Starting phenix.real_space_refine on Fri Mar 6 07:53:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u6o_26377/03_2026/7u6o_26377.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u6o_26377/03_2026/7u6o_26377.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7u6o_26377/03_2026/7u6o_26377.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u6o_26377/03_2026/7u6o_26377.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7u6o_26377/03_2026/7u6o_26377.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u6o_26377/03_2026/7u6o_26377.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.037 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 168 5.16 5 C 18618 2.51 5 N 5022 2.21 5 O 5616 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29424 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 4904 Classifications: {'peptide': 636} Link IDs: {'PTRANS': 33, 'TRANS': 602} Chain breaks: 3 Chain: "B" Number of atoms: 4904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 4904 Classifications: {'peptide': 636} Link IDs: {'PTRANS': 33, 'TRANS': 602} Chain breaks: 3 Chain: "C" Number of atoms: 4904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 4904 Classifications: {'peptide': 636} Link IDs: {'PTRANS': 33, 'TRANS': 602} Chain breaks: 3 Chain: "D" Number of atoms: 4904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 4904 Classifications: {'peptide': 636} Link IDs: {'PTRANS': 33, 'TRANS': 602} Chain breaks: 3 Chain: "E" Number of atoms: 4904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 4904 Classifications: {'peptide': 636} Link IDs: {'PTRANS': 33, 'TRANS': 602} Chain breaks: 3 Chain: "F" Number of atoms: 4904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 4904 Classifications: {'peptide': 636} Link IDs: {'PTRANS': 33, 'TRANS': 602} Chain breaks: 3 Time building chain proxies: 6.01, per 1000 atoms: 0.20 Number of scatterers: 29424 At special positions: 0 Unit cell: (167.932, 178.347, 88.5224, 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 168 16.00 O 5616 8.00 N 5022 7.00 C 18618 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.35 Conformation dependent library (CDL) restraints added in 1.1 seconds 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7032 Finding SS restraints... Secondary structure from input PDB file: 152 helices and 42 sheets defined 54.9% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 44 through 53 removed outlier: 3.857A pdb=" N TYR A 51 " --> pdb=" O VAL A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 56 No H-bonds generated for 'chain 'A' and resid 54 through 56' Processing helix chain 'A' and resid 58 through 65 removed outlier: 3.837A pdb=" N LEU A 62 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN A 64 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY A 65 " --> pdb=" O LEU A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 89 Processing helix chain 'A' and resid 131 through 137 Processing helix chain 'A' and resid 191 through 213 removed outlier: 3.552A pdb=" N MET A 213 " --> pdb=" O MET A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 241 Processing helix chain 'A' and resid 243 through 249 Processing helix chain 'A' and resid 278 through 293 Processing helix chain 'A' and resid 317 through 338 removed outlier: 3.959A pdb=" N ASP A 322 " --> pdb=" O ILE A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 382 Processing helix chain 'A' and resid 385 through 410 removed outlier: 7.109A pdb=" N ASP A 403 " --> pdb=" O ASP A 399 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU A 404 " --> pdb=" O LYS A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 417 removed outlier: 3.633A pdb=" N ASP A 415 " --> pdb=" O PRO A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 446 Processing helix chain 'A' and resid 499 through 523 Processing helix chain 'A' and resid 526 through 539 Processing helix chain 'A' and resid 540 through 542 No H-bonds generated for 'chain 'A' and resid 540 through 542' Processing helix chain 'A' and resid 551 through 560 Processing helix chain 'A' and resid 566 through 573 Processing helix chain 'A' and resid 576 through 586 Processing helix chain 'A' and resid 590 through 623 Processing helix chain 'A' and resid 623 through 632 Processing helix chain 'A' and resid 636 through 656 Processing helix chain 'A' and resid 658 through 687 removed outlier: 4.360A pdb=" N MET A 674 " --> pdb=" O ARG A 670 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N VAL A 675 " --> pdb=" O LEU A 671 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG A 687 " --> pdb=" O GLU A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 703 Processing helix chain 'B' and resid 44 through 53 removed outlier: 3.844A pdb=" N TYR B 51 " --> pdb=" O VAL B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 