Starting phenix.real_space_refine on Fri Sep 27 23:22:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c26_7336/09_2024/6c26_7336_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c26_7336/09_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_7336/09_2024/6c26_7336.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c26_7336/09_2024/6c26_7336.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c26_7336/09_2024/6c26_7336_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c26_7336/09_2024/6c26_7336_neut.cif" } 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. Time to flip 33 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 10.00, per 1000 atoms: 0.58 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 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: 4.71 Conformation dependent library (CDL) restraints added in 2.2 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... Secondary structure from input PDB file: 64 helices and 22 sheets defined 41.4% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.29 Creating SS restraints... Processing helix chain 'A' and resid 5 through 25 Processing helix chain 'A' and resid 25 through 32 removed outlier: 4.089A pdb=" N ILE A 29 " --> pdb=" O PHE A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 38 removed outlier: 3.727A pdb=" N ILE A 37 " --> pdb=" O LEU A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 55 removed outlier: 4.411A pdb=" N ASN A 51 " --> pdb=" O ASP A 47 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N TYR A 52 " --> pdb=" O PRO A 48 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG A 53 " --> pdb=" O TRP A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 61 removed outlier: 3.519A pdb=" N ASN A 60 " --> pdb=" O TYR A 57 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASN A 61 " --> pdb=" O LEU A 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 57 through 61' Processing helix chain 'A' and resid 63 through 68 removed outlier: 3.714A pdb=" N LEU A 67 " --> pdb=" O PHE A 63 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASN A 68 " --> pdb=" O TYR A 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 63 through 68' Processing helix chain 'A' and resid 91 through 104 removed outlier: 3.554A pdb=" N ASN A 103 " --> pdb=" O HIS A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 117 Processing helix chain 'A' and resid 118 through 138 removed outlier: 3.674A pdb=" N PHE A 122 " --> pdb=" O PHE A 118 " (cutoff:3.500A) 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 142 through 150 removed outlier: 3.500A pdb=" N ILE A 150 " --> pdb=" O ALA A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 188 removed outlier: 3.514A pdb=" N ALA A 171 " --> pdb=" O ASN A 167 " (cutoff:3.500A) 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 206 removed outlier: 3.688A pdb=" N SER A 206 " --> pdb=" O PHE A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 216 Processing helix chain 'A' and resid 217 through 228 removed outlier: 3.671A pdb=" N LEU A 227 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N MET A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 251 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) Processing helix chain 'A' and resid 258 through 263 removed outlier: 3.653A pdb=" N ARG A 262 " --> pdb=" O PHE A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 282 removed outlier: 3.888A pdb=" N PHE A 281 " --> pdb=" O GLN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 288 Processing helix chain 'A' and resid 292 through 297 Processing helix chain 'A' and resid 356 through 363 removed outlier: 4.250A pdb=" N PHE A 360 " --> pdb=" O TRP A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 379 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 384 through 399 removed outlier: 4.335A pdb=" N VAL A 388 " --> pdb=" O GLU A 384 " (cutoff:3.500A) 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) Processing helix chain 'A' and resid 409 through 417 removed outlier: 4.082A pdb=" N VAL A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 429 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) removed outlier: 3.716A pdb=" N LEU A 429 " --> pdb=" O PHE A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 473 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) removed outlier: 3.799A pdb=" N ALA A 473 " --> pdb=" O VAL A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 506 removed outlier: 3.565A pdb=" N TYR A 501 " --> pdb=" O ARG A 497 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LEU A 503 " --> pdb=" O ALA A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 518 No H-bonds generated for 'chain 'A' and resid 516 through 518' Processing helix chain 'A' and resid 519 through 527 removed outlier: 3.519A pdb=" N ILE A 523 " --> pdb=" O TYR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 550 Processing helix chain 'A' and resid 553 through 563 removed outlier: 4.558A pdb=" N GLU A 559 " --> pdb=" O GLU A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 594 removed outlier: 3.871A pdb=" N MET A 590 " --> pdb=" O LYS A 586 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE A 591 " --> pdb=" O PHE A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 632 removed outlier: 3.785A pdb=" N LYS A 631 " --> pdb=" O SER A 627 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N MET A 632 " --> pdb=" O LEU A 628 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 627 through 632' Processing helix chain 'A' and resid 641 through 645 removed outlier: 3.774A pdb=" N GLY A 644 " --> pdb=" O PHE A 641 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN A 645 " --> pdb=" O ASN A 642 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 641 through 645' Processing helix chain 'A' and resid 691 through 701 removed outlier: 3.744A pdb=" N GLY A 696 " --> pdb=" O LEU A 692 " (cutoff:3.500A) Processing helix chain '1' and resid 191 through 195 removed outlier: 3.711A pdb=" N LEU 1 194 " --> pdb=" O ASP 1 191 " (cutoff:3.500A) Processing helix chain '1' and resid 269 through 279 removed outlier: 3.912A pdb=" N LEU 1 273 " --> pdb=" O SER 1 269 " (cutoff:3.500A) Processing helix chain '1' and resid 344 through 347 removed outlier: 3.981A pdb=" N ASP 1 347 " --> pdb=" O LYS 1 344 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 344 through 347' Processing helix chain '1' and resid 442 through 447 removed outlier: 4.012A pdb=" N PHE 1 447 " --> pdb=" O LYS 1 443 " (cutoff:3.500A) Processing helix chain '1' and resid 448 through 469 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 12 removed outlier: 3.696A pdb=" N HIS 5 11 " --> pdb=" O TYR 5 7 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER 5 12 " --> pdb=" O LYS 5 8 " (cutoff:3.500A) Processing helix chain '5' and resid 24 through 46 removed outlier: 3.868A pdb=" N PHE 5 28 " --> pdb=" O THR 5 24 " (cutoff:3.500A) 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) Processing helix chain '5' and resid 52 through 80 removed outlier: 4.256A pdb=" N LEU 5 73 " --> pdb=" O LEU 5 69 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN 5 80 " --> pdb=" O VAL 5 76 " (cutoff:3.500A) Processing helix chain '4' and resid 3 through 32 removed outlier: 3.517A pdb=" N LEU 4 7 " --> pdb=" O SER 4 3 " (cutoff:3.500A) 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 41 removed outlier: 3.848A pdb=" N GLN 2 37 " --> pdb=" O ALA 2 33 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR 2 41 " --> pdb=" O GLN 2 37 " (cutoff:3.500A) Processing helix chain '2' and resid 43 