Starting phenix.real_space_refine on Fri Mar 15 00:46:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk7_32561/03_2024/7wk7_32561_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk7_32561/03_2024/7wk7_32561.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk7_32561/03_2024/7wk7_32561.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk7_32561/03_2024/7wk7_32561.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk7_32561/03_2024/7wk7_32561_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk7_32561/03_2024/7wk7_32561_updated.pdb" } resolution = 3.49 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= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 6658 2.51 5 N 1684 2.21 5 O 1822 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 39": "NH1" <-> "NH2" Residue "A ARG 79": "NH1" <-> "NH2" Residue "A PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 536": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 586": "NH1" <-> "NH2" Residue "A ARG 587": "NH1" <-> "NH2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B ARG 79": "NH1" <-> "NH2" Residue "B PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 536": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 586": "NH1" <-> "NH2" Residue "B ARG 587": "NH1" <-> "NH2" Residue "B PHE 667": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10206 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5099 Classifications: {'peptide': 665} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 26, 'TRANS': 638} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 6} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 5099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5099 Classifications: {'peptide': 665} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 26, 'TRANS': 638} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 6} Unresolved non-hydrogen planarities: 30 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'BCT': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'BCT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.52, per 1000 atoms: 0.54 Number of scatterers: 10206 At special positions: 0 Unit cell: (86.818, 127.612, 118.198, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 1822 8.00 N 1684 7.00 C 6658 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.05 Conformation dependent library (CDL) restraints added in 2.0 seconds 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2472 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 56 helices and 2 sheets defined 59.2% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.04 Creating SS restraints... Processing helix chain 'A' and resid 30 through 33 No H-bonds generated for 'chain 'A' and resid 30 through 33' Processing helix chain 'A' and resid 46 through 53 Processing helix chain 'A' and resid 58 through 68 Processing helix chain 'A' and resid 70 through 74 removed outlier: 3.910A pdb=" N TRP A 74 " --> pdb=" O ILE A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 107 removed outlier: 4.950A pdb=" N LEU A 85 " --> pdb=" O LYS A 81 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N LEU A 107 " --> pdb=" O MET A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 119 removed outlier: 3.591A pdb=" N LEU A 117 " --> pdb=" O VAL A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 142 through 155 Processing helix chain 'A' and resid 180 through 205 Processing helix chain 'A' and resid 210 through 214 removed outlier: 3.921A pdb=" N TYR A 214 " --> pdb=" O ILE A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 240 Processing helix chain 'A' and resid 252 through 263 Processing helix chain 'A' and resid 269 through 291 Processing helix chain 'A' and resid 302 through 316 Processing helix chain 'A' and resid 350 through 373 Processing helix chain 'A' and resid 381 through 398 removed outlier: 3.537A pdb=" N PHE A 397 " --> pdb=" O VAL A 393 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE A 398 " --> pdb=" O PHE A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 415 removed outlier: 3.901A pdb=" N GLN A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 436 removed outlier: 3.610A pdb=" N ILE A 430 " --> pdb=" O ILE A 426 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL A 431 " --> pdb=" O SER A 427 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL A 436 " --> pdb=" O MET A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 444 Proline residue: A 444 - end of helix No H-bonds generated for 'chain 'A' and resid 441 through 444' Processing helix chain 'A' and resid 447 through 473 removed outlier: 3.757A pdb=" N VAL A 453 " --> pdb=" O VAL A 449 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL A 454 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ILE A 455 " --> pdb=" O ALA A 451 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LYS A 459 " --> pdb=" O ILE A 455 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N GLY A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N MET A 461 " --> pdb=" O ASN A 457 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN A 464 " --> pdb=" O GLY A 460 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N VAL A 465 " --> pdb=" O MET A 461 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N CYS A 466 " --> pdb=" O PHE A 462 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N ASP A 467 " --> pdb=" O MET A 463 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N VAL A 468 " --> pdb=" O GLN A 464 " (cutoff:3.500A) Proline residue: A 469 - end of helix removed outlier: 3.676A pdb=" N LYS A 473 " --> pdb=" O PRO A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 491 removed outlier: 3.786A pdb=" N ILE A 490 " --> pdb=" O CYS A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 514 removed outlier: 3.696A pdb=" N LEU A 499 " --> pdb=" O ASP A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 570 Processing helix chain 'A' and resid 574 through 594 removed outlier: 3.834A pdb=" N TYR A 578 " --> pdb=" O ALA A 574 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG A 586 " --> pdb=" O LEU A 582 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ARG A 587 " --> pdb=" O LYS A 583 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE A 588 " --> pdb=" O ALA A 584 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS A 590 " --> pdb=" O ARG A 586 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE A 592 " --> pdb=" O ILE A 588 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LYS A 593 " --> pdb=" O GLN A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 685 removed outlier: 4.131A pdb=" N SER A 675 " --> pdb=" O VAL A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 705 removed outlier: 3.624A pdb=" N LYS A 702 " --> pdb=" O ASP A 698 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN A 705 " --> pdb=" O GLU A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 717 No H-bonds generated for 'chain 'A' and resid 715 through 717' Processing helix chain 'A' and resid 722 through 735 removed outlier: 3.553A pdb=" N ILE A 726 " --> pdb=" O VAL A 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'B' and resid 46 through 53 removed outlier: 3.805A pdb=" N LEU B 50 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA B 51 " --> pdb=" O ARG B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 68 removed outlier: 3.540A pdb=" N VAL B 65 " --> pdb=" O ALA B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 74 removed outlier: 3.794A pdb=" N TRP B 74 " --> pdb=" O ILE B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 109 removed outlier: 3.633A pdb=" N LEU B 84 " --> pdb=" O VAL B 80 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N LEU B 85 " --> pdb=" O LYS B 81 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER B 86 " --> pdb=" O GLU B 82 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE B 89 " --> pdb=" O LEU B 85 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL B 92 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N MET B 103 " --> pdb=" O THR B 99 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA B 106 " --> pdb=" O GLY B 102 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LEU B 107 " --> pdb=" O MET B 103 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU B 108 " --> pdb=" O ALA B 104 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA B 109 " --> pdb=" O TYR B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 120 removed outlier: 3.818A pdb=" N TYR B 118 " --> pdb=" O GLN B 114 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER B 119 " --> pdb=" O PHE B 115 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 114 through 120' Processing helix chain 'B' and resid 122 through 128 removed outlier: 3.652A pdb=" N PHE B 128 " --> pdb=" O ILE B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 155 removed outlier: 3.685A pdb=" N VAL B 151 " --> pdb=" O MET B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 