_start: 0.7508 (p0) cc_final: 0.7276 (p0) REVERT: A 565 ASP cc_start: 0.8201 (t0) cc_final: 0.7714 (t70) REVERT: A 582 ASP cc_start: 0.8833 (p0) cc_final: 0.8595 (p0) REVERT: A 663 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7091 (pp) REVERT: 1 84 TYR cc_start: 0.7516 (m-80) cc_final: 0.7198 (m-10) REVERT: 1 165 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8664 (tt) REVERT: 1 197 LYS cc_start: 0.7407 (mttt) cc_final: 0.6795 (ptmt) REVERT: 1 203 PHE cc_start: 0.8138 (OUTLIER) cc_final: 0.7735 (m-10) REVERT: 1 242 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8423 (tt) REVERT: 1 244 HIS cc_start: 0.8878 (OUTLIER) cc_final: 0.8359 (t-90) REVERT: 4 14 PHE cc_start: 0.8587 (OUTLIER) cc_final: 0.7891 (m-80) REVERT: 2 98 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7981 (tp) REVERT: C 69 ASN cc_start: 0.8223 (t0) cc_final: 0.8003 (t0) REVERT: C 109 TYR cc_start: 0.8432 (m-10) cc_final: 0.8194 (m-10) REVERT: C 148 GLU cc_start: 0.7264 (tp30) cc_final: 0.6820 (tp30) REVERT: C 275 SER cc_start: 0.8922 (m) cc_final: 0.8609 (p) REVERT: B 53 LYS cc_start: 0.8222 (ptpt) cc_final: 0.7931 (ptmt) REVERT: B 299 TRP cc_start: 0.8336 (t60) cc_final: 0.7903 (t-100) REVERT: B 325 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8394 (pp) outliers start: 99 outliers final: 73 residues processed: 270 average time/residue: 0.2621 time to fit residues: 110.4931 Evaluate side-chains 261 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 179 time to evaluate : 1.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 496 PHE Chi-restraints excluded: chain A residue 508 ASP Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 538 TRP Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain 1 residue 50 THR Chi-restraints excluded: chain 1 residue 79 SER Chi-restraints excluded: chain 1 residue 85 PHE Chi-restraints excluded: chain 1 residue 86 THR Chi-restraints excluded: chain 1 residue 132 VAL Chi-restraints excluded: chain 1 residue 160 THR Chi-restraints excluded: chain 1 residue 165 LEU Chi-restraints excluded: chain 1 residue 180 SER Chi-restraints excluded: chain 1 residue 194 LEU Chi-restraints excluded: chain 1 residue 203 PHE Chi-restraints excluded: chain 1 residue 230 LEU Chi-restraints excluded: chain 1 residue 233 VAL Chi-restraints excluded: chain 1 residue 242 LEU Chi-restraints excluded: chain 1 residue 244 HIS Chi-restraints excluded: chain 1 residue 250 GLN Chi-restraints excluded: chain 1 residue 288 VAL Chi-restraints excluded: chain 1 residue 293 MET Chi-restraints excluded: chain 1 residue 308 VAL Chi-restraints excluded: chain 1 residue 313 THR Chi-restraints excluded: chain 1 residue 342 THR Chi-restraints excluded: chain 1 residue 377 VAL Chi-restraints excluded: chain 1 residue 420 THR Chi-restraints excluded: chain 1 residue 427 ILE Chi-restraints excluded: chain 1 residue 466 VAL Chi-restraints excluded: chain 5 residue 69 LEU Chi-restraints excluded: chain 5 residue 84 VAL Chi-restraints excluded: chain 4 residue 14 PHE Chi-restraints excluded: chain 4 residue 30 SER Chi-restraints excluded: chain 2 residue 28 LYS Chi-restraints excluded: chain 2 residue 55 VAL Chi-restraints excluded: chain 2 residue 60 ILE Chi-restraints excluded: chain 2 residue 96 LEU Chi-restraints excluded: chain 2 residue 98 LEU Chi-restraints excluded: chain 3 residue 208 LYS Chi-restraints excluded: chain 3 residue 283 LEU Chi-restraints excluded: chain 3 residue 329 THR Chi-restraints excluded: chain C residue 94 MET Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 