through 68 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) removed outlier: 3.654A pdb=" N ILE 2 68 " --> pdb=" O PHE 2 64 " (cutoff:3.500A) Processing helix chain '2' and resid 73 through 100 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) removed outlier: 3.828A pdb=" N ASN 2 100 " --> pdb=" O LEU 2 96 " (cutoff:3.500A) Processing helix chain '2' and resid 108 through 125 removed outlier: 3.929A pdb=" N ALA 2 112 " --> pdb=" O ASN 2 108 " (cutoff:3.500A) 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 209 through 216 Processing helix chain '3' and resid 217 through 233 removed outlier: 3.695A pdb=" N SER 3 233 " --> pdb=" O ILE 3 229 " (cutoff:3.500A) Processing helix chain '3' and resid 234 through 241 removed outlier: 3.897A pdb=" N ASN 3 238 " --> pdb=" O ALA 3 234 " (cutoff:3.500A) Processing helix chain '3' and resid 268 through 289 removed outlier: 3.654A pdb=" N VAL 3 272 " --> pdb=" O ILE 3 268 " (cutoff:3.500A) Processing helix chain '3' and resid 291 through 297 removed outlier: 3.584A pdb=" N ARG 3 295 " --> pdb=" O ILE 3 291 " (cutoff:3.500A) Processing helix chain '3' and resid 305 through 335 removed outlier: 3.773A pdb=" N ASP 3 309 " --> pdb=" O ALA 3 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 127 removed outlier: 3.533A pdb=" N GLU C 125 " --> pdb=" O ALA C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 217 removed outlier: 3.936A pdb=" N LEU C 208 " --> pdb=" O PHE C 204 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER C 217 " --> pdb=" O THR C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 254 removed outlier: 3.806A pdb=" N PHE C 234 " --> pdb=" O THR C 230 " (cutoff:3.500A) 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) removed outlier: 3.928A pdb=" N GLY C 254 " --> pdb=" O ARG C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 283 removed outlier: 3.984A pdb=" N THR C 260 " --> pdb=" O SER C 256 " (cutoff:3.500A) Proline residue: C 270 - end of helix removed outlier: 3.581A pdb=" N GLY C 283 " --> pdb=" O LEU C 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 39 No H-bonds generated for 'chain 'B' and resid 37 through 39' Processing helix chain 'B' and resid 40 through 50 removed outlier: 3.841A pdb=" N LEU B 44 " --> pdb=" O TYR B 40 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASP B 46 " --> pdb=" O VAL B 42 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ARG B 50 " --> pdb=" O ASP B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 94 removed outlier: 3.846A pdb=" N ALA B 91 " --> pdb=" O GLY B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 104 removed outlier: 3.561A pdb=" N LEU B 99 " --> pdb=" O PRO B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 130 Processing helix chain 'B' and resid 246 through 257 removed outlier: 3.648A pdb=" N ALA B 250 " --> pdb=" O ASN B 246 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 412 removed outlier: 3.862A pdb=" N ILE B 396 " --> pdb=" O SER B 392 " (cutoff:3.500A) 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=AA1, first strand: chain 'A' and resid 70 through 71 removed outlier: 3.582A pdb=" N ASP A 71 " --> pdb=" O ARG A 80 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG A 80 " --> pdb=" O ASP A 71 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 530 through 531 removed outlier: 3.633A pdb=" N VAL A 513 " --> pdb=" O THR A 530 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LYS A 512 " --> pdb=" O TYR A 568 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N LEU A 570 " --> pdb=" O LYS A 512 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ALA A 514 " --> pdb=" O LEU A 570 " (cutoff:3.500A) removed outlier: 8.886A pdb=" N ILE A 572 " --> pdb=" O ALA A 514 " (cutoff:3.500A) 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=AA3, first strand: chain 'A' and resid 646 through 647 Processing sheet with id=AA4, first strand: chain '1' and resid 129 through 136 removed outlier: 6.777A pdb=" N SER 1 48 " --> pdb=" O ILE 1 40 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ILE 1 40 " --> pdb=" O SER 1 48 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N THR 1 50 " --> pdb=" O ARG 1 38 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ARG 1 38 " --> pdb=" O THR 1 50 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLU 1 52 " --> pdb=" O TYR 1 36 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N TYR 1 36 " --> pdb=" O GLU 1 52 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N THR 1 54 " --> pdb=" O VAL 1 34 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLU 1 32 " --> pdb=" O LYS 1 56 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N SER 1 174 " --> pdb=" O VAL 1 34 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TYR 1 36 " --> pdb=" O SER 1 174 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N THR 1 176 " --> pdb=" O TYR 1 36 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ARG 1 38 " --> pdb=" O THR 1 176 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ILE 1 178 " --> pdb=" O ARG 1 38 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ILE 1 40 " --> pdb=" O ILE 1 178 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU 1 177 " --> pdb=" O PHE 1 203 " (cutoff:3.500A) Processing sheet with id=AA5, 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=AA6, first strand: chain '1' and resid 142 through 143 removed outlier: 3.721A pdb=" N GLN 1 154 " --> pdb=" O HIS 1 226 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '1' and resid 426 through 427 removed outlier: 9.159A pdb=" N GLN 1 232 " --> pdb=" O TYR 1 374 " (cutoff:3.500A) removed outlier: 9.374A pdb=" N ASN 1 376 " --> pdb=" O GLN 1 232 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL 1 234 " --> pdb=" O ASN 1 376 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N GLU 1 378 " --> pdb=" O VAL 1 234 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU 1 236 " --> pdb=" O GLU 1 378 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N SER 1 380 " --> pdb=" O LEU 1 236 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ARG 1 238 " --> pdb=" O SER 1 380 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N PHE 1 382 " --> pdb=" O ARG 1 238 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ILE 1 240 " --> pdb=" O PHE 1 382 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '1' and resid 231 through 242 current: chain '1' and resid 303 through 305 Processing sheet with id=AA8, first strand: chain '1' and resid 401 through 406 removed outlier: 3.522A pdb=" N VAL 1 417 " --> pdb=" O LEU 1 383 " (cutoff:3.500A) removed outlier: 9.159A pdb=" N GLN 1 232 " --> pdb=" O TYR 1 374 " (cutoff:3.500A) removed outlier: 9.374A pdb=" N ASN 1 376 " --> pdb=" O GLN 1 232 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL 1 234 " --> pdb=" O ASN 1 376 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N GLU 1 378 " --> pdb=" O VAL 1 234 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU 1 236 " --> pdb=" O GLU 1 378 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N SER 1 380 " --> pdb=" O LEU 1 236 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ARG 1 238 " --> pdb=" O SER 1 380 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N PHE 1 382 " --> pdb=" O ARG 1 238 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ILE 1 240 " --> pdb=" O PHE 1 382 " (cutoff:3.500A) Processing sheet with id=AA9, 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: 9.159A pdb=" N GLN 1 232 " --> pdb=" O TYR 1 374 " (cutoff:3.500A) removed outlier: 9.374A pdb=" N ASN 1 376 " --> pdb=" O GLN 