160 No H-bonds generated for 'chain 'B' and resid 158 through 160' Processing helix chain 'B' and resid 181 through 205 removed outlier: 3.738A pdb=" N ARG B 185 " --> pdb=" O ARG B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 212 No H-bonds generated for 'chain 'B' and resid 210 through 212' Processing helix chain 'B' and resid 217 through 240 removed outlier: 3.627A pdb=" N PHE B 229 " --> pdb=" O THR B 225 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE B 238 " --> pdb=" O SER B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 262 Processing helix chain 'B' and resid 269 through 291 removed outlier: 3.617A pdb=" N ALA B 274 " --> pdb=" O ALA B 270 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR B 278 " --> pdb=" O ALA B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 316 removed outlier: 3.727A pdb=" N THR B 307 " --> pdb=" O GLU B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 373 removed outlier: 3.941A pdb=" N SER B 355 " --> pdb=" O ALA B 351 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TYR B 361 " --> pdb=" O ALA B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 398 removed outlier: 3.876A pdb=" N PHE B 385 " --> pdb=" O GLY B 381 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE B 386 " --> pdb=" O ASN B 382 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE B 397 " --> pdb=" O VAL B 393 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N PHE B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 415 removed outlier: 3.552A pdb=" N VAL B 412 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN B 413 " --> pdb=" O ARG B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 436 removed outlier: 3.539A pdb=" N VAL B 431 " --> pdb=" O SER B 427 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL B 436 " --> pdb=" O MET B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 473 removed outlier: 4.015A pdb=" N VAL B 454 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ILE B 455 " --> pdb=" O ALA B 451 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN B 457 " --> pdb=" O VAL B 453 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU B 458 " --> pdb=" O VAL B 454 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LYS B 459 " --> pdb=" O ILE B 455 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLY B 460 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N MET B 461 " --> pdb=" O ASN B 457 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN B 464 " --> pdb=" O GLY B 460 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N VAL B 465 " --> pdb=" O MET B 461 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N CYS B 466 " --> pdb=" O PHE B 462 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N ASP B 467 " --> pdb=" O MET B 463 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N VAL B 468 " --> pdb=" O GLN B 464 " (cutoff:3.500A) Proline residue: B 469 - end of helix removed outlier: 3.651A pdb=" N LYS B 473 " --> pdb=" O PRO B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 491 removed outlier: 3.770A pdb=" N ILE B 490 " --> pdb=" O CYS B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 514 removed outlier: 3.646A pdb=" N LEU B 499 " --> pdb=" O ASP B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 570 removed outlier: 3.612A pdb=" N LYS B 563 " --> pdb=" O VAL B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 594 removed outlier: 3.885A pdb=" N TYR B 578 " --> pdb=" O ALA B 574 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ARG B 587 " --> pdb=" O LYS B 583 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE B 588 " --> pdb=" O ALA B 584 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS B 590 " --> pdb=" O ARG B 586 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE B 592 " --> pdb=" O ILE B 588 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LYS B 593 " --> pdb=" O GLN B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 685 removed outlier: 4.855A pdb=" N SER B 675 " --> pdb=" O VAL B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 697 through 705 removed outlier: 3.824A pdb=" N LYS B 702 " --> pdb=" O ASP B 698 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN B 705 " --> pdb=" O GLU B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 717 No H-bonds generated for 'chain 'B' and resid 715 through 717' Processing helix chain 'B' and resid 722 through 735 removed outlier: 3.513A pdb=" N ILE B 726 " --> pdb=" O VAL B 722 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 545 through 549 removed outlier: 6.666A pdb=" N SER A 657 " --> pdb=" O LYS A 546 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N LEU A 548 " --> pdb=" O SER A 657 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL A 659 " --> pdb=" O LEU A 548 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ASN A 689 " --> pdb=" O LEU A 658 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N LEU A 660 " --> pdb=" O ASN A 689 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N TYR A 691 " --> pdb=" O LEU A 660 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'B' and resid 545 through 549 removed outlier: 6.739A pdb=" N SER B 657 " --> pdb=" O LYS B 546 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N LEU B 548 " --> pdb=" O SER B 657 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL B 659 " --> pdb=" O LEU B 548 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ASN B 689 " --> pdb=" O LEU B 658 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N LEU B 660 " --> pdb=" O ASN B 689 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TYR B 691 " --> pdb=" O LEU B 660 " (cutoff:3.500A) No H-bonds generated for sheet with id= B 469 hydrogen bonds defined for protein. 1329 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: 2.64 Time building geometry restraints manager: 4.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3203 1.34 - 1.46: 1355 1.46 - 1.57: 5784 1.57 - 1.69: 0 1.69 - 1.81: 64 Bond restraints: 10406 Sorted by residual: bond pdb=" C BCT B 800 " pdb=" O3 BCT B 800 " ideal model delta sigma weight residual 1.389 1.436 -0.047 2.00e-02 2.50e+03 5.50e+00 bond pdb=" C BCT A 800 " pdb=" O3 BCT A 800 " ideal model delta sigma weight residual 1.389 1.435 -0.046 2.00e-02 2.50e+03 5.34e+00 bond pdb=" C VAL B 653 " pdb=" N PRO B 654 " ideal model delta sigma weight residual 1.334 1.355 -0.021 2.34e-02 1.83e+03 8.24e-01 bond pdb=" C VAL A 653 " pdb=" N PRO A 654 " ideal model delta sigma weight residual 1.334 1.354 -0.021 2.34e-02 1.83e+03 7.75e-01 bond pdb=" N ASN A 167 " pdb=" CA ASN A 167 " ideal model delta sigma weight residual 1.457 1.468 -0.010 1.29e-02 6.01e+03 6.27e-01 ... (remaining 10401 not shown) Histogram of bond angle deviations from ideal: 100.76 - 107.42: 296 107.42 - 114.08: 6183 114.08 - 120.74: 4476 120.74 - 127.39: 3110 127.39 - 134.05: 77 Bond angle restraints: 14142 Sorted by residual: angle pdb=" C ARG B 79 " pdb=" N VAL B 80 " pdb=" CA VAL B 80 " ideal model delta sigma weight residual 120.62 124.97 -4.35 1.64e+00 3.72e-01 7.03e+00 angle pdb=" N LEU A 521 " pdb=" CA LEU A 521 " pdb=" C LEU A 521 " ideal model delta sigma weight residual 110.42 113.96 -3.54 1.46e+00 4.69e-01 5.86e+00 angle pdb=" N LEU B 521 " pdb=" CA LEU B 521 " pdb=" C LEU B 521 " ideal model delta sigma weight residual 110.42 113.93 -3.51 1.46e+00 4.69e-01 5.79e+00 angle pdb=" C ALA B 434 " pdb=" N ILE B 435 " pdb=" CA ILE B 435 " ideal model delta sigma weight residual 122.66 120.34 2.32 9.70e-01 1.06e+00 5.71e+00 angle pdb=" C GLY A 520 " pdb=" N LEU A 521 " pdb=" CA LEU A 521 " ideal model delta sigma weight residual 121.56 125.25 -3.69 1.56e+00 4.11e-01 5.59e+00 ... (remaining 14137 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.24: 5994 17.24 - 34.49: 153 34.49 - 51.73: 24 51.73 - 68.97: 3 68.97 - 86.22: 8 Dihedral angle restraints: 6182 sinusoidal: 2346 harmonic: 3836 Sorted by residual: dihedral pdb=" N LEU A 496 " pdb=" CA LEU A 496 " pdb=" CB LEU A 496 " pdb=" CG LEU A 496 " ideal model delta sinusoidal sigma weight residual -180.00 -123.81 -56.19 3 1.50e+01 4.44e-03 9.39e+00 dihedral pdb=" CB GLU A 303 " pdb=" CG GLU A 303 " pdb=" CD GLU A 303 " pdb=" OE1 GLU A 303 " ideal model delta sinusoidal sigma weight residual 0.00 -82.21 82.21 1 3.00e+01 1.11e-03 9.22e+00 dihedral pdb=" N LEU B 727 " pdb=" CA LEU B 727 " pdb=" CB LEU B 727 " pdb=" CG LEU B 727 " ideal model delta sinusoidal sigma weight residual -180.00 -127.36 -52.64 3 1.50e+01 4.44e-03 9.13e+00 ... (remaining 6179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 975 0.026 - 0.052: 469 0.052 - 0.077: 181 0.077 - 0.103: 75 0.103 - 0.129: 18 Chirality restraints: 1718 Sorted by residual: chirality pdb=" CA PRO B 553 " pdb=" N PRO B 553 " pdb=" C PRO B 553 " pdb=" CB PRO B 553 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.16e-01 chirality pdb=" CA PRO A 553 " pdb=" N PRO A 553 " pdb=" C PRO A 553 " pdb=" CB PRO A 553 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.09e-01 chirality pdb=" CA LEU A 668 " pdb=" N LEU A 668 " pdb=" C LEU A 668 " pdb=" CB LEU A 668 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.86e-01 ... (remaining 1715 not shown) Planarity restraints: 1760 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 552 " 0.021 5.00e-02 4.00e+02 3.14e-02 1.57e+00 pdb=" N PRO B 553 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO B 553 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 553 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 552 " 0.020 5.00e-02 4.00e+02 3.04e-02 1.48e+00 pdb=" N PRO A 553 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 553 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 553 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 300 " 0.020 5.00e-02 4.00e+02 2.99e-02 1.43e+00 pdb=" N PRO B 301 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO B 301 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 301 " 0.017 5.00e-02 4.00e+02 ... (remaining 1757 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1095 2.74 - 3.28: 10921 3.28 - 3.82: 16714 3.82 - 4.36: 19786 4.36 - 4.90: 33419 Nonbonded interactions: 81935 Sorted by model distance: nonbonded pdb=" OH TYR A 78 " pdb=" OD2 ASP A 87 " model vdw 2.206 2.440 nonbonded pdb=" OG SER A 90 " pdb=" O GLY A 417 " model vdw 2.221 2.440 nonbonded pdb=" OD1 ASN B 475 " pdb=" OG1 THR B 477 " model vdw 2.227 2.440 nonbonded pdb=" OD1 ASN A 475 " pdb=" OG1 THR A 477 " model vdw 2.229 2.440 nonbonded pdb=" O THR A 485 " pdb=" OG SER A 489 " model vdw 2.237 2.440 ... (remaining 81930 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 6.990 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 29.490 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 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 : 0.002 0.047 10406 Z= 0.116 Angle : 0.440 5.051 14142 Z= 0.246 Chirality : 0.037 0.129 1718 Planarity : 0.003 0.031 1760 Dihedral : 8.683 86.216 3710 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.54 % Favored : 95.39 % Rotamer: Outliers : 3.12 % Allowed : 5.17 % Favored : 91.71 % 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: -3.90 (0.18), residues: 1322 helix: -2.07 (0.14), residues: 838 sheet: -4.06 (0.61), residues: 34 loop : -3.22 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 83 HIS 0.001 0.000 HIS B 656 PHE 0.009 0.001 PHE B 555 TYR 0.009 0.001 TYR A 127 ARG 0.001 0.000 ARG A 512 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 438 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASP cc_start: 0.8008 (t70) cc_final: 0.7682 (p0) REVERT: A 195 LEU cc_start: 0.8361 (tp) cc_final: 0.8161 (tp) REVERT: A 213 ARG cc_start: 0.7653 (mtt180) cc_final: 0.7424 (mtm-85) REVERT: A 236 LEU cc_start: 0.8466 (tp) cc_final: 0.8144 (tt) REVERT: A 237 LYS cc_start: 0.8670 (ttpp) cc_final: 0.8377 (tttt) REVERT: A 244 THR cc_start: 0.8102 (p) cc_final: 0.7341 (p) REVERT: A 245 LYS cc_start: 0.7687 (ttmm) cc_final: 0.7344 (ttmm) REVERT: A 247 TYR cc_start: 0.7572 (m-10) cc_final: 0.6639 (m-10) REVERT: A 262 GLN cc_start: 0.7474 (mt0) cc_final: 0.7184 (mt0) REVERT: A 276 LEU cc_start: 0.8432 (tp) cc_final: 0.7941 (tt) REVERT: A 280 ILE cc_start: 0.8409 (mt) cc_final: 0.8033 (mm) REVERT: A 350 LEU cc_start: 0.6770 (OUTLIER) cc_final: 0.6449 (tm) REVERT: A 361 TYR cc_start: 0.8286 (t80) cc_final: 0.8029 (t80) REVERT: A 369 LYS cc_start: 0.8130 (mmtt) cc_final: 0.7733 (mmtt) REVERT: A 384 GLU cc_start: 0.6957 (mm-30) cc_final: 0.6573 (mm-30) REVERT: A 385 PHE cc_start: 0.8293 (OUTLIER) cc_final: 0.8005 (t80) REVERT: A 391 SER cc_start: 0.8553 (m) cc_final: 0.8224 (p) REVERT: A 394 PHE cc_start: 0.8343 (t80) cc_final: 0.7437 (t80) REVERT: A 398 PHE cc_start: 0.7707 (m-80) cc_final: 0.7392 (m-80) REVERT: A 432 MET cc_start: 0.7318 (tpt) cc_final: 0.6933 (tpt) REVERT: A 447 LYS cc_start: 0.8776 (mtpt) cc_final: 0.8322 (mtpp) REVERT: A 448 SER cc_start: 0.9040 (m) cc_final: 0.8530 (t) REVERT: A 470 ARG cc_start: 0.7426 (tpp80) cc_final: 0.7180 (tpp80) REVERT: A 475 ASN cc_start: 0.7165 (t0) cc_final: 0.6658 (t0) REVERT: A 478 ASP cc_start: 0.6763 (m-30) cc_final: 0.6187 (m-30) REVERT: A 484 PHE cc_start: 0.8603 (t80) cc_final: 0.8345 (t80) REVERT: A 503 LEU cc_start: 0.8278 (mt) cc_final: 0.7953 (mp) REVERT: A 556 TYR cc_start: 0.8097 (p90) cc_final: 0.7760 (p90) REVERT: A 560 ASP cc_start: 0.7819 (m-30) cc_final: 0.6417 (m-30) REVERT: A 563 LYS cc_start: 0.8521 (mmmt) cc_final: 0.8109 (mtpp) REVERT: A 684 GLN cc_start: 0.8627 (tp40) cc_final: 0.8384 (tp-100) REVERT: A 698 ASP cc_start: 0.7124 (t0) cc_final: 0.6828 (t0) REVERT: B 71 ILE cc_start: 0.8640 (tt) cc_final: 0.8374 (tp) REVERT: B 105 TYR cc_start: 0.8455 (m-10) cc_final: 0.8240 (m-80) REVERT: B 160 HIS cc_start: 0.7694 (t-90) cc_final: 0.7386 (t-90) REVERT: B 195 LEU cc_start: 0.8254 (tp) cc_final: 0.7987 (tp) REVERT: B 207 GLN cc_start: 0.7978 (tp40) cc_final: 0.7354 (mm110) REVERT: B 213 ARG cc_start: 0.7589 (mtt180) cc_final: 0.7183 (mtt180) REVERT: B 244 THR cc_start: 0.7957 (p) cc_final: 0.7295 (p) REVERT: B 247 TYR cc_start: 0.7667 (m-10) cc_final: 0.6907 (m-10) REVERT: B 276 LEU cc_start: 0.8647 (tp) cc_final: 0.8312 (tt) REVERT: B 277 LEU cc_start: 0.8523 (tp) cc_final: 0.8257 (tp) REVERT: B 286 LYS cc_start: 0.8721 (tppt) cc_final: 0.8360 (ttmm) REVERT: B 287 GLU cc_start: 0.7710 (tp30) cc_final: 0.6739 (tp30) REVERT: B 303 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7344 (mp0) REVERT: B 309 ILE cc_start: 0.8478 (tp) cc_final: 0.8240 (pt) REVERT: B 311 THR cc_start: 0.7678 (p) cc_final: 0.7410 (t) REVERT: B 355 SER cc_start: 0.8654 (m) cc_final: 0.8059 (p) REVERT: B 366 SER cc_start: 0.8430 (t) cc_final: 0.7883 (p) REVERT: B 377 TYR cc_start: 0.7857 (p90) cc_final: 0.7190 (p90) REVERT: B 378 VAL cc_start: 0.8437 (t) cc_final: 0.7893 (p) REVERT: B 391 SER cc_start: 0.8479 (m) cc_final: 0.8137 (p) REVERT: B 394 PHE cc_start: 0.8446 (t80) cc_final: 0.7316 (t80) REVERT: B 398 PHE cc_start: 0.7613 (m-80) cc_final: 0.7390 (m-80) REVERT: B 414 GLU cc_start: 0.7167 (tm-30) cc_final: 0.6769 (tm-30) REVERT: B 422 VAL cc_start: 0.7738 (t) cc_final: 0.7268 (p) REVERT: B 432 MET cc_start: 0.7453 (tpt) cc_final: 0.7085 (tpt) REVERT: B 447 LYS cc_start: 0.8636 (mtpt) cc_final: 0.8307 (mtpt) REVERT: B 448 SER cc_start: 0.9105 (m) cc_final: 0.8706 (t) REVERT: B 473 LYS cc_start: 0.8400 (mtpt) cc_final: 0.8125 (mtpt) REVERT: B 475 ASN cc_start: 0.7284 (t0) cc_final: 0.6543 (t0) REVERT: B 478 ASP cc_start: 0.7002 (m-30) cc_final: 0.6217 (m-30) REVERT: B 503 LEU cc_start: 0.8397 (mt) cc_final: 0.8103 (mp) REVERT: B 573 ASP cc_start: 0.7590 (t0) cc_final: 0.5764 (t0) REVERT: B 727 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7623 (mm) outliers start: 35 outliers final: 9 residues processed: 464 average time/residue: 0.2583 time to fit residues: 159.3524 Evaluate side-chains 380 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 367 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 727 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 0.3980 chunk 103 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 62 optimal weight: 0.0870 chunk 77 optimal weight: 0.2980 chunk 119 optimal weight: 0.9980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN A 382 ASN A 656 HIS B 101 GLN ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 GLN B 457 ASN B 464 GLN B 474 GLN B 731 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10406 Z= 0.215 Angle : 0.588 8.239 14142 Z= 0.301 Chirality : 0.042 0.190 1718 Planarity : 0.005 0.039 1760 Dihedral : 5.938 80.327 1443 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 3.92 % Allowed : 16.67 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.21), residues: 1322 helix: -0.67 (0.16), residues: 848 sheet: -3.52 (0.76), residues: 36 loop : -2.84 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 74 HIS 0.013 0.001 HIS A 656 PHE 0.024 0.001 PHE A 130 TYR 0.016 0.001 TYR A 377 ARG 0.005 0.000 ARG A 717 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 377 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 TYR cc_start: 0.7637 (m-10) cc_final: 0.7404 (m-10) REVERT: A 36 ARG cc_start: 0.7900 (tpp-160) cc_final: 0.7621 (mpp-170) REVERT: A 94 THR cc_start: 0.8094 (m) cc_final: 0.7716 (p) REVERT: A 135 HIS cc_start: 0.6745 (m170) cc_final: 0.6538 (m170) REVERT: A 182 ASP cc_start: 0.7388 (p0) cc_final: 0.7183 (p0) REVERT: A 195 LEU cc_start: 0.8161 (tp) cc_final: 0.7939 (tp) REVERT: A 236 LEU cc_start: 0.8591 (tp) cc_final: 0.8060 (tt) REVERT: A 245 LYS cc_start: 0.7916 (ttmm) cc_final: 0.7652 (ttmm) REVERT: A 247 TYR cc_start: 0.7584 (m-10) cc_final: 0.6692 (m-10) REVERT: A 251 LEU cc_start: 0.8687 (mt) cc_final: 0.8460 (mm) REVERT: A 353 SER cc_start: 0.8348 (m) cc_final: 0.8082 (t) REVERT: A 369 LYS cc_start: 0.8134 (mmtt) cc_final: 0.7879 (mmtt) REVERT: A 370 VAL cc_start: 0.8743 (t) cc_final: 