185 HIS Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 387 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 189 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 143 optimal weight: 0.0670 chunk 165 optimal weight: 0.0980 chunk 109 optimal weight: 4.9990 chunk 195 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 119 optimal weight: 0.0470 chunk 90 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 overall best weight: 0.8420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 HIS 2 61 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17627 Z= 0.171 Angle : 0.621 10.845 23885 Z= 0.297 Chirality : 0.045 0.369 2688 Planarity : 0.004 0.064 2928 Dihedral : 13.270 159.482 2756 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 4.86 % Allowed : 17.29 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.18), residues: 2043 helix: 1.08 (0.19), residues: 773 sheet: -1.29 (0.28), residues: 335 loop : -2.73 (0.17), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 98 HIS 0.003 0.001 HIS A 542 PHE 0.023 0.001 PHE 3 293 TYR 0.016 0.001 TYR 2 41 ARG 0.003 0.000 ARG A 497 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 203 time to evaluate : 1.795 Fit side-chains REVERT: A 286 LYS cc_start: 0.7707 (ttmm) cc_final: 0.7454 (ttpt) REVERT: A 404 ARG cc_start: 0.8156 (ptt180) cc_final: 0.7655 (ptt180) REVERT: A 412 VAL cc_start: 0.8441 (OUTLIER) cc_final: 0.7884 (p) REVERT: A 431 PHE cc_start: 0.7060 (p90) cc_final: 0.6842 (p90) REVERT: A 481 LEU cc_start: 0.8399 (mm) cc_final: 0.7674 (tp) REVERT: A 510 ASP cc_start: 0.7471 (p0) cc_final: 0.7230 (p0) REVERT: A 565 ASP cc_start: 0.8149 (t0) cc_final: 0.7680 (t70) REVERT: A 663 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.6970 (pp) REVERT: 1 84 TYR cc_start: 0.7357 (m-80) cc_final: 0.7025 (m-10) REVERT: 1 165 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8671 (tt) REVERT: 1 197 LYS cc_start: 0.7326 (mttt) cc_final: 0.6703 (ptmt) REVERT: 1 203 PHE cc_start: 0.8170 (OUTLIER) cc_final: 0.7805 (m-10) REVERT: 1 418 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8323 (ttpt) REVERT: 4 14 PHE cc_start: 0.8567 (OUTLIER) cc_final: 0.7865 (m-80) REVERT: 2 83 ILE cc_start: 0.7286 (OUTLIER) cc_final: 0.6962 (tt) REVERT: 2 98 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7800 (tp) REVERT: 3 340 PHE cc_start: 0.8549 (OUTLIER) cc_final: 0.8049 (p90) REVERT: C 109 TYR cc_start: 0.8403 (m-10) cc_final: 0.8104 (m-10) REVERT: C 275 SER cc_start: 0.8918 (m) cc_final: 0.8607 (p) REVERT: B 53 LYS cc_start: 0.8191 (ptpt) cc_final: 0.7877 (ptmt) REVERT: B 325 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8309 (pp) outliers start: 89 outliers final: 59 residues processed: 278 average time/residue: 0.2646 time to fit residues: 113.6911 Evaluate side-chains 247 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 178 time to evaluate : 1.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 496 PHE Chi-restraints excluded: chain A residue 508 ASP Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain 1 residue 50 THR Chi-restraints excluded: chain 1 residue 79 SER Chi-restraints excluded: chain 1 residue 85 PHE Chi-restraints excluded: chain 1 residue 160 THR Chi-restraints excluded: chain 1 residue 165 LEU Chi-restraints excluded: chain 1 residue 180 SER Chi-restraints excluded: chain 1 residue 194 LEU Chi-restraints excluded: chain 1 residue 203 PHE Chi-restraints excluded: chain 1 residue 220 LEU Chi-restraints excluded: chain 1 residue 230 LEU