1 232 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL 1 234 " --> pdb=" O ASN 1 376 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N GLU 1 378 " --> pdb=" O VAL 1 234 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU 1 236 " --> pdb=" O GLU 1 378 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N SER 1 380 " --> pdb=" O LEU 1 236 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ARG 1 238 " --> pdb=" O SER 1 380 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N PHE 1 382 " --> pdb=" O ARG 1 238 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ILE 1 240 " --> pdb=" O PHE 1 382 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '1' and resid 255 through 259 removed outlier: 9.159A pdb=" N GLN 1 232 " --> pdb=" O TYR 1 374 " (cutoff:3.500A) removed outlier: 9.374A pdb=" N ASN 1 376 " --> pdb=" O GLN 1 232 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL 1 234 " --> pdb=" O ASN 1 376 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N GLU 1 378 " --> pdb=" O VAL 1 234 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU 1 236 " --> pdb=" O GLU 1 378 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N SER 1 380 " --> pdb=" O LEU 1 236 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ARG 1 238 " --> pdb=" O SER 1 380 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N PHE 1 382 " --> pdb=" O ARG 1 238 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ILE 1 240 " --> pdb=" O PHE 1 382 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL 1 417 " --> pdb=" O LEU 1 383 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '1' and resid 291 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=AB3, 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=AB4, first strand: chain 'C' and resid 25 through 27 Processing sheet with id=AB5, first strand: chain 'C' and resid 92 through 96 removed outlier: 6.976A pdb=" N ALA C 135 " --> pdb=" O ILE C 154 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU C 137 " --> pdb=" O ARG C 152 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG C 152 " --> pdb=" O LEU C 137 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 28 through 29 removed outlier: 5.185A pdb=" N MET B 112 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N PHE B 216 " --> pdb=" O ASN B 193 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ASN B 193 " --> pdb=" O PHE B 216 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL B 218 " --> pdb=" O ILE B 191 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 69 through 70 Processing sheet with id=AB8, first strand: chain 'B' and resid 131 through 133 Processing sheet with id=AB9, 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=AC1, 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=AC2, first strand: chain 'B' and resid 263 through 273 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) removed outlier: 4.697A pdb=" N ALA B 269 " --> pdb=" O SER B 293 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N SER B 293 " --> pdb=" O ALA B 269 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N HIS B 271 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ILE B 291 " --> pdb=" O HIS B 271 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N HIS B 273 " --> pdb=" O LYS B 289 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N LYS B 289 " --> pdb=" O HIS B 273 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 304 through 305 Processing sheet with id=AC4, first strand: chain 'B' and resid 321 through 326 removed outlier: 3.706A pdb=" N TYR B 323 " --> pdb=" O LEU B 316 " (cutoff:3.500A) 650 hydrogen bonds defined for protein. 1866 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.37 Time building geometry restraints manager: 5.48 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: 0.00 - 4.58: 23472 4.58 - 9.16: 357 9.16 - 13.74: 43 13.74 - 18.32: 10 18.32 - 22.90: 3 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: 10216 3.06 - 3.67: 23568 3.67 - 4.29: 32830 4.29 - 4.90: 56324 Nonbonded interactions: 122987 Sorted by model distance: nonbonded pdb=" NZ LYS C 77 " pdb=" OG1 THR C 143 " model vdw 1.833 3.120 nonbonded pdb=" OH TYR B 69 " pdb=" ND2 ASN B 105 " model vdw 1.955 3.120 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 3.040 nonbonded pdb=" CG2 ILE B 291 " pdb=" O GLY B 342 " model vdw 2.139 3.460 ... (remaining 122982 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 1.010 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: 0.020 Extract box with map and model: 0.580 Check model and map are aligned: 0.120 Set scattering table: 0.130 Process input model: 40.080 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.940 ------------------------------------------------------------------------------- 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= 0.740 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 : 1.825 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: 0.3032 time to fit residues: 180.5213 Evaluate side-chains 228 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 208 time to evaluate : 1.893 ------------------------------------------------------------------------------- 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: 2.9990 chunk 153 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 159 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 266 HIS ** A 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 ASN A 540 ASN A 674 ASN 1 284 GLN 1 343 ASN ** 1 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 GLN B 259 ASN B 307 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2196 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= 0.231 Angle : 0.754 13.683 23885 Z= 0.373 Chirality : 0.048 0.405 2688 Planarity : 0.005 0.055 2928 Dihedral : 18.517 156.878 2781 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 4.58 % Allowed : 11.40 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.16), residues: 2043 helix: -1.04 (0.17), residues: 802 sheet: -1.88 (0.27), residues: 350 loop : -3.29 (0.16), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 208 HIS 0.004 0.001 HIS A 542 PHE 0.042 0.002 PHE 1 398 TYR 0.023 0.002 TYR 3 235 ARG 0.007 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 320 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 236 time to evaluate : 1.846 Fit side-chains revert: symmetry clash REVERT: A 25 PHE cc_start: 0.7831 (t80) cc_final: 0.6686 (m-10) REVERT: A 65 LYS cc_start: 0.8530 (mttp) cc_final: 0.8287 (mtpt) REVERT: A 122 PHE cc_start: 0.8178 (OUTLIER) cc_final: 0.7705 (m-80) REVERT: A 217 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7965 (tt) REVERT: A 286 LYS cc_start: 0.7846 (ttmm) cc_final: 0.7563 (ttpt) REVERT: A 412 VAL cc_start: 0.8626 (OUTLIER) cc_final: 0.8357 (p) REVERT: A 481 LEU cc_start: 0.8387 (mm) cc_final: 0.7727 (tp) REVERT: A 495 ASP cc_start: 0.8513 (p0) cc_final: 0.8237 (p0) REVERT: A 565 ASP cc_start: 0.8246 (t0) cc_final: 0.7798 (t70) REVERT: A 624 MET cc_start: 0.8966 (tpt) cc_final: 0.8624 (tpt) REVERT: A 663 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7058 (pp) REVERT: A 676 MET cc_start: 0.7831 (ttm) cc_final: 0.7379 (ttm) REVERT: 1 84 TYR cc_start: 0.7563 (m-80) cc_final: 0.7258 (m-10) REVERT: 1 153 GLU cc_start: 0.8263 (mm-30) cc_final: 0.8055 (mm-30) REVERT: 1 197 LYS cc_start: 0.7496 (mttt) cc_final: 0.6958 (ptmt) REVERT: 1 203 PHE cc_start: 0.7962 (OUTLIER) cc_final: 0.7353 (m-10) REVERT: 1 209 GLU cc_start: 0.9004 (OUTLIER) cc_final: 0.8348 (mp0) REVERT: 1 222 ILE cc_start: 0.8906 (OUTLIER) cc_final: 0.8705 (mp) REVERT: 1 242 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8468 (tt) REVERT: 1 371 ASP cc_start: 0.7748 (t0) cc_final: 0.7511 (t0) REVERT: 5 7 TYR cc_start: 0.8717 (t80) cc_final: 0.8424 (t80) REVERT: 4 14 PHE cc_start: 0.8615 (OUTLIER) cc_final: 0.8047 (m-80) REVERT: 2 98 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7994 (tp) REVERT: 3 260 ASN cc_start: 0.8220 (t0) cc_final: 0.8017 (t0) REVERT: C 275 SER cc_start: 0.8858 (m) cc_final: 0.8437 (p) REVERT: B 112 MET cc_start: 0.8139 (ptp) cc_final: 0.7865 (ptt) REVERT: B 299 TRP cc_start: 0.8285 (t60) cc_final: 0.8054 (t-100) REVERT: B 325 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8381 (pp) REVERT: B 348 ASP cc_start: 0.8282 (t0) cc_final: 0.7989 (t0) outliers start: 84 outliers final: 38 residues processed: 306 average time/residue: 0.2723 time to fit residues: 128.3006 Evaluate side-chains 242 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 193 time to evaluate : 1.