0.8526 (p) REVERT: A 384 GLU cc_start: 0.7091 (mm-30) cc_final: 0.6598 (mm-30) REVERT: A 385 PHE cc_start: 0.8355 (OUTLIER) cc_final: 0.7768 (t80) REVERT: A 391 SER cc_start: 0.8600 (m) cc_final: 0.8312 (p) REVERT: A 394 PHE cc_start: 0.8376 (t80) cc_final: 0.7534 (t80) REVERT: A 395 SER cc_start: 0.8118 (m) cc_final: 0.7916 (p) REVERT: A 398 PHE cc_start: 0.7740 (m-80) cc_final: 0.7413 (m-80) REVERT: A 432 MET cc_start: 0.7342 (tpt) cc_final: 0.6931 (tpt) REVERT: A 436 VAL cc_start: 0.8751 (OUTLIER) cc_final: 0.8494 (m) REVERT: A 447 LYS cc_start: 0.8662 (mtpt) cc_final: 0.8231 (mtpp) REVERT: A 470 ARG cc_start: 0.7517 (tpp80) cc_final: 0.6945 (tpp80) REVERT: A 475 ASN cc_start: 0.7258 (t0) cc_final: 0.6559 (t0) REVERT: A 484 PHE cc_start: 0.8701 (t80) cc_final: 0.8454 (t80) REVERT: A 556 TYR cc_start: 0.8263 (p90) cc_final: 0.7829 (p90) REVERT: A 560 ASP cc_start: 0.7845 (m-30) cc_final: 0.6395 (m-30) REVERT: A 581 ARG cc_start: 0.7704 (mmt180) cc_final: 0.7485 (mtp85) REVERT: A 677 ARG cc_start: 0.7869 (ptm-80) cc_final: 0.7229 (ttt90) REVERT: A 698 ASP cc_start: 0.7172 (t0) cc_final: 0.6845 (t0) REVERT: B 100 LEU cc_start: 0.8873 (tp) cc_final: 0.8592 (tp) REVERT: B 195 LEU cc_start: 0.8355 (tp) cc_final: 0.7940 (tp) REVERT: B 213 ARG cc_start: 0.7597 (mtt180) cc_final: 0.7148 (mtt180) REVERT: B 244 THR cc_start: 0.8238 (p) cc_final: 0.7543 (t) REVERT: B 259 GLU cc_start: 0.7875 (tt0) cc_final: 0.7283 (tt0) REVERT: B 276 LEU cc_start: 0.8614 (tp) cc_final: 0.8357 (tt) REVERT: B 287 GLU cc_start: 0.7737 (tp30) cc_final: 0.6800 (tp30) REVERT: B 304 VAL cc_start: 0.8653 (t) cc_final: 0.8363 (m) REVERT: B 309 ILE cc_start: 0.8375 (tp) cc_final: 0.8171 (pt) REVERT: B 318 ASN cc_start: 0.8268 (t0) cc_final: 0.8034 (t0) REVERT: B 355 SER cc_start: 0.8454 (m) cc_final: 0.8002 (p) REVERT: B 361 TYR cc_start: 0.8164 (t80) cc_final: 0.7791 (t80) REVERT: B 366 SER cc_start: 0.8409 (t) cc_final: 0.8157 (p) REVERT: B 370 VAL cc_start: 0.8964 (t) cc_final: 0.8740 (p) REVERT: B 384 GLU cc_start: 0.7548 (mm-30) cc_final: 0.6958 (mm-30) REVERT: B 391 SER cc_start: 0.8571 (m) cc_final: 0.8245 (p) REVERT: B 394 PHE cc_start: 0.8382 (t80) cc_final: 0.7181 (t80) REVERT: B 398 PHE cc_start: 0.7702 (m-80) cc_final: 0.7426 (m-80) REVERT: B 414 GLU cc_start: 0.7184 (tm-30) cc_final: 0.6746 (tm-30) REVERT: B 432 MET cc_start: 0.7654 (tpt) cc_final: 0.7256 (tpt) REVERT: B 447 LYS cc_start: 0.8602 (mtpt) cc_final: 0.8271 (mtpt) REVERT: B 473 LYS cc_start: 0.8385 (mtpt) cc_final: 0.8094 (mtpt) REVERT: B 475 ASN cc_start: 0.7452 (t0) cc_final: 0.6187 (t0) REVERT: B 530 TYR cc_start: 0.8562 (m-10) cc_final: 0.8295 (m-10) REVERT: B 531 LYS cc_start: 0.8449 (mmmt) cc_final: 0.7927 (mmmt) REVERT: B 682 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7470 (mt-10) REVERT: B 684 GLN cc_start: 0.8578 (tp40) cc_final: 0.8378 (tp40) outliers start: 44 outliers final: 25 residues processed: 399 average time/residue: 0.2601 time to fit residues: 137.7143 Evaluate side-chains 365 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 338 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 656 HIS Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 681 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 81 optimal weight: 8.9990 chunk 33 optimal weight: 0.2980 chunk 120 optimal weight: 0.7980 chunk 129 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 119 optimal weight: 0.6980 chunk 40 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN ** A 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS A 684 GLN A 731 ASN B 160 HIS B 382 ASN B 457 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10406 Z= 0.248 Angle : 0.610 9.466 14142 Z= 0.311 Chirality : 0.043 0.157 1718 Planarity : 0.004 0.042 1760 Dihedral : 5.374 80.961 1433 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 4.72 % Allowed : 19.79 % Favored : 75.49 % 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: -1.67 (0.22), residues: 1322 helix: -0.31 (0.17), residues: 864 sheet: -3.01 (0.85), residues: 36 loop : -2.48 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 74 HIS 0.011 0.001 HIS B 160 PHE 0.019 0.001 PHE B 272 TYR 0.015 0.001 TYR B 105 ARG 0.009 0.001 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 363 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 TYR cc_start: 0.7857 (m-10) cc_final: 0.7389 (m-10) REVERT: A 182 ASP cc_start: 0.7455 (p0) cc_final: 0.7252 (p0) REVERT: A 195 LEU cc_start: 0.8108 (tp) cc_final: 0.7893 (tp) REVERT: A 236 LEU cc_start: 0.8609 (tp) cc_final: 0.8065 (tt) REVERT: A 245 LYS cc_start: 0.8014 (ttmm) cc_final: 0.7672 (ttmm) REVERT: A 247 TYR cc_start: 0.7616 (m-10) cc_final: 0.6750 (m-10) REVERT: A 251 LEU cc_start: 0.8741 (mt) cc_final: 0.7774 (mm) REVERT: A 271 ASP cc_start: 0.7464 (m-30) cc_final: 0.7201 (m-30) REVERT: A 318 ASN cc_start: 0.8253 (t0) cc_final: 0.8036 (t0) REVERT: A 348 ASP cc_start: 0.5022 (OUTLIER) cc_final: 0.4609 (p0) REVERT: A 353 SER cc_start: 0.8397 (m) cc_final: 0.8196 (t) REVERT: A 369 LYS cc_start: 0.8152 (mmtt) cc_final: 0.7939 (mmtt) REVERT: A 370 VAL cc_start: 0.8803 (t) cc_final: 0.8561 (p) REVERT: A 384 GLU cc_start: 0.7203 (mm-30) cc_final: 0.6782 (mm-30) REVERT: A 385 PHE cc_start: 0.8387 (OUTLIER) cc_final: 0.7835 (t80) REVERT: A 391 SER cc_start: 0.8643 (m) cc_final: 0.8319 (p) REVERT: A 394 PHE cc_start: 0.8383 (t80) cc_final: 0.7625 (t80) REVERT: A 395 SER cc_start: 0.8140 (m) cc_final: 0.7938 (p) REVERT: A 398 PHE cc_start: 0.7772 (m-80) cc_final: 0.7417 (m-80) REVERT: A 432 MET cc_start: 0.7328 (tpt) cc_final: 0.6928 (tpt) REVERT: A 436 VAL cc_start: 0.8748 (OUTLIER) cc_final: 0.8501 (m) REVERT: A 447 LYS cc_start: 0.8671 (mtpt) cc_final: 0.8205 (ttmt) REVERT: A 470 ARG cc_start: 0.7443 (tpp80) cc_final: 0.7181 (tpp80) REVERT: A 475 ASN cc_start: 0.7068 (t0) cc_final: 0.6527 (t0) REVERT: A 484 PHE cc_start: 0.8745 (t80) cc_final: 0.8451 (t80) REVERT: A 523 SER cc_start: 0.8141 (t) cc_final: 0.7937 (t) REVERT: A 556 TYR cc_start: 0.8318 (p90) cc_final: 0.7989 (p90) REVERT: A 563 LYS cc_start: 0.8570 (mmmt) cc_final: 0.8091 (mmmt) REVERT: A 581 ARG cc_start: 0.7728 (mmt180) cc_final: 0.7482 (mtp85) REVERT: A 677 ARG cc_start: 0.7940 (ptm-80) cc_final: 0.7395 (ttt90) REVERT: A 698 ASP cc_start: 0.7210 (t0) cc_final: 0.6817 (t0) REVERT: B 21 THR cc_start: 0.8552 (OUTLIER) cc_final: 0.8342 (p) REVERT: B 155 MET cc_start: 0.7581 (mpp) cc_final: 0.7162 (mpp) REVERT: B 181 ARG cc_start: 0.8290 (ttt-90) cc_final: 0.8084 (ttt-90) REVERT: B 195 LEU cc_start: 0.8354 (tp) cc_final: 0.7982 (tp) REVERT: B 213 ARG cc_start: 0.7606 (mtt180) cc_final: 0.7344 (mtt180) REVERT: B 276 LEU cc_start: 0.8594 (tp) cc_final: 0.8379 (tt) REVERT: B 287 GLU cc_start: 0.7825 (tp30) cc_final: 0.6842 (tp30) REVERT: B 304 VAL cc_start: 0.8756 (t) cc_final: 0.8452 (m) REVERT: B 309 ILE cc_start: 0.8376 (tp) cc_final: 0.8142 (pt) REVERT: B 318 ASN cc_start: 0.8336 (t0) cc_final: 0.8087 (t0) REVERT: B 348 ASP cc_start: 0.5256 (OUTLIER) cc_final: 0.5051 (p0) REVERT: B 361 TYR cc_start: 0.8337 (t80) cc_final: 0.7924 (t80) REVERT: B 366 SER cc_start: 0.8439 (t) cc_final: 0.8152 (p) REVERT: B 378 VAL cc_start: 0.8511 (t) cc_final: 0.8267 (m) REVERT: B 391 SER cc_start: 0.8599 (m) cc_final: 0.8168 (p) REVERT: B 394 PHE cc_start: 0.8418 (t80) cc_final: 0.7333 (t80) REVERT: B 398 PHE cc_start: 0.7712 (m-80) cc_final: 0.7447 (m-80) REVERT: B 414 GLU cc_start: 0.7256 (tm-30) cc_final: 0.6769 (tm-30) REVERT: B 432 MET cc_start: 0.7680 (tpt) cc_final: 0.7290 (tpt) REVERT: B 447 LYS cc_start: 0.8671 (mtpt) cc_final: 0.8291 (mtpt) REVERT: B 459 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8470 (ttpp) REVERT: B 473 LYS cc_start: 0.8345 (mtpt) cc_final: 0.8042 (mtpt) REVERT: B 475 ASN cc_start: 0.7343 (t0) cc_final: 0.6926 (t0) REVERT: B 476 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8350 (mtmm) REVERT: B 478 ASP cc_start: 0.8026 (p0) cc_final: 0.7462 (p0) REVERT: B 677 ARG cc_start: 0.8142 (ptm160) cc_final: 0.7830 (tpt-90) REVERT: B 714 ARG cc_start: 0.7967 (mtm-85) cc_final: 0.7551 (mtm-85) outliers start: 53 outliers final: 29 residues processed: 390 average time/residue: 0.2577 time to fit residues: 133.3239 Evaluate side-chains 365 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 329 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 656 HIS Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 459 LYS Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 721 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.3980 chunk 90 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 57 optimal weight: 0.0040 chunk 80 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 chunk 127 optimal weight: 0.3980 chunk 114 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN A 656 HIS A 684 GLN A 731 ASN B 382 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10406 Z= 0.210 Angle : 0.594 9.292 14142 Z= 0.303 Chirality : 0.042 