Chi-restraints excluded: chain 1 residue 233 VAL Chi-restraints excluded: chain 1 residue 250 GLN Chi-restraints excluded: chain 1 residue 288 VAL Chi-restraints excluded: chain 1 residue 293 MET Chi-restraints excluded: chain 1 residue 308 VAL Chi-restraints excluded: chain 1 residue 313 THR Chi-restraints excluded: chain 1 residue 342 THR Chi-restraints excluded: chain 1 residue 377 VAL Chi-restraints excluded: chain 1 residue 418 LYS Chi-restraints excluded: chain 5 residue 84 VAL Chi-restraints excluded: chain 4 residue 14 PHE Chi-restraints excluded: chain 4 residue 30 SER Chi-restraints excluded: chain 2 residue 28 LYS Chi-restraints excluded: chain 2 residue 60 ILE Chi-restraints excluded: chain 2 residue 61 GLN Chi-restraints excluded: chain 2 residue 83 ILE Chi-restraints excluded: chain 2 residue 96 LEU Chi-restraints excluded: chain 2 residue 98 LEU Chi-restraints excluded: chain 3 residue 208 LYS Chi-restraints excluded: chain 3 residue 283 LEU Chi-restraints excluded: chain 3 residue 340 PHE Chi-restraints excluded: chain C residue 94 MET Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 185 HIS Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 387 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 78 optimal weight: 5.9990 chunk 116 optimal weight: 0.9990 chunk 58 optimal weight: 0.0570 chunk 38 optimal weight: 0.9980 chunk 37 optimal weight: 8.9990 chunk 124 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 chunk 96 optimal weight: 0.3980 chunk 18 optimal weight: 5.9990 chunk 153 optimal weight: 5.9990 chunk 177 optimal weight: 0.9980 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 17 GLN 2 61 GLN ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17627 Z= 0.163 Angle : 0.620 10.770 23885 Z= 0.295 Chirality : 0.044 0.362 2688 Planarity : 0.004 0.062 2928 Dihedral : 12.963 159.741 2755 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 4.36 % Allowed : 18.17 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.19), residues: 2043 helix: 1.30 (0.19), residues: 772 sheet: -1.22 (0.28), residues: 347 loop : -2.66 (0.18), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 98 HIS 0.003 0.000 HIS A 385 PHE 0.023 0.001 PHE 3 293 TYR 0.014 0.001 TYR 2 41 ARG 0.002 0.000 ARG A 497 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 190 time to evaluate : 1.944 Fit side-chains REVERT: A 286 LYS cc_start: 0.7700 (ttmm) cc_final: 0.7440 (ttpt) REVERT: A 404 ARG cc_start: 0.8175 (ptt180) cc_final: 0.7621 (ptt180) REVERT: A 412 VAL cc_start: 0.8464 (OUTLIER) cc_final: 0.7911 (p) REVERT: A 510 ASP cc_start: 0.7560 (p0) cc_final: 0.7327 (p0) REVERT: A 565 ASP cc_start: 0.8141 (t0) cc_final: 0.7680 (t70) REVERT: A 663 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.6934 (pp) REVERT: 1 84 TYR cc_start: 0.7281 (m-80) cc_final: 0.6926 (m-10) REVERT: 1 165 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8694 (tt) REVERT: 1 197 LYS cc_start: 0.7322 (mttt) cc_final: 0.6723 (ptmt) REVERT: 1 203 PHE cc_start: 0.8104 (OUTLIER) cc_final: 0.7762 (m-10) REVERT: 4 14 PHE cc_start: 0.8561 (OUTLIER) cc_final: 0.7874 (m-80) REVERT: 2 28 LYS cc_start: 0.7340 (ptpp) cc_final: 0.7120 (ptpp) REVERT: 2 31 LYS cc_start: 0.8207 (ttmm) cc_final: 0.7542 (mtmt) REVERT: 2 83 ILE cc_start: 0.7262 (OUTLIER) cc_final: 0.6962 (tt) REVERT: 2 98 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7767 (tp) REVERT: 3 340 PHE cc_start: 0.8548 (OUTLIER) cc_final: 0.8062 (p90) REVERT: C 97 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7389 (pp20) REVERT: C 109 TYR cc_start: 0.8436 (m-10) cc_final: 0.8064 (m-10) REVERT: C 275 SER cc_start: 0.9029 (m) cc_final: 0.8725 (p) REVERT: B 53 LYS cc_start: 0.8177 (ptpt) cc_final: 0.7846 (ptmt) REVERT: B 325 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8296 (pp) outliers start: 80 outliers final: 61 residues processed: 253 average time/residue: 0.2686 time to fit residues: 105.5030 Evaluate side-chains 251 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 181 time to evaluate : 1.