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 59 VAL 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 217 LEU Chi-restraints excluded: chain A residue 250 SER 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 576 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 177 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 222 ILE 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 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 14 PHE Chi-restraints excluded: chain 4 residue 30 SER Chi-restraints excluded: chain 2 residue 55 VAL Chi-restraints excluded: chain 2 residue 66 ILE Chi-restraints excluded: chain 2 residue 98 LEU 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 182 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 343 GLU 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: 0.9990 chunk 57 optimal weight: 9.9990 chunk 153 optimal weight: 0.1980 chunk 125 optimal weight: 3.9990 chunk 50 optimal weight: 0.0370 chunk 184 optimal weight: 3.9990 chunk 199 optimal weight: 0.9980 chunk 164 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 148 optimal weight: 6.9990 overall best weight: 0.6460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 HIS A 216 ASN ** A 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 17 GLN 4 26 HIS 2 61 GLN C 160 ASN B 32 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17627 Z= 0.179 Angle : 0.676 13.751 23885 Z= 0.328 Chirality : 0.046 0.391 2688 Planarity : 0.005 0.062 2928 Dihedral : 15.854 161.587 2762 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 3.82 % Allowed : 13.86 % Favored : 82.32 % 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: -2.30 (0.17), residues: 2043 helix: 0.03 (0.18), residues: 804 sheet: -1.66 (0.28), residues: 335 loop : -2.98 (0.17), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 49 HIS 0.004 0.001 HIS 1 416 PHE 0.050 0.001 PHE 1 398 TYR 0.017 0.001 TYR 2 41 ARG 0.020 0.001 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 300 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 230 time to evaluate : 2.022 Fit side-chains revert: symmetry clash REVERT: A 25 PHE cc_start: 0.7820 (t80) cc_final: 0.6638 (m-10) REVERT: A 65 LYS cc_start: 0.8482 (mttp) cc_final: 0.8205 (mtpp) REVERT: A 122 PHE cc_start: 0.8035 (OUTLIER) cc_final: 0.7510 (m-80) REVERT: A 217 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7822 (tt) REVERT: A 286 LYS cc_start: 0.7871 (ttmm) cc_final: 0.7603 (ttpt) REVERT: A 402 MET cc_start: 0.7975 (mtt) cc_final: 0.7462 (mtt) REVERT: A 412 VAL cc_start: 0.8521 (OUTLIER) cc_final: 0.8194 (p) REVERT: A 481 LEU cc_start: 0.8421 (mm) cc_final: 0.7798 (tp) REVERT: A 495 ASP cc_start: 0.8445 (p0) cc_final: 0.8131 (m-30) REVERT: A 565 ASP cc_start: 0.8240 (t0) cc_final: 0.7841 (t70) REVERT: A 628 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8927 (tm) REVERT: A 663 LEU cc_start: 0.7469 (OUTLIER) cc_final: 0.6904 (pp) REVERT: 1 84 TYR cc_start: 0.7436 (m-80) cc_final: 0.6963 (m-10) REVERT: 1 153 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7931 (mm-30) REVERT: 1 165 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8582 (tt) REVERT: 1 197 LYS cc_start: 0.7470 (mttt) cc_final: 0.6885 (ptmt) REVERT: 1 203 PHE cc_start: 0.7933 (OUTLIER) cc_final: 0.7335 (m-10) REVERT: 1 391 ASP cc_start: 0.7213 (t0) cc_final: 0.6963 (t0) REVERT: 4 14 PHE cc_start: 0.8613 (OUTLIER) cc_final: 0.8034 (m-80) REVERT: 2 98 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7827 (tp) REVERT: 3 260 ASN cc_start: 0.8336 (t0) cc_final: 0.8057 (t0) REVERT: 3 334 LYS cc_start: 0.7938 (tppt) cc_final: 0.7706 (tptt) REVERT: C 69 ASN cc_start: 0.8120 (t0) cc_final: 0.7833 (t0) REVERT: C 275 SER cc_start: 0.8809 (m) cc_final: 0.8529 (p) REVERT: B 112 MET cc_start: 0.8070 (ptp) cc_final: 0.7862 (ptm) REVERT: B 299 TRP cc_start: 0.8239 (t60) cc_final: 0.7964 (t-100) REVERT: B 325 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8330 (pp) REVERT: B 348 ASP cc_start: 0.8276 (t0) cc_final: 0.7966 (t0) REVERT: B 415 THR cc_start: 0.9474 (OUTLIER) cc_final: 0.9067 (p) outliers start: 70 outliers final: 33 residues processed: 285 average time/residue: 0.2751 time to fit residues: 120.0056 Evaluate side-chains 243 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 199 time to evaluate : 1.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 217 LEU 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 530 THR Chi-restraints excluded: chain A residue 576 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 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 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 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 185 HIS Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain B residue 27 LEU 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 343 GLU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 387 TRP Chi-restraints excluded: chain B residue 415 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 182 optimal weight: 0.5980 chunk 138 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 chunk 185 optimal weight: 1.9990 chunk 196 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 175 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 1 429 GLN 2 61 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2990 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= 0.214 Angle : 0.658 11.829 23885 Z= 0.321 Chirality : 0.046 0.394 2688 Planarity : 0.004 0.053 2928 Dihedral : 14.687 161.108 2756 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 4.42 % Allowed : 14.68 % Favored : 80.91 % 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: -1.93 (0.18), residues: 2043 helix: 0.50 (0.19), residues: 810 sheet: -1.55 (0.28), residues: 334 loop : -2.94 (0.17), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 98 HIS 0.004 0.001 HIS A 542 PHE 0.018 0.001 PHE 1 398 TYR 0.018 0.001 TYR 2 41 ARG 0.003 0.000 ARG A 649 *********************** 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 291 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 210 time to evaluate : 2.137 Fit side-chains REVERT: A 65 LYS cc_start: 0.8540 (mttp) cc_final: 0.8255 (mtpp) REVERT: A 122 PHE cc_start: 0.8023 (OUTLIER) cc_final: 0.7512 (m-80) REVERT: A 217 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7788 (tt) REVERT: A 286 LYS cc_start: 0.7865 (ttmm) cc_final: 0.7605 (ttpt) REVERT: A 402 MET cc_start: 0.7983 (mtt) cc_final: 0.7437 (mtt) REVERT: A 412 VAL cc_start: 0.8530 (OUTLIER) cc_final: 0.8174 (p) REVERT: A 481 LEU cc_start: 0.8422 (mm) cc_final: 0.7790 (tp) REVERT: A 510 ASP cc_start: 