0.177 1718 Planarity : 0.004 0.042 1760 Dihedral : 5.466 82.938 1433 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.35 % Favored : 93.57 % Rotamer: Outliers : 4.55 % Allowed : 21.75 % Favored : 73.71 % 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: -1.33 (0.23), residues: 1322 helix: -0.01 (0.17), residues: 854 sheet: -2.77 (0.87), residues: 36 loop : -2.41 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 74 HIS 0.006 0.001 HIS A 656 PHE 0.011 0.001 PHE A 115 TYR 0.032 0.001 TYR A 361 ARG 0.010 0.001 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 347 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 ILE cc_start: 0.7390 (mm) cc_final: 0.7073 (mm) REVERT: A 94 THR cc_start: 0.8373 (t) cc_final: 0.7973 (p) REVERT: A 195 LEU cc_start: 0.7981 (tp) cc_final: 0.7734 (tp) REVERT: A 229 PHE cc_start: 0.7934 (OUTLIER) cc_final: 0.7594 (t80) REVERT: A 236 LEU cc_start: 0.8691 (tp) cc_final: 0.8143 (tt) REVERT: A 237 LYS cc_start: 0.8730 (ttpt) cc_final: 0.8496 (tttt) REVERT: A 245 LYS cc_start: 0.8023 (ttmm) cc_final: 0.7701 (ttmm) REVERT: A 247 TYR cc_start: 0.7628 (m-10) cc_final: 0.6868 (m-10) REVERT: A 271 ASP cc_start: 0.7430 (m-30) cc_final: 0.7185 (m-30) REVERT: A 318 ASN cc_start: 0.8219 (t0) cc_final: 0.8004 (t0) REVERT: A 348 ASP cc_start: 0.4972 (OUTLIER) cc_final: 0.4541 (p0) REVERT: A 361 TYR cc_start: 0.8349 (t80) cc_final: 0.8086 (t80) REVERT: A 369 LYS cc_start: 0.8212 (mmtt) cc_final: 0.8003 (mmtt) REVERT: A 370 VAL cc_start: 0.8849 (t) cc_final: 0.8607 (p) REVERT: A 384 GLU cc_start: 0.7261 (mm-30) cc_final: 0.6809 (mm-30) REVERT: A 391 SER cc_start: 0.8654 (m) cc_final: 0.8306 (p) REVERT: A 394 PHE cc_start: 0.8377 (t80) cc_final: 0.8152 (t80) REVERT: A 405 THR cc_start: 0.8281 (m) cc_final: 0.8052 (p) REVERT: A 414 GLU cc_start: 0.7513 (tm-30) cc_final: 0.7073 (tm-30) REVERT: A 432 MET cc_start: 0.7318 (tpt) cc_final: 0.6918 (tpt) REVERT: A 447 LYS cc_start: 0.8657 (mtpt) cc_final: 0.8192 (ttmt) REVERT: A 470 ARG cc_start: 0.7427 (tpp80) cc_final: 0.7170 (tpp80) REVERT: A 475 ASN cc_start: 0.7046 (t0) cc_final: 0.6562 (t0) REVERT: A 484 PHE cc_start: 0.8741 (t80) cc_final: 0.8424 (t80) REVERT: A 556 TYR cc_start: 0.8335 (p90) cc_final: 0.7918 (p90) REVERT: A 563 LYS cc_start: 0.8588 (mmmt) cc_final: 0.8116 (mmmt) REVERT: A 581 ARG cc_start: 0.7731 (mmt180) cc_final: 0.7440 (mtp85) REVERT: A 677 ARG cc_start: 0.8051 (ptm-80) cc_final: 0.7484 (ttt90) REVERT: A 698 ASP cc_start: 0.7191 (t0) cc_final: 0.6797 (t0) REVERT: B 21 THR cc_start: 0.8604 (OUTLIER) cc_final: 0.8378 (p) REVERT: B 155 MET cc_start: 0.7578 (mpp) cc_final: 0.7223 (mpp) REVERT: B 195 LEU cc_start: 0.8379 (tp) cc_final: 0.8010 (tp) REVERT: B 236 LEU cc_start: 0.8766 (tt) cc_final: 0.8433 (tt) REVERT: B 276 LEU cc_start: 0.8586 (tp) cc_final: 0.8384 (tt) REVERT: B 287 GLU cc_start: 0.7835 (tp30) cc_final: 0.6857 (tp30) REVERT: B 309 ILE cc_start: 0.8380 (tp) cc_final: 0.8146 (pt) REVERT: B 318 ASN cc_start: 0.8336 (t0) cc_final: 0.8079 (t0) REVERT: B 361 TYR cc_start: 0.8346 (t80) cc_final: 0.7976 (t80) REVERT: B 366 SER cc_start: 0.8347 (t) cc_final: 0.8139 (p) REVERT: B 378 VAL cc_start: 0.8512 (t) cc_final: 0.8293 (m) REVERT: B 382 ASN cc_start: 0.8528 (OUTLIER) cc_final: 0.7935 (t0) REVERT: B 391 SER cc_start: 0.8610 (m) cc_final: 0.8147 (p) REVERT: B 394 PHE cc_start: 0.8423 (t80) cc_final: 0.7343 (t80) REVERT: B 398 PHE cc_start: 0.7710 (m-80) cc_final: 0.7415 (m-80) REVERT: B 414 GLU cc_start: 0.7226 (tm-30) cc_final: 0.6702 (tm-30) REVERT: B 432 MET cc_start: 0.7612 (tpt) cc_final: 0.7199 (tpt) REVERT: B 447 LYS cc_start: 0.8672 (mtpt) cc_final: 0.8270 (mtpt) REVERT: B 459 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8455 (ttpp) REVERT: B 473 LYS cc_start: 0.8309 (mtpt) cc_final: 0.8098 (mtpt) REVERT: B 475 ASN cc_start: 0.7268 (t0) cc_final: 0.6886 (t0) REVERT: B 476 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8411 (mtmm) REVERT: B 478 ASP cc_start: 0.7974 (p0) cc_final: 0.7480 (p0) REVERT: B 674 ARG cc_start: 0.7462 (mtt180) cc_final: 0.7162 (mtm-85) REVERT: B 677 ARG cc_start: 0.8187 (ptm160) cc_final: 0.7633 (ttt90) REVERT: B 681 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.8120 (ttmm) REVERT: B 684 GLN cc_start: 0.8513 (tp40) cc_final: 0.8278 (tp40) outliers start: 51 outliers final: 33 residues processed: 373 average time/residue: 0.2472 time to fit residues: 124.0885 Evaluate side-chains 370 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 330 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 580 LYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 656 HIS Chi-restraints excluded: chain A residue 684 GLN Chi-restraints excluded: chain A residue 703 MET Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 459 LYS Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 681 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 114 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN A 656 HIS A 684 GLN A 728 HIS B 33 GLN B 160 HIS B 382 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 10406 Z= 0.318 Angle : 0.653 9.823 14142 Z= 0.335 Chirality : 0.046 0.276 1718 Planarity : 0.004 0.051 1760 Dihedral : 5.578 81.220 1433 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 4.90 % Allowed : 21.57 % Favored : 73.53 % 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 (0.23), residues: 1322 helix: 0.06 (0.18), residues: 848 sheet: -2.74 (0.87), residues: 36 loop : -2.46 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 74 HIS 0.013 0.001 HIS B 160 PHE 0.013 0.001 PHE B 667 TYR 0.024 0.002 TYR B 105 ARG 0.011 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 327 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 THR cc_start: 0.8426 (t) cc_final: 0.8067 (p) REVERT: A 155 MET cc_start: 0.7165 (mpp) cc_final: 0.6932 (mpp) REVERT: A 195 LEU cc_start: 0.8002 (tp) cc_final: 0.7784 (tp) REVERT: A 236 LEU cc_start: 0.8695 (tp) cc_final: 0.8181 (tt) REVERT: A 240 LEU cc_start: 0.8601 (mm) cc_final: 0.8161 (mp) REVERT: A 245 LYS cc_start: 0.8061 (ttmm) cc_final: 0.7734 (ttmm) REVERT: A 247 TYR cc_start: 0.7655 (m-10) cc_final: 0.6844 (m-10) REVERT: A 251 LEU cc_start: 0.8811 (mt) cc_final: 0.8592 (mt) REVERT: A 271 ASP cc_start: 0.7558 (m-30) cc_final: 0.7301 (m-30) REVERT: A 318 ASN cc_start: 0.8297 (t0) cc_final: 0.8046 (t0) REVERT: A 348 ASP cc_start: 0.5121 (OUTLIER) cc_final: 0.4730 (p0) REVERT: A 370 VAL cc_start: 0.8930 (t) cc_final: 0.8687 (p) REVERT: A 391 SER cc_start: 0.8750 (m) cc_final: 0.8353 (p) REVERT: A 394 PHE cc_start: 0.8462 (t80) cc_final: 0.7888 (t80) REVERT: A 398 PHE cc_start: 0.7868 (m-80) cc_final: 0.7201 (m-10) REVERT: A 405 THR cc_start: 0.8310 (m) cc_final: 0.8084 (m) REVERT: A 414 GLU cc_start: 0.7614 (tm-30) cc_final: 0.7156 (tm-30) REVERT: A 432 MET cc_start: 0.7407 (tpt) cc_final: 0.7107 (tpt) REVERT: A 436 VAL cc_start: 0.8717 (OUTLIER) cc_final: 0.8478 (m) REVERT: A 447 LYS cc_start: 0.8699 (mtpt) cc_final: 0.8289 (mtpt) REVERT: A 470 ARG cc_start: 0.7536 (tpp80) cc_final: 0.7274 (tpp80) REVERT: A 475 ASN cc_start: 0.7067 (t0) cc_final: 0.6649 (t0) REVERT: A 484 PHE cc_start: 0.8772 (t80) cc_final: 0.8457 (t80) REVERT: A 560 ASP cc_start: 0.7760 (m-30) cc_final: 0.7469 (m-30) REVERT: A 581 ARG cc_start: 0.7716 (mmt180) cc_final: 0.7401 (mtp85) REVERT: A 677 ARG cc_start: 0.8106 (ptm-80) cc_final: 0.7328 (ttt90) REVERT: A 698 ASP cc_start: 0.7223 (t0) cc_final: 0.6846 (t0) REVERT: A 704 GLU cc_start: 0.7577 (tm-30) cc_final: 0.7340 (tm-30) REVERT: B 21 THR cc_start: 0.8755 (OUTLIER) cc_final: 0.8497 (p) REVERT: B 155 MET cc_start: 0.7636 (mpp) cc_final: 0.7218 (mpp) REVERT: B 195 LEU cc_start: 0.8409 (tp) cc_final: 0.8063 (tp) REVERT: B 207 GLN cc_start: 0.8022 (mm110) cc_final: 0.7630 (mm-40) REVERT: B 237 LYS cc_start: 0.8727 (ttpt) cc_final: 0.8505 (tttt) REVERT: B 240 LEU cc_start: 0.8737 (mm) cc_final: 0.8515 (mp) REVERT: B 287 GLU cc_start: 0.7869 (tp30) cc_final: 0.6862 (tp30) REVERT: B 309 ILE cc_start: 0.8435 (tp) cc_final: 0.8193 (pt) REVERT: B 318 ASN cc_start: 0.8340 (t0) cc_final: 0.8094 (t0) REVERT: B 349 MET cc_start: 0.5554 (mtp) cc_final: 0.5216 (mtm) REVERT: B 355 SER cc_start: 0.8389 (m) cc_final: 0.7936 (p) REVERT: B 366 SER cc_start: 0.8415 (t) cc_final: 0.8144 (p) REVERT: B 382 ASN cc_start: 0.8456 (OUTLIER) cc_final: 0.7860 (t0) REVERT: B 383 GLN cc_start: 0.8400 (tp40) cc_final: 0.8152 (tp40) REVERT: B 391 SER cc_start: 0.8624 (m) cc_final: 0.8135 (p) REVERT: B 394 PHE cc_start: 0.8464 (t80) cc_final: 0.7442 (t80) REVERT: B 398 PHE cc_start: 0.7736 (m-80) cc_final: 0.7428 (m-80) REVERT: B 414 GLU cc_start: 0.7264 (tm-30) cc_final: 0.6857 (tm-30) REVERT: B 432 MET cc_start: 0.7630 (tpt) cc_final: 0.7266 (tpt) REVERT: B 447 LYS cc_start: 0.8717 (mtpt) cc_final: 0.8295 (mtpt) REVERT: B 459 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8482 (ttpp) REVERT: B 473 LYS cc_start: 0.8408 (mtpt) cc_final: 0.8190 (mtpt) REVERT: B 475 ASN cc_start: 0.7310 (t0) cc_final: 0.6980 (t0) REVERT: B 476 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8393 (mtmm) REVERT: B 478 ASP cc_start: 0.7964 (p0) cc_final: 0.7502 (p0) REVERT: B 674 ARG cc_start: 0.7473 (mtt180) cc_final: 0.7168 (mtm-85) REVERT: B 677 ARG cc_start: 0.8266 (ptm160) cc_final: 0.7531 (ttt90) REVERT: B 681 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.8112 (ttmm) REVERT: B 684 GLN cc_start: 0.8522 (tp40) cc_final: 0.8303 (tp-100) outliers start: 55 outliers final: 35 residues processed: 362 average time/residue: 0.2451 time to fit residues: 119.4576 Evaluate side-chains 354 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 312 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 656 HIS Chi-restraints excluded: chain A residue 684 GLN Chi-restraints excluded: chain A residue 703 MET Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 33 GLN Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 255 TYR Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 459 LYS Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 681 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 31 optimal weight: 0.4980 chunk 127 optimal weight: 0.9990 chunk 106 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 67 optimal weight: 0.0870 chunk 123 optimal weight: 2.