56 No H-bonds generated for 'chain 'B' and resid 54 through 56' Processing helix chain 'B' and resid 58 through 65 removed outlier: 3.845A pdb=" N LEU B 62 " --> pdb=" O SER B 58 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN B 64 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY B 65 " --> pdb=" O LEU B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 89 Processing helix chain 'B' and resid 131 through 137 Processing helix chain 'B' and resid 191 through 213 Processing helix chain 'B' and resid 237 through 241 Processing helix chain 'B' and resid 243 through 249 Processing helix chain 'B' and resid 278 through 293 Processing helix chain 'B' and resid 317 through 338 removed outlier: 3.991A pdb=" N ASP B 322 " --> pdb=" O ILE B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 382 Processing helix chain 'B' and resid 385 through 410 removed outlier: 7.141A pdb=" N ASP B 403 " --> pdb=" O ASP B 399 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU B 404 " --> pdb=" O LYS B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 417 removed outlier: 3.637A pdb=" N ASP B 415 " --> pdb=" O PRO B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 446 Processing helix chain 'B' and resid 499 through 523 Processing helix chain 'B' and resid 526 through 539 Processing helix chain 'B' and resid 540 through 542 No H-bonds generated for 'chain 'B' and resid 540 through 542' Processing helix chain 'B' and resid 551 through 560 removed outlier: 3.686A pdb=" N GLU B 555 " --> pdb=" O ALA B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 573 Processing helix chain 'B' and resid 576 through 586 Processing helix chain 'B' and resid 590 through 623 Processing helix chain 'B' and resid 623 through 632 Processing helix chain 'B' and resid 636 through 656 Processing helix chain 'B' and resid 658 through 672 Processing helix chain 'B' and resid 672 through 687 removed outlier: 3.618A pdb=" N ARG B 687 " --> pdb=" O GLU B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 697 through 703 Processing helix chain 'C' and resid 44 through 53 removed outlier: 3.853A pdb=" N TYR C 51 " --> pdb=" O VAL C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 56 No H-bonds generated for 'chain 'C' and resid 54 through 56' Processing helix chain 'C' and resid 58 through 65 removed outlier: 3.841A pdb=" N LEU C 62 " --> pdb=" O SER C 58 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN C 64 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY C 65 " --> pdb=" O LEU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 89 Processing helix chain 'C' and resid 131 through 137 Processing helix chain 'C' and resid 191 through 213 Processing helix chain 'C' and resid 237 through 241 Processing helix chain 'C' and resid 243 through 249 Processing helix chain 'C' and resid 278 through 293 removed outlier: 3.503A pdb=" N MET C 282 " --> pdb=" O ALA C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 338 removed outlier: 4.042A pdb=" N ASP C 322 " --> pdb=" O ILE C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 382 Processing helix chain 'C' and resid 385 through 410 removed outlier: 3.654A pdb=" N LEU C 389 " --> pdb=" O GLU C 385 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASP C 403 " --> pdb=" O ASP C 399 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU C 404 " --> pdb=" O LYS C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 417 removed outlier: 3.594A pdb=" N ASP C 415 " --> pdb=" O PRO C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 446 Processing helix chain 'C' and resid 499 through 523 Processing helix chain 'C' and resid 526 through 539 Processing helix chain 'C' and resid 540 through 542 No H-bonds generated for 'chain 'C' and resid 540 through 542' Processing helix chain 'C' and resid 551 through 560 removed outlier: 3.745A pdb=" N GLU C 555 " --> pdb=" O ALA C 551 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 573 Processing helix chain 'C' and resid 576 through 586 Processing helix chain 'C' and resid 590 through 623 Processing helix chain 'C' and resid 623 through 632 Processing helix chain 'C' and resid 636 through 656 Processing helix chain 'C' and resid 658 through 687 removed outlier: 4.177A pdb=" N MET C 674 " --> pdb=" O ARG C 670 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N VAL C 675 " --> pdb=" O LEU C 671 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG C 687 " --> pdb=" O GLU C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 697 through 703 Processing helix chain 'D' and resid 44 through 53 removed outlier: 3.854A pdb=" N TYR D 51 " --> pdb=" O VAL D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 56 No H-bonds generated for 'chain 'D' and resid 54 through 56' Processing helix chain 'D' and resid 58 through 65 removed outlier: 