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 496 PHE Chi-restraints excluded: chain A residue 508 ASP Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain 1 residue 50 THR Chi-restraints excluded: chain 1 residue 79 SER Chi-restraints excluded: chain 1 residue 85 PHE Chi-restraints excluded: chain 1 residue 86 THR Chi-restraints excluded: chain 1 residue 160 THR Chi-restraints excluded: chain 1 residue 165 LEU Chi-restraints excluded: chain 1 residue 180 SER Chi-restraints excluded: chain 1 residue 194 LEU Chi-restraints excluded: chain 1 residue 203 PHE Chi-restraints excluded: chain 1 residue 230 LEU Chi-restraints excluded: chain 1 residue 233 VAL Chi-restraints excluded: chain 1 residue 288 VAL Chi-restraints excluded: chain 1 residue 293 MET Chi-restraints excluded: chain 1 residue 308 VAL Chi-restraints excluded: chain 1 residue 313 THR Chi-restraints excluded: chain 1 residue 342 THR Chi-restraints excluded: chain 1 residue 377 VAL Chi-restraints excluded: chain 1 residue 420 THR Chi-restraints excluded: chain 1 residue 455 CYS Chi-restraints excluded: chain 5 residue 84 VAL Chi-restraints excluded: chain 4 residue 14 PHE Chi-restraints excluded: chain 4 residue 30 SER Chi-restraints excluded: chain 2 residue 60 ILE Chi-restraints excluded: chain 2 residue 83 ILE Chi-restraints excluded: chain 2 residue 96 LEU Chi-restraints excluded: chain 2 residue 98 LEU Chi-restraints excluded: chain 3 residue 208 LYS Chi-restraints excluded: chain 3 residue 329 THR Chi-restraints excluded: chain 3 residue 340 PHE Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 94 MET Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 185 HIS Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 387 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 187 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 182 optimal weight: 9.9990 chunk 109 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 143 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 164 optimal weight: 6.9990 chunk 172 optimal weight: 2.9990 chunk 181 optimal weight: 4.9990 chunk 119 optimal weight: 0.0370 overall best weight: 1.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 61 GLN ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17627 Z= 0.222 Angle : 0.636 10.953 23885 Z= 0.305 Chirality : 0.045 0.370 2688 Planarity : 0.004 0.062 2928 Dihedral : 12.883 159.003 2755 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 4.64 % Allowed : 17.95 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.18), residues: 2043 helix: 1.35 (0.19), residues: 770 sheet: -1.23 (0.28), residues: 350 loop : -2.62 (0.18), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 98 HIS 0.003 0.001 HIS A 542 PHE 0.024 0.001 PHE 3 293 TYR 0.015 0.001 TYR 2 41 ARG 0.003 0.000 ARG C 37 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 182 time to evaluate : 1.978 Fit side-chains REVERT: A 286 LYS cc_start: 0.7710 (ttmm) cc_final: 0.7449 (ttpt) REVERT: A 402 MET cc_start: 0.8126 (mtt) cc_final: 0.7585 (mtt) REVERT: A 404 ARG