0.7438 (p0) cc_final: 0.7211 (p0) REVERT: A 565 ASP cc_start: 0.8262 (t0) cc_final: 0.7847 (t70) REVERT: A 663 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.6952 (pp) REVERT: 1 84 TYR cc_start: 0.7435 (m-80) cc_final: 0.6962 (m-10) REVERT: 1 153 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7879 (mm-30) REVERT: 1 165 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8651 (tt) REVERT: 1 197 LYS cc_start: 0.7474 (mttt) cc_final: 0.6872 (ptmt) REVERT: 1 239 ASP cc_start: 0.7884 (p0) cc_final: 0.7646 (p0) REVERT: 1 391 ASP cc_start: 0.7103 (t0) cc_final: 0.6825 (t0) REVERT: 5 7 TYR cc_start: 0.8664 (t80) cc_final: 0.8384 (t80) REVERT: 4 14 PHE cc_start: 0.8630 (OUTLIER) cc_final: 0.7999 (m-80) REVERT: 2 28 LYS cc_start: 0.7232 (ptpp) cc_final: 0.7031 (ptpp) REVERT: 2 98 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7934 (tp) REVERT: 3 260 ASN cc_start: 0.8341 (t0) cc_final: 0.8020 (t0) REVERT: C 69 ASN cc_start: 0.8330 (t0) cc_final: 0.8042 (t0) REVERT: C 275 SER cc_start: 0.8892 (m) cc_final: 0.8561 (p) REVERT: B 299 TRP cc_start: 0.8261 (t60) cc_final: 0.7916 (t-100) REVERT: B 325 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8393 (pp) REVERT: B 348 ASP cc_start: 0.8269 (t0) cc_final: 0.8038 (t0) REVERT: B 415 THR cc_start: 0.9472 (OUTLIER) cc_final: 0.9045 (p) outliers start: 81 outliers final: 52 residues processed: 274 average time/residue: 0.2801 time to fit residues: 118.9346 Evaluate side-chains 259 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 198 time to evaluate : 1.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 59 VAL 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 217 LEU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 381 LEU 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 530 THR Chi-restraints excluded: chain A residue 576 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 165 LEU Chi-restraints excluded: chain 1 residue 180 SER Chi-restraints excluded: chain 1 residue 194 LEU Chi-restraints excluded: chain 1 residue 195 LEU Chi-restraints excluded: chain 1 residue 203 PHE 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 377 VAL Chi-restraints excluded: chain 1 residue 420 THR Chi-restraints excluded: chain 1 residue 459 THR 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 83 ILE Chi-restraints excluded: chain 2 residue 96 LEU Chi-restraints excluded: chain 2 residue 98 LEU Chi-restraints excluded: chain 3 residue 280 LEU Chi-restraints excluded: chain 3 residue 293 PHE Chi-restraints excluded: chain C residue 57 ILE 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 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 70 ASP Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 343 GLU 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 Chi-restraints excluded: chain B residue 415 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 163 optimal weight: 10.0000 chunk 111 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 146 optimal weight: 0.3980 chunk 80 optimal weight: 2.9990 chunk 167 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 176 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- 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** 1 280 GLN ** 1 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 17627 Z= 0.324 Angle : 0.707 11.518 23885 Z= 0.347 Chirality : 0.048 0.389 2688 Planarity : 0.005 0.070 2928 Dihedral : 14.263 160.376 2756 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 5.67 % Allowed : 14.24 % Favored : 80.09 % 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: -1.80 (0.18), residues: 2043 helix: 0.64 (0.19), residues: 812 sheet: -1.49 (0.28), residues: 335 loop : -2.90 (0.17), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 299 HIS 0.007 0.001 HIS A 542 PHE 0.019 0.002 PHE B 216 TYR 0.014 0.002 TYR 1 441 ARG 0.006 0.000 ARG A 605 *********************** 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 299 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 195 time to evaluate : 1.731 Fit side-chains REVERT: A 24 ILE cc_start: 0.8061 (OUTLIER) cc_final: 0.7810 (mt) REVERT: A 122 PHE cc_start: 0.8072 (OUTLIER) cc_final: 0.7541 (m-80) REVERT: A 217 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7798 (tt) REVERT: A 286 LYS cc_start: 0.7839 (ttmm) cc_final: 0.7581 (ttpt) REVERT: A 402 MET cc_start: 0.8040 (mtt) cc_final: 0.7478 (mtt) REVERT: A 404 ARG cc_start: 0.8186 (ptt180) cc_final: 0.7754 (ptt180) REVERT: A 412 VAL cc_start: 0.8659 (OUTLIER) cc_final: 0.8253 (p) REVERT: A 481 LEU cc_start: 0.8383 (mm) cc_final: 0.7677 (tp) REVERT: A 565 ASP cc_start: 0.8240 (t0) cc_final: 0.7736 (t0) REVERT: A 663 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7111 (pp) REVERT: 1 84 TYR cc_start: 0.7461 (m-80) cc_final: 0.7079 (m-10) REVERT: 1 153 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7882 (mm-30) REVERT: 1 165 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8665 (tt) REVERT: 1 197 LYS cc_start: 0.7418 (mttt) cc_final: 0.6785 (ptmt) REVERT: 1 244 HIS cc_start: 0.8891 (OUTLIER) cc_final: 0.8403 (t-90) REVERT: 1 391 ASP cc_start: 0.7104 (t0) cc_final: 0.6813 (t0) REVERT: 1 418 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8387 (ttpt) REVERT: 4 14 PHE cc_start: 0.8677 (OUTLIER) cc_final: 0.8021 (m-80) REVERT: 2 98 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8161 (tp) REVERT: 3 260 ASN cc_start: 0.8352 (t0) cc_final: 0.8127 (t0) REVERT: C 275 SER cc_start: 0.9033 (m) cc_final: 0.8739 (p) REVERT: B 299 TRP cc_start: 0.8338 (t60) cc_final: 0.7869 (t-100) REVERT: B 325 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8416 (pp) outliers start: 104 outliers final: 66 residues processed: 278 average time/residue: 0.2605 time to fit residues: 112.6937 Evaluate side-chains 266 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 189 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 59 VAL 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 217 LEU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 374 VAL 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 530 THR Chi-restraints excluded: chain A residue 576 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 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 177 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 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 377 VAL Chi-restraints excluded: chain 1 residue 418 LYS Chi-restraints excluded: chain 1 residue 420 THR Chi-restraints excluded: chain 1 residue 459 THR 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 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 293 PHE 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 70 ASP Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 343 GLU 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: 7.9990 chunk 176 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 115 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 196 optimal weight: 0.9980 chunk 163 optimal weight: 8.9990 chunk 90 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 425 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.3277 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= 0.220 Angle : 0.661 11.525 23885 Z= 0.323 Chirality : 0.046 0.379 2688 Planarity : 0.004 0.065 2928 Dihedral : 13.736 160.855 2755 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 4.75 % Allowed : 15.88 % Favored : 79.38 % 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: -1.52 (0.18), residues: 2043 helix: 0.93 (0.19), residues: 810 sheet: -1.34 (0.29), residues: 334 loop : -2.80 (0.17), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 98 HIS 0.004 0.001 HIS A 542 PHE 0.021 0.001 PHE 1 398 TYR 0.014 0.001 TYR 2 41 ARG 0.003 0.000 ARG A 649 *********************** 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 289 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 202 time to evaluate : 1.754 Fit side-chains REVERT: A 122 PHE cc_start: 0.8014 (OUTLIER) cc_final: 0.7493 (m-80) REVERT: A 217 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7754 (tt) REVERT: A 286 LYS cc_start: 0.7830 (ttmm) cc_final: 0.7590 (ttpt) REVERT: A 402 MET cc_start: 0.8171 (mtt) cc_final: 0.7615 (mtt) REVERT: A 404 ARG cc_start: 0.8196 (ptt180) cc_final: 0.7735 (ptt180) REVERT: A 412 VAL cc_start: 0.8581 (OUTLIER) cc_final: 0.8170 (p) REVERT: A 481 LEU cc_start: 0.8357 (mm) cc_final: 0.7657 (tp) REVERT: A 510 ASP cc_start: 0.7445 (p0) cc_final: 0.7217 (p0) REVERT: A 565 ASP cc_start: 0.8237 (t0) cc_final: 0.7714 (t70) REVERT: A 663 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7040 (pp) REVERT: 1 84 TYR cc_start: 0.7462 (m-80) cc_final: 0.7048 (m-10) REVERT: 1 112 ILE cc_start: 0.8323 (mp) cc_final: 0.8113 (mt) REVERT: 1 153 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7917 (mm-30) REVERT: 1 165 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8714 (tt) REVERT: 1 197 LYS cc_start: 0.7388 (mttt) cc_final: 0.6789 (ptmt) REVERT: 1 391 ASP cc_start: 0.7046 (t0) cc_final: 0.6692 (t0) REVERT: 4 14 PHE cc_start: 0.8605 (OUTLIER) cc_final: 0.7920 (m-80) REVERT: 2 98 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.8015 (tp) REVERT: 3 260 ASN cc_start: 0.8343 (t0) cc_final: 0.8123 (t0) REVERT: C 109 TYR cc_start: 0.8467 (m-10) cc_final: 0.8258 (m-10) REVERT: C 275 SER cc_start: 0.8917 (m) cc_final: 0.8606 (p) REVERT: B 53 LYS cc_start: 0.8173 (ptpt) cc_final: 0.7922 (ptpt) REVERT: B 150 GLU cc_start: 0.7382 (mp0) cc_final: 0.7036 (pm20) REVERT: B 299 TRP cc_start: 0.8324 (t60) cc_final: 0.7910 (t-100) REVERT: B 325 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8355 (pp) outliers start: 87 outliers final: 56 residues processed: 273 average time/residue: 0.2535 time to fit residues: 107.8276 Evaluate side-chains 254 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 190 time to evaluate : 1.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 59 VAL 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 183 ILE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 381 LEU 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 530 THR Chi-restraints excluded: chain A residue 576 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 1 residue 50 THR 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 177 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 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 377 VAL Chi-restraints excluded: chain 1 residue 420 THR Chi-restraints excluded: chain 1 residue 455 CYS Chi-restraints excluded: chain 1 residue 459 THR 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 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 2 residue 124 VAL Chi-restraints excluded: chain 3 residue 283 LEU 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 112 MET 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 343 GLU 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: 2.9990 chunk 22 optimal weight: 0.2980 chunk 111 optimal weight: 6.9990 chunk 143 optimal weight: 8.9990 chunk 165 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 195 optimal weight: 0.9980 chunk 122 optimal weight: 5.9990 chunk 119 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 HIS B 247 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17627 Z= 0.233 Angle : 0.664 11.084 23885 Z= 0.323 Chirality : 0.046 0.373 2688 Planarity : 0.004 0.065 2928 Dihedral : 13.418 160.951 2755 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 4.91 % Allowed : 15.82 % Favored : 79.27 % 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: -1.37 (0.18), residues: 2043 helix: 1.08 (0.19), residues: 810 sheet: -1.30 (0.29), residues: 335 loop : -2.73 (0.18), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 98 HIS 0.005 0.001 HIS A 542 PHE 0.013 0.001 PHE 1 398 TYR 0.012 0.001 TYR 2 41 ARG 0.002 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 290 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 200 time to evaluate : 1.873 Fit side-chains REVERT: A 122 PHE cc_start: 0.8013 (OUTLIER) cc_final: 0.7583 (m-80) REVERT: A 217 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7767 (tt) REVERT: A 286 LYS cc_start: 0.7804 (ttmm) cc_final: 0.7563 (ttpt) REVERT: A 368 TRP cc_start: 0.7946 (OUTLIER) cc_final: 0.7598 (t60) REVERT: A 402 MET cc_start: 0.8135 (mtt) cc_final: 0.7593 (mtt) REVERT: A 404 ARG cc_start: 0.8194 (ptt180) cc_final: 0.7778 (ptt180) REVERT: A 412 VAL cc_start: 0.8529 (OUTLIER) cc_final: 0.8085 (p) REVERT: A 510 ASP cc_start: 0.7487 (p0) cc_final: 0.7269 (p0) REVERT: A 550 MET cc_start: 0.8031 (tpp) cc_final: 0.7719 (tpp) REVERT: A 663 LEU cc_start: 0.7599 (OUTLIER) cc_final: 0.7041 (pp) REVERT: 1 84 TYR cc_start: 0.7404 (m-80) cc_final: 0.7041 (m-10) REVERT: 1 112 ILE cc_start: 0.8299 (mp) cc_final: 0.8080 (mt) REVERT: 1 153 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7881 (mm-30) REVERT: 1 165 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8714 (tt) REVERT: 1 197 LYS cc_start: 0.7407 (mttt) cc_final: 0.6794 (ptmt) REVERT: 1 244 HIS cc_start: 0.8859 (OUTLIER) cc_final: 0.8368 (t-90) REVERT: 1 391 ASP cc_start: 0.7025 (t0) cc_final: 0.6662 (t0) REVERT: 1 418 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8505 (ttpt) REVERT: 4 14 PHE cc_start: 0.8636 (OUTLIER) cc_final: 0.7943 (m-80) REVERT: 2 98 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.8018 (tp) REVERT: 3 260 ASN cc_start: 0.8323 (t0) cc_final: 0.8043 (t0) REVERT: C 275 SER cc_start: 0.8927 (m) cc_final: 0.8620 (p) REVERT: B 53 LYS cc_start: 0.8220 (ptpt) cc_final: 0.7873 (ptmt) REVERT: B 150 GLU cc_start: 0.7316 (mp0) cc_final: 0.6829 (pm20) REVERT: B 176 GLU cc_start: 0.7602 (mp0) cc_final: 0.7130 (mt-10) REVERT: B 299 TRP cc_start: 0.8331 (t60) cc_final: 0.7902 (t-100) REVERT: B 325 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8385 (pp) outliers start: 90 outliers final: 65 residues processed: 270 average time/residue: 0.2790 time to fit residues: 116.4301 Evaluate side-chains 268 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 192 time to evaluate : 1.