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN A 656 HIS A 684 GLN B 33 GLN B 382 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 10406 Z= 0.218 Angle : 0.630 9.721 14142 Z= 0.314 Chirality : 0.043 0.203 1718 Planarity : 0.004 0.045 1760 Dihedral : 5.519 82.269 1431 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.58 % Favored : 93.34 % Rotamer: Outliers : 5.17 % Allowed : 23.44 % Favored : 71.39 % 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: -1.12 (0.23), residues: 1322 helix: 0.18 (0.18), residues: 848 sheet: -2.48 (0.93), residues: 36 loop : -2.37 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 482 HIS 0.008 0.001 HIS A 656 PHE 0.012 0.001 PHE B 667 TYR 0.020 0.001 TYR B 105 ARG 0.011 0.001 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 316 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ILE cc_start: 0.7419 (OUTLIER) cc_final: 0.7118 (mm) REVERT: A 94 THR cc_start: 0.8378 (t) cc_final: 0.7981 (p) REVERT: A 229 PHE cc_start: 0.7927 (OUTLIER) cc_final: 0.7598 (t80) REVERT: A 236 LEU cc_start: 0.8692 (tp) cc_final: 0.8134 (tt) REVERT: A 251 LEU cc_start: 0.8782 (mt) cc_final: 0.8553 (mt) REVERT: A 271 ASP cc_start: 0.7539 (m-30) cc_final: 0.7258 (m-30) REVERT: A 318 ASN cc_start: 0.8280 (t0) cc_final: 0.8019 (t0) REVERT: A 329 LYS cc_start: 0.8067 (pttt) cc_final: 0.7724 (ptmm) REVERT: A 348 ASP cc_start: 0.5089 (OUTLIER) cc_final: 0.4686 (p0) REVERT: A 370 VAL cc_start: 0.8909 (t) cc_final: 0.8670 (p) REVERT: A 391 SER cc_start: 0.8732 (m) cc_final: 0.8334 (p) REVERT: A 394 PHE cc_start: 0.8439 (t80) cc_final: 0.8022 (t80) REVERT: A 398 PHE cc_start: 0.7804 (m-80) cc_final: 0.7492 (m-10) REVERT: A 405 THR cc_start: 0.8244 (m) cc_final: 0.8026 (p) REVERT: A 414 GLU cc_start: 0.7559 (tm-30) cc_final: 0.7163 (tm-30) REVERT: A 432 MET cc_start: 0.7347 (tpt) cc_final: 0.6963 (tpt) REVERT: A 436 VAL cc_start: 0.8714 (OUTLIER) cc_final: 0.8485 (m) REVERT: A 470 ARG cc_start: 0.7485 (tpp80) cc_final: 0.7213 (tpp80) REVERT: A 475 ASN cc_start: 0.6987 (t0) cc_final: 0.6529 (t0) REVERT: A 484 PHE cc_start: 0.8747 (t80) cc_final: 0.8450 (t80) REVERT: A 560 ASP cc_start: 0.7699 (m-30) cc_final: 0.7481 (m-30) REVERT: A 563 LYS cc_start: 0.8586 (mmmt) cc_final: 0.8382 (mmmt) REVERT: A 581 ARG cc_start: 0.7757 (mmt180) cc_final: 0.7445 (mtp85) REVERT: A 677 ARG cc_start: 0.8008 (ptm-80) cc_final: 0.7535 (tpt-90) REVERT: A 698 ASP cc_start: 0.7214 (t0) cc_final: 0.6821 (t0) REVERT: A 704 GLU cc_start: 0.7567 (tm-30) cc_final: 0.7325 (tm-30) REVERT: B 21 THR cc_start: 0.8741 (OUTLIER) cc_final: 0.8475 (p) REVERT: B 155 MET cc_start: 0.7497 (mpp) cc_final: 0.7210 (mpp) REVERT: B 195 LEU cc_start: 0.8396 (tp) cc_final: 0.8037 (tp) REVERT: B 207 GLN cc_start: 0.7991 (mm110) cc_final: 0.7577 (mm-40) REVERT: B 240 LEU cc_start: 0.8731 (mm) cc_final: 0.8365 (mp) REVERT: B 287 GLU cc_start: 0.7871 (tp30) cc_final: 0.6873 (tp30) REVERT: B 309 ILE cc_start: 0.8409 (tp) cc_final: 0.8167 (pt) REVERT: B 318 ASN cc_start: 0.8284 (t0) cc_final: 0.8064 (t0) REVERT: B 355 SER cc_start: 0.8382 (m) cc_final: 0.7935 (p) REVERT: B 366 SER cc_start: 0.8405 (t) cc_final: 0.8155 (p) REVERT: B 382 ASN cc_start: 0.8416 (OUTLIER) cc_final: 0.8003 (t0) REVERT: B 383 GLN cc_start: 0.8383 (tp40) cc_final: 0.8172 (tp40) REVERT: B 391 SER cc_start: 0.8629 (m) cc_final: 0.8130 (p) REVERT: B 394 PHE cc_start: 0.8419 (t80) cc_final: 0.7404 (t80) REVERT: B 398 PHE cc_start: 0.7669 (m-80) cc_final: 0.7342 (m-80) REVERT: B 414 GLU cc_start: 0.7284 (tm-30) cc_final: 0.6903 (tm-30) REVERT: B 432 MET cc_start: 0.7572 (tpt) cc_final: 0.7202 (tpt) REVERT: B 447 LYS cc_start: 0.8691 (mtpt) cc_final: 0.8271 (mtpt) REVERT: B 459 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8475 (ttpp) REVERT: B 473 LYS cc_start: 0.8455 (mtpt) cc_final: 0.8223 (mtpt) REVERT: B 475 ASN cc_start: 0.7197 (t0) cc_final: 0.6753 (t0) REVERT: B 476 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8416 (mtmm) REVERT: B 478 ASP cc_start: 0.7933 (p0) cc_final: 0.7476 (p0) REVERT: B 674 ARG cc_start: 0.7404 (mtt180) cc_final: 0.7167 (mtm-85) REVERT: B 677 ARG cc_start: 0.8286 (ptm160) cc_final: 0.7787 (ttt90) REVERT: B 684 GLN cc_start: 0.8500 (tp40) cc_final: 0.8262 (tp-100) outliers start: 58 outliers final: 38 residues processed: 351 average time/residue: 0.2417 time to fit residues: 114.2231 Evaluate side-chains 358 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 312 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 656 HIS Chi-restraints excluded: chain A residue 684 GLN Chi-restraints excluded: chain A residue 703 MET Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 255 TYR Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 261 PHE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 459 LYS Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 700 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 93 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 127 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 77 optimal weight: 0.0270 chunk 58 optimal weight: 0.4980 chunk 78 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN A 457 ASN A 656 HIS B 382 ASN ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 10406 Z= 0.236 Angle : 0.640 9.772 14142 Z= 0.322 Chirality : 0.043 0.235 1718 Planarity : 0.004 0.047 1760 Dihedral : 5.541 82.464 1431 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.20 % Favored : 93.72 % Rotamer: Outliers : 5.26 % Allowed : 24.15 % Favored : 70.59 % 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: -1.09 (0.24), residues: 1322 helix: 0.14 (0.18), residues: 860 sheet: -2.22 (1.00), residues: 36 loop : -2.29 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 74 HIS 0.004 0.001 HIS A 656 PHE 0.012 0.001 PHE B 667 TYR 0.017 0.001 TYR B 105 ARG 0.006 0.001 ARG A 714 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 312 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 ILE cc_start: 0.7429 (OUTLIER) cc_final: 0.7124 (mm) REVERT: A 94 THR cc_start: 0.8394 (t) cc_final: 0.8048 (p) REVERT: A 155 MET cc_start: 0.7081 (mpp) cc_final: 0.6866 (mpp) REVERT: A 229 PHE cc_start: 0.7930 (OUTLIER) cc_final: 0.7605 (t80) REVERT: A 236 LEU cc_start: 0.8718 (tp) cc_final: 0.8221 (tt) REVERT: A 240 LEU cc_start: 0.8600 (mm) cc_final: 0.8226 (mp) REVERT: A 247 TYR cc_start: 0.7536 (m-10) cc_final: 0.7291 (m-10) REVERT: A 251 LEU cc_start: 0.8773 (mt) cc_final: 0.8540 (mt) REVERT: A 271 ASP cc_start: 0.7578 (m-30) cc_final: 0.7363 (m-30) REVERT: A 318 ASN cc_start: 0.8286 (t0) cc_final: 0.8015 (t0) REVERT: A 329 LYS cc_start: 0.8076 (pttt) cc_final: 0.7730 (ptmm) REVERT: A 348 ASP cc_start: 0.5097 (OUTLIER) cc_final: 0.4763 (p0) REVERT: A 370 VAL cc_start: 0.8911 (t) cc_final: 0.8666 (p) REVERT: A 391 SER cc_start: 0.8708 (m) cc_final: 0.8333 (p) REVERT: A 394 PHE cc_start: 0.8441 (t80) cc_final: 0.7989 (t80) REVERT: A 398 PHE cc_start: 0.7778 (m-80) cc_final: 0.7470 (m-10) REVERT: A 405 THR cc_start: 0.8231 (m) cc_final: 0.8027 (p) REVERT: A 414 GLU cc_start: 0.7426 (tm-30) cc_final: 0.7152 (tm-30) REVERT: A 432 MET cc_start: 0.7344 (tpt) cc_final: 0.7019 (tpt) REVERT: A 436 VAL cc_start: 0.8693 (OUTLIER) cc_final: 0.8454 (m) REVERT: A 470 ARG cc_start: 0.7501 (tpp80) cc_final: 0.7229 (tpp80) REVERT: A 475 ASN cc_start: 0.6953 (t0) cc_final: 0.6512 (t0) REVERT: A 563 LYS cc_start: 0.8593 (mmmt) cc_final: 0.8289 (mmmm) REVERT: A 581 ARG cc_start: 0.7759 (mmt180) cc_final: 0.7436 (mtp85) REVERT: A 677 ARG cc_start: 0.7990 (ptm-80) cc_final: 0.7484 (tpt-90) REVERT: A 698 ASP cc_start: 0.7197 (t0) cc_final: 0.6807 (t0) REVERT: A 704 GLU cc_start: 0.7579 (tm-30) cc_final: 0.7327 (tm-30) REVERT: B 21 THR cc_start: 0.8776 (OUTLIER) cc_final: 0.8484 (p) REVERT: B 155 MET cc_start: 0.7483 (mpp) cc_final: 0.7187 (mpp) REVERT: B 195 LEU cc_start: 0.8401 (tp) cc_final: 0.8067 (tp) REVERT: B 207 GLN cc_start: 0.8020 (mm110) cc_final: 0.7574 (mm-40) REVERT: B 240 LEU cc_start: 0.8743 (mm) cc_final: 0.8398 (mp) REVERT: B 318 ASN cc_start: 0.8301 (t0) cc_final: 0.8073 (t0) REVERT: B 355 SER cc_start: 0.8422 (m) cc_final: 0.7971 (p) REVERT: B 366 SER cc_start: 0.8406 (t) cc_final: 0.8153 (p) REVERT: B 382 ASN cc_start: 0.8398 (OUTLIER) cc_final: 0.7985 (t0) REVERT: B 383 GLN cc_start: 0.8429 (tp40) cc_final: 0.8221 (tp40) REVERT: B 391 SER cc_start: 0.8638 (m) cc_final: 0.8135 (p) REVERT: B 394 PHE cc_start: 0.8406 (t80) cc_final: 0.7391 (t80) REVERT: B 398 PHE cc_start: 0.7671 (m-80) cc_final: 0.7327 (m-80) REVERT: B 414 GLU cc_start: 0.7297 (tm-30) cc_final: 0.6948 (tm-30) REVERT: B 432 MET cc_start: 0.7599 (tpt) cc_final: 0.7214 (tpt) REVERT: B 447 LYS cc_start: 0.8694 (mtpt) cc_final: 0.8273 (mtpt) REVERT: B 459 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8504 (ttpp) REVERT: B 473 LYS cc_start: 0.8448 (mtpt) cc_final: 0.8185 (mtpt) REVERT: B 475 ASN cc_start: 0.7041 (t0) cc_final: 0.6681 (t0) REVERT: B 476 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8407 (mtmm) REVERT: B 478 ASP cc_start: 0.7813 (p0) cc_final: 0.7351 (p0) REVERT: B 674 ARG cc_start: 0.7427 (mtt180) cc_final: 0.7194 (mtm-85) REVERT: B 677 ARG cc_start: 0.8282 (ptm160) cc_final: 0.7787 (ttt90) REVERT: B 684 GLN cc_start: 0.8469 (tp40) cc_final: 0.8244 (tp-100) outliers start: 59 outliers final: 42 residues processed: 351 average time/residue: 0.2362 time to fit residues: 112.2525 Evaluate side-chains 356 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 306 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain A residue 255 TYR Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 382 ASN Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 489 SER Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 656 HIS Chi-restraints excluded: chain A residue 689 ASN Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 255 TYR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 459 LYS Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain B residue 700 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 24 optimal weight: 0.2980 chunk 80 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 62 optimal weight: 0.4980 chunk 11 optimal weight: 0.4980 chunk 100 optimal weight: 0.9990 chunk 115 optimal weight: 0.8980 chunk 121 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 ASN A 656 HIS A 684 GLN B 382 ASN ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 10406 Z= 0.231 Angle : 0.646 10.571 14142 Z= 0.323 Chirality : 0.044 0.249 1718 Planarity : 0.004 0.046 1760 Dihedral : 5.581 82.629 1431 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.51 % Favored : 93.42 % Rotamer: Outliers : 5.53 % Allowed : 24.06 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.24), residues: 1322 helix: 0.20 (0.18), residues: 856 sheet: -2.15 (1.00), residues: 36 loop : -2.25 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 482 HIS 0.005 0.001 HIS A 656 PHE 0.014 0.001 PHE A 115 TYR 0.017 0.001 TYR B 105 ARG 0.007 0.001 ARG B 714 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 314 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 ILE cc_start: 0.7434 (OUTLIER) cc_final: 0.7139 (mm) REVERT: A 94 THR cc_start: 0.8370 (t) cc_final: 0.7977 (p) REVERT: A 229 PHE cc_start: 0.7929 (OUTLIER) cc_final: 0.7619 (t80) REVERT: A 236 LEU cc_start: 0.8712 (tp) cc_final: 0.8185 (tt) REVERT: A 240 LEU cc_start: 0.8607 (mm) cc_final: 0.8211 (mp) REVERT: A 271 ASP cc_start: 0.7578 (m-30) cc_final: 0.7243 (m-30) REVERT: A 318 ASN cc_start: 0.8300 (t0) cc_final: 0.7776 (t0) REVERT: A 324 ASN cc_start: 0.8582 (t0) cc_final: 0.8231 (t0) REVERT: A 329 LYS cc_start: 0.8094 (pttt) cc_final: 0.7750 (ptmm) REVERT: A 348 ASP cc_start: 0.5102 (OUTLIER) cc_final: 0.4780 (p0) REVERT: A 370 VAL cc_start: 0.8897 (t) cc_final: 0.8619 (p) REVERT: A 378 VAL cc_start: 0.8233 (t) cc_final: 0.7945 (p) REVERT: A 391 SER cc_start: 0.8706 (m) cc_final: 0.8321 (p) REVERT: A 394 PHE cc_start: 0.8435 (t80) cc_final: 0.8003 (t80) REVERT: A 398 PHE cc_start: 0.7728 (m-80) cc_final: 0.7438 (m-10) REVERT: A 414 GLU cc_start: 0.7532 (tm-30) cc_final: 0.7146 (tm-30) REVERT: A 432 MET cc_start: 0.7314 (tpt) cc_final: 0.6999 (tpt) REVERT: A 436 VAL cc_start: 0.8670 (OUTLIER) cc_final: 0.8449 (m) REVERT: A 470 ARG cc_start: 0.7514 (tpp80) cc_final: 0.7234 (tpp80) REVERT: A 475 ASN cc_start: 0.6938 (t0) cc_final: 0.6485 (t0) REVERT: A 563 LYS cc_start: 0.8585 (mmmt) cc_final: 0.7999 (mmmm) REVERT: A 567 ASN cc_start: 0.7966 (m-40) cc_final: 0.7684 (m110) REVERT: A 581 ARG cc_start: 0.7764 (mmt180) cc_final: 0.7433 (mtp85) REVERT: A 677 ARG cc_start: 0.7988 (ptm-80) cc_final: 0.7578 (ttt90) REVERT: A 698 ASP cc_start: 0.7199 (t0) cc_final: 0.6820 (t0) REVERT: A 704 GLU cc_start: 0.7581 (tm-30) cc_final: 0.7342 (tm-30) REVERT: B 21 THR cc_start: 0.8784 (OUTLIER) cc_final: 0.8495 (p) REVERT: B 155 MET cc_start: 0.7461 (mpp) cc_final: 0.7160 (mpp) REVERT: B 195 LEU cc_start: 0.8412 (tp) cc_final: 0.8065 (tp) REVERT: B 207 GLN cc_start: 0.8015 (mm110) cc_final: 0.7553 (mm-40) REVERT: B 240 LEU cc_start: 0.8722 (mm) cc_final: 0.8408 (mp) REVERT: B 288 LEU cc_start: 0.8889 (tp) cc_final: 0.8639 (tp) REVERT: B 318 ASN cc_start: 0.8298 (t0) cc_final: 0.8089 (t0) REVERT: B 366 SER cc_start: 0.8394 (t) cc_final: 0.8153 (p) REVERT: B 382 ASN cc_start: 0.8391 (OUTLIER) cc_final: 0.8120 (t0) REVERT: B 383 GLN cc_start: 0.8414 (tp40) cc_final: 0.8207 (tp40) REVERT: B 385 PHE cc_start: 0.8734 (OUTLIER) cc_final: 0.8056 (m-10) REVERT: B 391 SER cc_start: 0.8647 (m) cc_final: 0.8145 (p) REVERT: B 394 PHE cc_start: 0.8392 (t80) cc_final: 0.7507 (t80) REVERT: B 398 PHE cc_start: 0.7658 (m-80) cc_final: 0.7327 (m-80) REVERT: B 414 GLU cc_start: 0.7292 (tm-30) cc_final: 0.6970 (tm-30) REVERT: B 432 MET cc_start: 0.7559 (tpt) cc_final: 0.7185 (tpt) REVERT: B 447 LYS cc_start: 0.8689 (mtpt) cc_final: 0.8277 (mtpt) REVERT: B 459 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8504 (ttpp) REVERT: B 473 LYS cc_start: 0.8433 (mtpt) cc_final: 0.8157 (mtpt) REVERT: B 475 ASN cc_start: 0.7087 (t0) cc_final: 0.6712 (t0) REVERT: B 476 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8414 (mtmm) REVERT: B 478 ASP cc_start: 0.7790 (p0) cc_final: 0.7376 (p0) REVERT: B 674 ARG cc_start: 0.7422 (mtt180) cc_final: 0.7187 (mtm-85) REVERT: B 677 ARG cc_start: 0.8287 (ptm160) cc_final: 0.7903 (ttt180) REVERT: B 684 GLN cc_start: 0.8477 (tp40) cc_final: 0.8243 (tp-100) outliers start: 62 outliers final: 44 residues processed: 357 average time/residue: 0.2426 time to fit residues: 117.7863 Evaluate side-chains 358 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 305 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain A residue 255 TYR Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 489 SER Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 656 HIS Chi-restraints excluded: chain A residue 684 GLN Chi-restraints excluded: chain A residue 689 ASN Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 255 TYR Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 459 LYS Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain B residue 697 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 3.9990 chunk 121 optimal weight: 0.7980 chunk 71 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 93 optimal weight: 7.9990 chunk 36 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 125 optimal weight: 0.6980 chunk 76 optimal weight: 0.0970 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN A 457 ASN ** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS A 684 GLN B 382 ASN ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.4224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 10406 Z= 0.231 Angle : 0.662 10.630 14142 Z= 0.332 Chirality : 0.044 0.308 1718 Planarity : 0.004 0.046 1760 Dihedral : 5.599 82.948 1431 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.73 % Favored : 93.19 % Rotamer: Outliers : 5.61 % Allowed : 24.78 % Favored : 69.