cc_start: 0.8220 (ptt180) cc_final: 0.7691 (ptt180) REVERT: A 412 VAL cc_start: 0.8509 (OUTLIER) cc_final: 0.7968 (p) REVERT: A 510 ASP cc_start: 0.7627 (p0) cc_final: 0.7386 (p0) REVERT: A 565 ASP cc_start: 0.8192 (t0) cc_final: 0.7707 (t70) REVERT: A 663 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.7071 (pp) REVERT: 1 84 TYR cc_start: 0.7352 (m-80) cc_final: 0.6996 (m-10) REVERT: 1 112 ILE cc_start: 0.8369 (mp) cc_final: 0.8112 (mt) REVERT: 1 165 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8757 (tt) REVERT: 1 197 LYS cc_start: 0.7333 (mttt) cc_final: 0.6728 (ptmt) REVERT: 1 203 PHE cc_start: 0.8146 (OUTLIER) cc_final: 0.7873 (m-10) REVERT: 1 232 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.8061 (pt0) REVERT: 1 244 HIS cc_start: 0.8864 (OUTLIER) cc_final: 0.8436 (t-90) REVERT: 1 418 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8363 (ttpt) REVERT: 4 14 PHE cc_start: 0.8587 (OUTLIER) cc_final: 0.7894 (m-80) REVERT: 2 28 LYS cc_start: 0.7359 (ptpp) cc_final: 0.7092 (ptpp) REVERT: 2 31 LYS cc_start: 0.8252 (ttmm) cc_final: 0.7562 (mtmt) REVERT: 2 83 ILE cc_start: 0.7319 (OUTLIER) cc_final: 0.7000 (tt) REVERT: 2 98 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7851 (tp) REVERT: 3 340 PHE cc_start: 0.8575 (OUTLIER) cc_final: 0.8084 (p90) REVERT: C 97 GLU cc_start: 0.7710 (tm-30) cc_final: 0.7439 (pp20) REVERT: C 109 TYR cc_start: 0.8488 (m-10) cc_final: 0.8122 (m-10) REVERT: C 275 SER cc_start: 0.9040 (m) cc_final: 0.8734 (p) REVERT: B 53 LYS cc_start: 0.8232 (ptpt) cc_final: 0.7961 (ptpt) REVERT: B 325 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8357 (pp) outliers start: 85 outliers final: 65 residues processed: 253 average time/residue: 0.2659 time to fit residues: 104.7153 Evaluate side-chains 263 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 186 time to evaluate : 1.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 496 PHE Chi-restraints excluded: chain A residue 508 ASP Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 538 TRP Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain 1 residue 50 THR Chi-restraints excluded: chain 1 residue 79 SER Chi-restraints excluded: chain 1 residue 85 PHE Chi-restraints excluded: chain 1 residue 86 THR Chi-restraints excluded: chain 1 residue 160 THR Chi-restraints excluded: chain 1 residue 165 LEU Chi-restraints excluded: chain 1 residue 180 SER Chi-restraints excluded: chain 1 residue 194 LEU Chi-restraints excluded: chain 1 residue 203 PHE Chi-restraints excluded: chain 1 residue 220 LEU Chi-restraints excluded: chain 1 residue 230 LEU Chi-restraints excluded: chain 1 residue 232 GLN Chi-restraints excluded: chain 1 residue 233 VAL Chi-restraints excluded: chain 1 residue 244 HIS Chi-restraints excluded: chain 1 residue 288 VAL Chi-restraints excluded: chain 1 residue 293 MET Chi-restraints excluded: chain 1 residue 308 VAL Chi-restraints excluded: chain 1 residue 313 THR Chi-restraints excluded: chain 1 residue 342 THR Chi-restraints excluded: chain 1 residue 377 VAL Chi-restraints excluded: chain 1 residue 418 LYS Chi-restraints excluded: chain 1 residue 420 THR Chi-restraints excluded: chain 1 residue 455 CYS Chi-restraints excluded: chain 5 residue 84 VAL Chi-restraints excluded: chain 4 residue 14 PHE Chi-restraints excluded: chain 4 residue 30 SER Chi-restraints excluded: chain 2 residue 59 VAL Chi-restraints excluded: chain 2 residue 60 ILE Chi-restraints excluded: chain 2 residue 61 GLN Chi-restraints excluded: chain 2 residue 83 ILE Chi-restraints