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 59 VAL 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 183 ILE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 368 TRP Chi-restraints excluded: chain A residue 381 LEU 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 530 THR Chi-restraints excluded: chain A residue 538 TRP Chi-restraints excluded: chain A residue 576 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 1 residue 50 THR 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 177 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 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 377 VAL Chi-restraints excluded: chain 1 residue 418 LYS Chi-restraints excluded: chain 1 residue 420 THR Chi-restraints excluded: chain 1 residue 459 THR 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 2 residue 124 VAL 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 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 112 MET 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 343 GLU 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: 4.9990 chunk 116 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 96 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 153 optimal weight: 8.9990 chunk 177 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17627 Z= 0.264 Angle : 0.679 11.456 23885 Z= 0.332 Chirality : 0.047 0.363 2688 Planarity : 0.004 0.066 2928 Dihedral : 13.240 160.330 2755 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 4.75 % Allowed : 16.48 % Favored : 78.78 % 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: -1.30 (0.18), residues: 2043 helix: 1.15 (0.19), residues: 809 sheet: -1.30 (0.28), residues: 346 loop : -2.70 (0.18), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 98 HIS 0.003 0.001 HIS 1 416 PHE 0.015 0.001 PHE B 216 TYR 0.012 0.001 TYR 2 41 ARG 0.003 0.000 ARG A 80 *********************** 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 284 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 197 time to evaluate : 1.840 Fit side-chains REVERT: A 122 PHE cc_start: 0.8062 (OUTLIER) cc_final: 0.7818 (m-80) REVERT: A 217 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7771 (tt) REVERT: A 286 LYS cc_start: 0.7850 (ttmm) cc_final: 0.7563 (ttpt) REVERT: A 368 TRP cc_start: 0.7914 (OUTLIER) cc_final: 0.7544 (t60) REVERT: A 402 MET cc_start: 0.8099 (mtt) cc_final: 0.7553 (mtt) REVERT: A 404 ARG cc_start: 0.8206 (ptt180) cc_final: 0.7745 (ptt180) REVERT: A 412 VAL cc_start: 0.8520 (OUTLIER) cc_final: 0.8023 (p) REVERT: A 431 PHE cc_start: 0.7143 (p90) cc_final: 0.6863 (p90) REVERT: A 550 MET cc_start: 0.8071 (tpp) cc_final: 0.7788 (tpp) REVERT: A 663 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7074 (pp) REVERT: 1 84 TYR cc_start: 0.7435 (m-80) cc_final: 0.7075 (m-10) REVERT: 1 112 ILE cc_start: 0.8324 (mp) cc_final: 0.8083 (mt) REVERT: 1 165 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8748 (tt) REVERT: 1 197 LYS cc_start: 0.7408 (mttt) cc_final: 0.6799 (ptmt) REVERT: 1 244 HIS cc_start: 0.8867 (OUTLIER) cc_final: 0.8394 (t-90) REVERT: 1 391 ASP cc_start: 0.7052 (t0) cc_final: 0.6664 (t0) REVERT: 1 418 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8502 (ttpt) REVERT: 4 14 PHE cc_start: 0.8620 (OUTLIER) cc_final: 0.7908 (m-80) REVERT: 2 98 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8138 (tp) REVERT: 3 260 ASN cc_start: 0.8390 (t0) cc_final: 0.8124 (t0) REVERT: 3 340 PHE cc_start: 0.8611 (OUTLIER) cc_final: 0.8123 (p90) REVERT: C 24 ASP cc_start: 0.7338 (p0) cc_final: 0.6774 (p0) REVERT: C 109 TYR cc_start: 0.8481 (m-10) cc_final: 0.8129 (m-10) REVERT: C 275 SER cc_start: 0.8933 (m) cc_final: 0.8622 (p) REVERT: B 53 LYS cc_start: 0.8253 (ptpt) cc_final: 0.7909 (ptmt) REVERT: B 150 GLU cc_start: 0.7305 (mp0) cc_final: 0.6818 (pm20) REVERT: B 299 TRP cc_start: 0.8335 (t60) cc_final: 0.7852 (t-100) REVERT: B 325 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8385 (pp) outliers start: 87 outliers final: 67 residues processed: 266 average time/residue: 0.2603 time to fit residues: 108.8411 Evaluate side-chains 272 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 193 time to evaluate : 1.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 59 VAL 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 183 ILE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 368 TRP Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 426 ASP 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 530 THR Chi-restraints excluded: chain A residue 538 TRP Chi-restraints excluded: chain A residue 542 HIS Chi-restraints excluded: chain A residue 576 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 1 residue 50 THR 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 177 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 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 377 VAL Chi-restraints excluded: chain 1 residue 418 LYS Chi-restraints excluded: chain 1 residue 420 THR Chi-restraints excluded: chain 1 residue 427 ILE Chi-restraints excluded: chain 1 residue 459 THR 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 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 2 residue 124 VAL 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 94 MET Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 185 HIS Chi-restraints excluded: chain C residue 214 TRP 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 112 MET Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 343 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 187 optimal weight: 2.9990 chunk 171 optimal weight: 0.9990 chunk 182 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 79 optimal weight: 7.9990 chunk 143 optimal weight: 9.9990 chunk 55 optimal weight: 0.8980 chunk 164 optimal weight: 3.9990 chunk 172 optimal weight: 0.7980 chunk 181 optimal weight: 8.9990 chunk 119 optimal weight: 9.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 224 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17627 Z= 0.284 Angle : 0.692 11.478 23885 Z= 0.341 Chirality : 0.047 0.366 2688 Planarity : 0.004 0.066 2928 Dihedral : 13.161 159.867 2755 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 5.07 % Allowed : 16.37 % Favored : 78.56 % 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: -1.29 (0.18), residues: 2043 helix: 1.22 (0.19), residues: 806 sheet: -1.32 (0.28), residues: 349 loop : -2.73 (0.18), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 98 HIS 0.004 0.001 HIS A 542 PHE 0.020 0.002 PHE C 70 TYR 0.014 0.001 TYR 2 41 ARG 0.003 0.000 ARG A 80 *********************** 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 283 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 190 time to evaluate : 1.895 Fit side-chains REVERT: A 204 MET cc_start: 0.8548 (tmm) cc_final: 0.8153 (ttt) REVERT: A 217 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7788 (tt) REVERT: A 286 LYS cc_start: 0.7845 (ttmm) cc_final: 0.7565 (ttpt) REVERT: A 368 TRP cc_start: 0.7932 (OUTLIER) cc_final: 0.7614 (t60) REVERT: A 402 MET cc_start: 0.8065 (mtt) cc_final: 0.7546 (mtt) REVERT: A 404 ARG cc_start: 0.8229 (ptt180) cc_final: 0.7750 (ptt180) REVERT: A 412 VAL cc_start: 0.8497 (OUTLIER) cc_final: 0.8010 (p) REVERT: A 431 PHE cc_start: 0.7165 (p90) cc_final: 0.6761 (p90) REVERT: A 510 ASP cc_start: 0.7502 (p0) cc_final: 0.7290 (p0) REVERT: A 550 MET cc_start: 0.8079 (tpp) cc_final: 0.7817 (tpp) REVERT: A 663 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7059 (pp) REVERT: 1 84 TYR cc_start: 0.7465 (m-80) cc_final: 0.7104 (m-10) REVERT: 1 112 ILE cc_start: 0.8332 (mp) cc_final: 0.8084 (mt) REVERT: 1 153 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7874 (mm-30) REVERT: 1 165 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8752 (tt) REVERT: 1 197 LYS cc_start: 0.7411 (mttt) cc_final: 0.6807 (ptmt) REVERT: 1 244 HIS cc_start: 0.8891 (OUTLIER) cc_final: 0.8425 (t-90) REVERT: 1 391 ASP cc_start: 0.7044 (t0) cc_final: 0.6631 (t0) REVERT: 1 418 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8504 (ttpt) REVERT: 4 14 PHE cc_start: 0.8662 (OUTLIER) cc_final: 0.7939 (m-80) REVERT: 2 98 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8176 (tp) REVERT: 3 260 ASN cc_start: 0.8397 (t0) cc_final: 0.8115 (t0) REVERT: 3 340 PHE cc_start: 0.8594 (OUTLIER) cc_final: 0.8119 (p90) REVERT: C 109 TYR cc_start: 0.8448 (m-10) cc_final: 0.8127 (m-10) REVERT: C 216 ASN cc_start: 0.8390 (t0) cc_final: 0.8144 (t0) REVERT: C 275 SER cc_start: 0.8948 (m) cc_final: 0.8641 (p) REVERT: B 53 LYS cc_start: 0.8256 (ptpt) cc_final: 0.7990 (ptpt) REVERT: B 150 GLU cc_start: 0.7312 (mp0) cc_final: 0.6816 (pm20) REVERT: B 176 GLU cc_start: 0.7618 (mp0) cc_final: 0.7213 (mt-10) REVERT: B 299 TRP cc_start: 0.8347 (t60) cc_final: 0.7820 (t-100) REVERT: B 325 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8426 (pp) outliers start: 93 outliers final: 69 residues processed: 267 average time/residue: 0.2636 time to fit residues: 110.4079 Evaluate side-chains 259 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 179 time to evaluate : 1.