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.24), residues: 1322 helix: 0.33 (0.18), residues: 842 sheet: -2.12 (0.99), residues: 36 loop : -2.26 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 482 HIS 0.010 0.001 HIS A 656 PHE 0.015 0.001 PHE A 115 TYR 0.015 0.001 TYR A 377 ARG 0.006 0.001 ARG B 714 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 317 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 THR cc_start: 0.8384 (t) cc_final: 0.8037 (p) REVERT: A 113 VAL cc_start: 0.8877 (OUTLIER) cc_final: 0.8597 (p) REVERT: A 229 PHE cc_start: 0.7927 (OUTLIER) cc_final: 0.7609 (t80) REVERT: A 236 LEU cc_start: 0.8706 (tp) cc_final: 0.8170 (tt) REVERT: A 271 ASP cc_start: 0.7556 (m-30) cc_final: 0.7341 (m-30) REVERT: A 318 ASN cc_start: 0.8310 (t0) cc_final: 0.8056 (t0) REVERT: A 324 ASN cc_start: 0.8581 (t0) cc_final: 0.8212 (t0) REVERT: A 329 LYS cc_start: 0.8095 (pttt) cc_final: 0.7760 (ptmm) REVERT: A 370 VAL cc_start: 0.8893 (t) cc_final: 0.8603 (p) REVERT: A 391 SER cc_start: 0.8689 (m) cc_final: 0.8294 (p) REVERT: A 394 PHE cc_start: 0.8435 (t80) cc_final: 0.7992 (t80) REVERT: A 398 PHE cc_start: 0.7716 (m-80) cc_final: 0.7433 (m-10) REVERT: A 414 GLU cc_start: 0.7509 (tm-30) cc_final: 0.7135 (tm-30) REVERT: A 432 MET cc_start: 0.7314 (tpt) cc_final: 0.6998 (tpt) REVERT: A 470 ARG cc_start: 0.7518 (tpp80) cc_final: 0.7232 (tpp80) REVERT: A 475 ASN cc_start: 0.6924 (t0) cc_final: 0.6411 (t0) REVERT: A 563 LYS cc_start: 0.8580 (mmmt) cc_final: 0.7998 (mmmm) REVERT: A 567 ASN cc_start: 0.7974 (m-40) cc_final: 0.7742 (m110) REVERT: A 581 ARG cc_start: 0.7763 (mmt180) cc_final: 0.7445 (mtp85) REVERT: A 677 ARG cc_start: 0.7974 (ptm-80) cc_final: 0.7573 (ttt90) REVERT: A 698 ASP cc_start: 0.7192 (t0) cc_final: 0.6820 (t0) REVERT: A 704 GLU cc_start: 0.7581 (tm-30) cc_final: 0.7347 (tm-30) REVERT: B 21 THR cc_start: 0.8796 (OUTLIER) cc_final: 0.8525 (p) REVERT: B 155 MET cc_start: 0.7452 (mpp) cc_final: 0.7150 (mpp) REVERT: B 195 LEU cc_start: 0.8402 (tp) cc_final: 0.8060 (tp) REVERT: B 207 GLN cc_start: 0.8020 (mm110) cc_final: 0.7539 (mm-40) REVERT: B 288 LEU cc_start: 0.8866 (tp) cc_final: 0.8621 (tp) REVERT: B 366 SER cc_start: 0.8341 (t) cc_final: 0.8131 (p) REVERT: B 382 ASN cc_start: 0.8331 (OUTLIER) cc_final: 0.8097 (t0) REVERT: B 385 PHE cc_start: 0.8703 (OUTLIER) cc_final: 0.8007 (m-10) REVERT: B 391 SER cc_start: 0.8663 (m) cc_final: 0.8165 (p) REVERT: B 394 PHE cc_start: 0.8389 (t80) cc_final: 0.7496 (t80) REVERT: B 398 PHE cc_start: 0.7654 (m-80) cc_final: 0.7322 (m-80) REVERT: B 414 GLU cc_start: 0.7291 (tm-30) cc_final: 0.6996 (tm-30) REVERT: B 432 MET cc_start: 0.7527 (tpt) cc_final: 0.7156 (tpt) REVERT: B 447 LYS cc_start: 0.8681 (mtpt) cc_final: 0.8260 (mtpt) REVERT: B 459 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8500 (ttpp) REVERT: B 473 LYS cc_start: 0.8452 (mtpt) cc_final: 0.8186 (mtpt) REVERT: B 475 ASN cc_start: 0.7140 (t0) cc_final: 0.6830 (t0) REVERT: B 476 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8402 (mtmm) REVERT: B 478 ASP cc_start: 0.7743 (p0) cc_final: 0.7330 (p0) REVERT: B 674 ARG cc_start: 0.7401 (mtt180) cc_final: 0.7183 (mtm-85) REVERT: B 684 GLN cc_start: 0.8474 (tp40) cc_final: 0.8236 (tp-100) outliers start: 63 outliers final: 44 residues processed: 359 average time/residue: 0.2325 time to fit residues: 114.0285 Evaluate side-chains 353 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 302 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 489 SER Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 656 HIS Chi-restraints excluded: chain A residue 684 GLN Chi-restraints excluded: chain A residue 689 ASN Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 261 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 459 LYS Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 668 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 chunk 131 optimal weight: 0.5980 chunk 121 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN A 457 ASN ** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS A 684 GLN B 382 ASN ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.4330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 10406 Z= 0.262 Angle : 0.677 10.867 14142 Z= 0.341 Chirality : 0.044 0.236 1718 Planarity : 0.004 0.048 1760 Dihedral : 5.650 82.874 1431 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.96 % Favored : 92.89 % Rotamer: Outliers : 4.63 % Allowed : 26.38 % Favored : 68.98 % 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: -0.99 (0.24), residues: 1322 helix: 0.21 (0.18), residues: 862 sheet: -2.11 (0.98), residues: 36 loop : -2.26 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 74 HIS 0.007 0.001 HIS A 656 PHE 0.015 0.001 PHE A 115 TYR 0.015 0.001 TYR A 377 ARG 0.007 0.001 ARG A 714 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 298 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 THR cc_start: 0.8396 (t) cc_final: 0.7997 (p) REVERT: A 229 PHE cc_start: 0.7937 (OUTLIER) cc_final: 0.7610 (t80) REVERT: A 236 LEU cc_start: 0.8728 (tp) cc_final: 0.8248 (tt) REVERT: A 271 ASP cc_start: 0.7570 (m-30) cc_final: 0.7352 (m-30) REVERT: A 277 LEU cc_start: 0.8534 (tp) cc_final: 0.8264 (tp) REVERT: A 318 ASN cc_start: 0.8319 (t0) cc_final: 0.8083 (t0) REVERT: A 329 LYS cc_start: 0.8121 (pttt) cc_final: 0.7786 (ptmm) REVERT: A 370 VAL cc_start: 0.8896 (t) cc_final: 0.8610 (p) REVERT: A 378 VAL cc_start: 0.8257 (t) cc_final: 0.7985 (p) REVERT: A 391 SER cc_start: 0.8679 (m) cc_final: 0.8288 (p) REVERT: A 398 PHE cc_start: 0.7696 (m-80) cc_final: 0.7475 (m-10) REVERT: A 414 GLU cc_start: 0.7504 (tm-30) cc_final: 0.7126 (tm-30) REVERT: A 432 MET cc_start: 0.7299 (tpt) cc_final: 0.6995 (tpt) REVERT: A 470 ARG cc_start: 0.7537 (tpp80) cc_final: 0.7255 (tpp80) REVERT: A 475 ASN cc_start: 0.6947 (t0) cc_final: 0.6435 (t0) REVERT: A 563 LYS cc_start: 0.8559 (mmmt) cc_final: 0.8284 (mmmm) REVERT: A 581 ARG cc_start: 0.7729 (mmt180) cc_final: 0.7409 (mtp85) REVERT: A 677 ARG cc_start: 0.7998 (ptm-80) cc_final: 0.7583 (ttt90) REVERT: A 698 ASP cc_start: 0.7205 (t0) cc_final: 0.6827 (t0) REVERT: A 704 GLU cc_start: 0.7593 (tm-30) cc_final: 0.7366 (tm-30) REVERT: B 21 THR cc_start: 0.8817 (OUTLIER) cc_final: 0.8536 (p) REVERT: B 155 MET cc_start: 0.7465 (mpp) cc_final: 0.7159 (mpp) REVERT: B 195 LEU cc_start: 0.8401 (tp) cc_final: 0.8059 (tp) REVERT: B 207 GLN cc_start: 0.8039 (mm110) cc_final: 0.7613 (mm-40) REVERT: B 240 LEU cc_start: 0.8719 (mm) cc_final: 0.8376 (mp) REVERT: B 288 LEU cc_start: 0.8873 (tp) cc_final: 0.8645 (tp) REVERT: B 355 SER cc_start: 0.8403 (m) cc_final: 0.7956 (p) REVERT: B 366 SER cc_start: 0.8355 (t) cc_final: 0.8139 (p) REVERT: B 385 PHE cc_start: 0.8706 (OUTLIER) cc_final: 0.8026 (m-10) REVERT: B 391 SER cc_start: 0.8663 (m) cc_final: 0.8173 (p) REVERT: B 398 PHE cc_start: 0.7671 (m-80) cc_final: 0.7327 (m-80) REVERT: B 414 GLU cc_start: 0.7311 (tm-30) cc_final: 0.7020 (tm-30) REVERT: B 432 MET cc_start: 0.7540 (tpt) cc_final: 0.7179 (tpt) REVERT: B 447 LYS cc_start: 0.8681 (mtpt) cc_final: 0.8264 (mtpt) REVERT: B 459 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8508 (ttpp) REVERT: B 473 LYS cc_start: 0.8447 (mtpt) cc_final: 0.8181 (mtpt) REVERT: B 475 ASN cc_start: 0.6966 (t0) cc_final: 0.6576 (t0) REVERT: B 476 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8362 (mtmm) REVERT: B 478 ASP cc_start: 0.7750 (p0) cc_final: 0.7414 (p0) REVERT: B 674 ARG cc_start: 0.7412 (mtt180) cc_final: 0.7194 (mtm-85) REVERT: B 682 GLU cc_start: 0.7599 (tt0) cc_final: 0.7389 (mt-10) REVERT: B 684 GLN cc_start: 0.8475 (tp40) cc_final: 0.8237 (tp-100) outliers start: 52 outliers final: 43 residues processed: 336 average time/residue: 0.2412 time to fit residues: 109.5774 Evaluate side-chains 352 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 304 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 489 SER Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 656 HIS Chi-restraints excluded: chain A residue 684 GLN Chi-restraints excluded: chain A residue 689 ASN Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 261 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 459 LYS Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 668 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 92 optimal weight: 0.6980 chunk 5 optimal weight: 0.0970 chunk 75 optimal weight: 0.5980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 457 ASN ** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS A 684 GLN B 382 ASN ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.119905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.101111 restraints weight = 17653.128| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.77 r_work: 0.3206 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 10406 Z= 0.250 Angle : 0.682 11.322 14142 Z= 0.342 Chirality : 0.045 0.337 1718 Planarity : 0.004 0.047 1760 Dihedral : 5.675 83.070 1431 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.96 % Favored : 92.89 % Rotamer: Outliers : 4.55 % Allowed : 26.92 % Favored : 68.54 % 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: -0.96 (0.24), residues: 1322 helix: 0.24 (0.18), residues: 862 sheet: -2.03 (0.99), residues: 36 loop : -2.28 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 74 HIS 0.006 0.001 HIS A 656 PHE 0.015 0.001 PHE A 115 TYR 0.015 0.001 TYR A 377 ARG 0.007 0.001 ARG A 440 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2944.51 seconds wall clock time: 53 minutes 21.49 seconds (3201.49 seconds total)