excluded: chain 2 residue 96 LEU Chi-restraints excluded: chain 2 residue 98 LEU Chi-restraints excluded: chain 3 residue 208 LYS Chi-restraints excluded: chain 3 residue 283 LEU Chi-restraints excluded: chain 3 residue 329 THR Chi-restraints excluded: chain 3 residue 340 PHE Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 94 MET Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 185 HIS Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 387 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 192 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 134 optimal weight: 0.8980 chunk 202 optimal weight: 0.6980 chunk 186 optimal weight: 7.9990 chunk 161 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 61 GLN ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17627 Z= 0.170 Angle : 0.620 10.812 23885 Z= 0.296 Chirality : 0.044 0.364 2688 Planarity : 0.004 0.060 2928 Dihedral : 12.713 159.394 2755 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 4.47 % Allowed : 18.33 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.19), residues: 2043 helix: 1.44 (0.19), residues: 774 sheet: -1.07 (0.28), residues: 344 loop : -2.58 (0.18), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 98 HIS 0.003 0.000 HIS A 385 PHE 0.022 0.001 PHE 3 293 TYR 0.015 0.001 TYR 2 41 ARG 0.003 0.000 ARG A 497 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 190 time to evaluate : 1.914 Fit side-chains REVERT: A 204 MET cc_start: 0.8548 (tmm) cc_final: 0.8101 (ttt) REVERT: A 286 LYS cc_start: 0.7748 (ttmm) cc_final: 0.7439 (ttpt) REVERT: A 402 MET cc_start: 0.8138 (mtt) cc_final: 0.7594 (mtt) REVERT: A 404 ARG cc_start: 0.8227 (ptt180) cc_final: 0.7694 (ptt180) REVERT: A 412 VAL cc_start: 0.8462 (OUTLIER) cc_final: 0.7963 (p) REVERT: A 481 LEU cc_start: 0.8465 (mm) cc_final: 0.7763 (tp) REVERT: A 510 ASP cc_start: 0.7629 (p0) cc_final: 0.7363 (p0) REVERT: A 565 ASP cc_start: 0.8186 (t0) cc_final: 0.7711 (t70) REVERT: A 663 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.6969 (pp) REVERT: 1 84 TYR cc_start: 0.7318 (m-80) cc_final: 0.6974 (m-10) REVERT: 1 85 PHE cc_start: 0.7544 (OUTLIER) cc_final: 0.7029 (t80) REVERT: 1 112 ILE cc_start: 0.8309 (mp) cc_final: 0.8043 (mt) REVERT: 1 165 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8752 (tt) REVERT: 1 197 LYS cc_start: 0.7375 (mttt) cc_final: 0.6812 (ptmt) REVERT: 1 203 PHE cc_start: 0.8124 (OUTLIER) cc_final: 0.7858 (m-10) REVERT: 1 232 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.8039 (pt0) REVERT: 1 418 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8342 (ttpt) REVERT: 4 14 PHE cc_start: 0.8568 (OUTLIER) cc_final: 0.7877 (m-80) REVERT: 2 28 LYS cc_start: 0.7366 (ptpp) cc_final: 0.7131 (ptpp) REVERT: 2 83 ILE cc_start: 0.7260 (OUTLIER) cc_final: 0.6964 (tt) REVERT: 2 98 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7775 (tp) REVERT: 3 340 PHE cc_start: 0.8555 (OUTLIER) cc_final: 0.8081 (p90) REVERT: C 97 GLU cc_start: 0.7706 (tm-30) cc_final: 0.7455 (pp20) REVERT: C 109 TYR cc_start: 0.8462 (m-10) cc_final: 0.8106 (m-10) REVERT: C 275 SER cc_start: 0.9032 (m) cc_final: 0.8726 (p) REVERT: B 53 LYS cc_start: 0.8223 (ptpt) cc_final: 0.7953 (ptpt) REVERT: B 325 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8320 (pp) outliers start: 82 outliers final: 64 residues processed: 257 average time/residue: 0.2595 time to fit residues: 104.5479 Evaluate side-chains 256 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 180 time to evaluate : 1.