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 59 VAL 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 130 THR Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 368 TRP 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 440 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 496 PHE Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 538 TRP Chi-restraints excluded: chain A residue 542 HIS Chi-restraints excluded: chain A residue 576 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 1 residue 50 THR 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 177 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 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 418 LYS Chi-restraints excluded: chain 1 residue 420 THR Chi-restraints excluded: chain 1 residue 427 ILE Chi-restraints excluded: chain 1 residue 459 THR 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 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 2 residue 124 VAL 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 94 MET Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 168 SER 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 112 MET Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 343 GLU 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: 2.9990 chunk 117 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 134 optimal weight: 0.9990 chunk 202 optimal weight: 0.5980 chunk 186 optimal weight: 7.9990 chunk 161 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 chunk 127 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 17 GLN C 224 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17627 Z= 0.184 Angle : 0.658 11.076 23885 Z= 0.321 Chirality : 0.045 0.358 2688 Planarity : 0.004 0.063 2928 Dihedral : 12.836 160.901 2755 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 3.87 % Allowed : 17.57 % Favored : 78.56 % 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: 1.45 (0.19), residues: 805 sheet: -1.22 (0.28), residues: 349 loop : -2.64 (0.18), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 98 HIS 0.003 0.001 HIS A 542 PHE 0.019 0.001 PHE C 204 TYR 0.014 0.001 TYR 2 41 ARG 0.004 0.000 ARG B 349 ********************** 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 262 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 191 time to evaluate : 1.936 Fit side-chains REVERT: A 217 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7790 (tt) REVERT: A 286 LYS cc_start: 0.7826 (ttmm) cc_final: 0.7544 (ttpt) REVERT: A 368 TRP cc_start: 0.7885 (OUTLIER) cc_final: 0.7587 (t60) REVERT: A 381 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7439 (mt) REVERT: A 402 MET cc_start: 0.8154 (mtt) cc_final: 0.7653 (mtt) REVERT: A 404 ARG cc_start: 0.8203 (ptt180) cc_final: 0.7763 (ptt180) REVERT: A 412 VAL cc_start: 0.8446 (OUTLIER) cc_final: 0.7998 (p) REVERT: A 431 PHE cc_start: 0.7267 (p90) cc_final: 0.6880 (p90) REVERT: A 495 ASP cc_start: 0.8601 (p0) cc_final: 0.8395 (p0) REVERT: A 510 ASP cc_start: 0.7477 (p0) cc_final: 0.7264 (p0) REVERT: A 550 MET cc_start: 0.7991 (tpp) cc_final: 0.7757 (tpp) REVERT: A 663 LEU cc_start: 0.7528 (OUTLIER) cc_final: 0.6992 (pp) REVERT: 1 84 TYR cc_start: 0.7417 (m-80) cc_final: 0.6982 (m-10) REVERT: 1 112 ILE cc_start: 0.8309 (mp) cc_final: 0.8052 (mt) REVERT: 1 165 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8751 (tt) REVERT: 1 197 LYS cc_start: 0.7387 (mttt) cc_final: 0.6807 (ptmt) REVERT: 1 244 HIS cc_start: 0.8850 (OUTLIER) cc_final: 0.8388 (t-90) REVERT: 1 391 ASP cc_start: 0.7001 (t0) cc_final: 0.6593 (t0) REVERT: 4 14 PHE cc_start: 0.8602 (OUTLIER) cc_final: 0.7881 (m-80) REVERT: 2 83 ILE cc_start: 0.7200 (OUTLIER) cc_final: 0.6934 (tt) REVERT: 2 98 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7970 (tp) REVERT: 3 260 ASN cc_start: 0.8366 (t0) cc_final: 0.8038 (t0) REVERT: 3 340 PHE cc_start: 0.8548 (OUTLIER) cc_final: 0.8096 (p90) REVERT: C 109 TYR cc_start: 0.8463 (m-10) cc_final: 0.8121 (m-10) REVERT: C 275 SER cc_start: 0.8933 (m) cc_final: 0.8626 (p) REVERT: B 53 LYS cc_start: 0.8243 (ptpt) cc_final: 0.7904 (ptmt) REVERT: B 176 GLU cc_start: 0.7664 (mp0) cc_final: 0.7193 (mt-10) REVERT: B 299 TRP cc_start: 0.8287 (t60) cc_final: 0.7848 (t-100) REVERT: B 325 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8356 (pp) outliers start: 71 outliers final: 55 residues processed: 248 average time/residue: 0.2747 time to fit residues: 106.2981 Evaluate side-chains 252 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 185 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 59 VAL 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 183 ILE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 368 TRP 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 440 ILE Chi-restraints excluded: chain A residue 496 PHE Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 538 TRP Chi-restraints excluded: chain A residue 576 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 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 177 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 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 377 VAL Chi-restraints excluded: chain 1 residue 455 CYS Chi-restraints excluded: chain 1 residue 459 THR 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 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 283 LEU Chi-restraints excluded: chain 3 residue 329 THR 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 185 HIS Chi-restraints excluded: chain C residue 214 TRP Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 112 MET 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 343 GLU 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: 0.9980 chunk 49 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 161 optimal weight: 0.9990 chunk 67 optimal weight: 6.9990 chunk 165 optimal weight: 6.9990 chunk 20 optimal weight: 0.4980 chunk 29 optimal weight: 5.9990 chunk 141 optimal weight: 7.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 118 GLN C 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.137835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.108417 restraints weight = 23907.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.107692 restraints weight = 33614.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.108928 restraints weight = 31627.449| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3716 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= 0.220 Angle : 0.667 11.091 23885 Z= 0.325 Chirality : 0.046 0.367 2688 Planarity : 0.004 0.062 2928 Dihedral : 12.693 160.618 2755 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 4.15 % Allowed : 17.62 % Favored : 78.23 % 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: -1.03 (0.19), residues: 2043 helix: 1.49 (0.19), residues: 804 sheet: -1.21 (0.28), residues: 350 loop : -2.62 (0.18), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 98 HIS 0.004 0.001 HIS A 542 PHE 0.019 0.001 PHE C 204 TYR 0.012 0.001 TYR 2 41 ARG 0.002 0.000 ARG A 80 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3327.62 seconds wall clock time: 60 minutes 43.05 seconds (3643.05 seconds total)