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 496 PHE Chi-restraints excluded: chain A residue 508 ASP Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain 1 residue 50 THR Chi-restraints excluded: chain 1 residue 79 SER Chi-restraints excluded: chain 1 residue 85 PHE Chi-restraints excluded: chain 1 residue 86 THR Chi-restraints excluded: chain 1 residue 160 THR Chi-restraints excluded: chain 1 residue 165 LEU Chi-restraints excluded: chain 1 residue 180 SER Chi-restraints excluded: chain 1 residue 194 LEU Chi-restraints excluded: chain 1 residue 203 PHE Chi-restraints excluded: chain 1 residue 220 LEU Chi-restraints excluded: chain 1 residue 230 LEU Chi-restraints excluded: chain 1 residue 232 GLN Chi-restraints excluded: chain 1 residue 233 VAL Chi-restraints excluded: chain 1 residue 288 VAL Chi-restraints excluded: chain 1 residue 293 MET Chi-restraints excluded: chain 1 residue 308 VAL Chi-restraints excluded: chain 1 residue 313 THR Chi-restraints excluded: chain 1 residue 342 THR Chi-restraints excluded: chain 1 residue 377 VAL Chi-restraints excluded: chain 1 residue 418 LYS Chi-restraints excluded: chain 1 residue 420 THR Chi-restraints excluded: chain 1 residue 455 CYS Chi-restraints excluded: chain 5 residue 84 VAL Chi-restraints excluded: chain 4 residue 14 PHE Chi-restraints excluded: chain 4 residue 30 SER Chi-restraints excluded: chain 2 residue 59 VAL Chi-restraints excluded: chain 2 residue 60 ILE Chi-restraints excluded: chain 2 residue 61 GLN Chi-restraints excluded: chain 2 residue 83 ILE Chi-restraints excluded: chain 2 residue 96 LEU Chi-restraints excluded: chain 2 residue 98 LEU Chi-restraints excluded: chain 3 residue 208 LYS Chi-restraints excluded: chain 3 residue 283 LEU Chi-restraints excluded: chain 3 residue 329 THR Chi-restraints excluded: chain 3 residue 340 PHE Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 94 MET Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 185 HIS Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 387 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 171 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 148 optimal weight: 10.0000 chunk 23 optimal weight: 0.0070 chunk 44 optimal weight: 1.9990 chunk 161 optimal weight: 0.8980 chunk 67 optimal weight: 8.9990 chunk 165 optimal weight: 8.9990 chunk 20 optimal weight: 0.2980 chunk 29 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 overall best weight: 1.4402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 61 GLN ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.137756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.108502 restraints weight = 23823.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.107406 restraints weight = 34771.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.108709 restraints weight = 35349.326| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17627 Z= 0.231 Angle : 0.643 10.952 23885 Z= 0.307 Chirality : 0.045 0.373 2688 Planarity : 0.004 0.062 2928 Dihedral : 12.696 158.830 2755 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 4.47 % Allowed : 18.71 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.19), residues: 2043 helix: 1.46 (0.19), residues: 772 sheet: -1.12 (0.28), residues: 350 loop : -2.55 (0.18), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 98 HIS 0.003 0.001 HIS A 542 PHE 0.023 0.001 PHE 3 293 TYR 0.014 0.001 TYR 2 41 ARG 0.003 0.000 ARG A 497 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3417.46 seconds wall clock time: 63 minutes 8.73 seconds (3788.73 seconds total)