3.840A pdb=" N LEU D 62 " --> pdb=" O SER D 58 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN D 64 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY D 65 " --> pdb=" O LEU D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 89 Processing helix chain 'D' and resid 131 through 137 Processing helix chain 'D' and resid 191 through 213 removed outlier: 3.556A pdb=" N MET D 213 " --> pdb=" O MET D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 241 Processing helix chain 'D' and resid 243 through 249 Processing helix chain 'D' and resid 278 through 293 Processing helix chain 'D' and resid 317 through 338 removed outlier: 3.953A pdb=" N ASP D 322 " --> pdb=" O ILE D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 382 Processing helix chain 'D' and resid 385 through 410 removed outlier: 7.107A pdb=" N ASP D 403 " --> pdb=" O ASP D 399 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU D 404 " --> pdb=" O LYS D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 417 removed outlier: 3.621A pdb=" N ASP D 415 " --> pdb=" O PRO D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 446 Processing helix chain 'D' and resid 499 through 523 Processing helix chain 'D' and resid 526 through 539 Processing helix chain 'D' and resid 540 through 542 No H-bonds generated for 'chain 'D' and resid 540 through 542' Processing helix chain 'D' and resid 551 through 560 removed outlier: 3.729A pdb=" N GLU D 555 " --> pdb=" O ALA D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 566 through 573 Processing helix chain 'D' and resid 576 through 586 Processing helix chain 'D' and resid 590 through 623 Processing helix chain 'D' and resid 623 through 632 Processing helix chain 'D' and resid 636 through 656 Processing helix chain 'D' and resid 658 through 687 removed outlier: 4.370A pdb=" N MET D 674 " --> pdb=" O ARG D 670 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N VAL D 675 " --> pdb=" O LEU D 671 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG D 687 " --> pdb=" O GLU D 683 " (cutoff:3.500A) Processing helix chain 'D' and resid 697 through 703 Processing helix chain 'E' and resid 44 through 53 removed outlier: 3.852A pdb=" N TYR E 51 " --> pdb=" O VAL E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 56 No H-bonds generated for 'chain 'E' and resid 54 through 56' Processing helix chain 'E' and resid 58 through 65 removed outlier: 3.851A pdb=" N LEU E 62 " --> pdb=" O SER E 58 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN E 64 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY E 65 " --> pdb=" O LEU E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 89 Processing helix chain 'E' and resid 131 through 137 Processing helix chain 'E' and resid 191 through 213 removed outlier: 3.531A pdb=" N MET E 213 " --> pdb=" O MET E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 241 Processing helix chain 'E' and resid 243 through 249 Processing helix chain 'E' and resid 278 through 293 Processing helix chain 'E' and resid 317 through 338 removed outlier: 4.002A pdb=" N ASP E 322 " --> pdb=" O ILE E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 382 Processing helix chain 'E' and resid 385 through 410 removed outlier: 7.103A pdb=" N ASP E 403 " --> pdb=" O ASP E 399 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU E 404 " --> pdb=" O LYS E 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 412 through 417 removed outlier: 3.631A pdb=" N ASP E 415 " --> pdb=" O PRO E 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 433 through 446 Processing helix chain 'E' and resid 499 through 523 Processing helix chain 'E' and resid 526 through 539 Processing helix chain 'E' and resid 540 through 542 No H-bonds generated for 'chain 'E' and resid 540 through 542' Processing helix chain 'E' and resid 551 through 560 removed outlier: 3.695A pdb=" N GLU E 555 " --> pdb=" O ALA E 551 " (cutoff:3.500A) Processing helix chain 'E' and resid 566 through 573 Processing helix chain 'E' and resid 576 through 586 Processing helix chain 'E' and resid 590 through 623 Processing helix chain 'E' and resid 623 through 632 Processing helix chain 'E' and resid 636 through 656 Processing helix chain 'E' and resid 658 through 672 Processing helix chain 'E' and resid 672 through 687 removed outlier: 3.607A pdb=" N ARG E 687 " --> pdb=" O GLU E 683 " (cutoff:3.500A) Processing helix chain 'E' and resid 697 through 703 Processing helix chain 'F' and resid 44 through 53 removed outlier: 3.850A pdb=" N TYR F 51 " --> pdb=" O VAL F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 56 No H-bonds generated for 'chain 'F' and resid 54 through 56' Processing helix chain 'F' and resid 58 through 65 removed outlier: 3.841A pdb=" N LEU F 62 " --> pdb=" O SER F 58 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN F 64 " --> pdb=" O THR F 60 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLY F 65 " --> pdb=" O LEU F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 89 Processing helix chain 'F' and resid 131 through 137 Processing helix chain 'F' and resid 191 through 212 Processing helix chain 'F' and resid 237 through 241 Processing helix chain 'F' and resid 243 through 249 Processing helix chain 'F' and resid 278 through 293 Processing helix chain 'F' and resid 317 through 338 removed outlier: 3.990A pdb=" N ASP F 322 " --> pdb=" O ILE F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 382 Processing helix chain 'F' and resid 385 through 410 removed outlier: 3.570A pdb=" N LEU F 389 " --> pdb=" O GLU F 385 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ASP F 403 " --> pdb=" O ASP F 399 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU F 404 " --> pdb=" O LYS F 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 412 through 417 removed outlier: 3.615A pdb=" N ASP F 415 " --> pdb=" O PRO F 412 " (cutoff:3.500A) Processing helix chain 'F' and resid 433 through 446 Processing helix chain 'F' and resid 499 through 523 Processing helix chain 'F' and resid 526 through 539 Processing helix chain 'F' and resid 540 through 542 No H-bonds generated for 'chain 'F' and resid 540 through 542' Processing helix chain 'F' and resid 551 through 560 removed outlier: 3.742A pdb=" N GLU F 555 " --> pdb=" O ALA F 551 " (cutoff:3.500A) Processing helix chain 'F' and resid 566 through 573 Processing helix chain 'F' and resid 576 through 586 Processing helix chain 'F' and resid 590 through 623 Processing helix chain 'F' and resid 623 through 632 Processing helix chain 'F' and resid 636 through 656 Processing helix chain 'F' and resid 658 through 687 removed outlier: 4.175A pdb=" N MET F 674 " --> pdb=" O ARG F 670 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N VAL F 675 " --> pdb=" O LEU F 671 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG F 687 " --> pdb=" O GLU F 683 " (cutoff:3.500A) Processing helix chain 'F' and resid 697 through 703 Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.292A pdb=" N ILE A 168 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL A 92 " --> pdb=" O VAL A 175 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N ILE A 177 " --> pdb=" O VAL A 92 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N CYS A 94 " --> pdb=" O ILE A 177 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ALA A 179 " --> pdb=" O CYS A 94 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N TRP A 96 " --> pdb=" O ALA A 179 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.292A pdb=" N ILE A 168 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 118 through 120 Processing sheet with id=AA4, first strand: chain 'A' and resid 298 through 301 removed outlier: 3.811A pdb=" N THR A 298 " --> pdb=" O ALA A 311 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 315 through 316 removed outlier: 3.527A pdb=" N HIS A 358 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 430 through 431 Processing sheet with id=AA7, first strand: chain 'A' and resid 455 through 458 Processing sheet with id=AA8, first strand: chain 'B' and resid 42 through 43 removed outlier: 4.356A pdb=" N ILE B 168 " --> pdb=" O PHE B 43 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL B 92 " --> pdb=" O VAL B 175 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ILE B 177 " --> pdb=" O VAL B 92 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N CYS B 94 " --> pdb=" O ILE B 177 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ALA B 179 " --> pdb=" O CYS B 94 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N TRP B 96 " --> pdb=" O ALA B 179 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 42 through 43 removed outlier: 4.356A pdb=" N ILE B 168 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 118 through 120 Processing sheet with id=AB2, first strand: chain 'B' and resid 298 through 301 removed outlier: 3.832A pdb=" N THR B 298 " --> pdb=" O ALA B 311 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 315 through 316 removed outlier: 3.525A pdb=" N HIS B 358 " --> pdb=" O GLU B 229 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 430 through 431 Processing sheet with id=AB5, first strand: chain 'B' and resid 455 through 458 Processing sheet with id=AB6, first strand: chain 'C' and resid 42 through 43 removed outlier: 4.378A pdb=" N ILE C 168 " --> pdb=" O PHE C 43 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL C 92 " --> pdb=" O VAL C 175 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N ILE C 177 " --> pdb=" O VAL C 92 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N CYS C 94 " --> pdb=" O ILE C 177 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ALA C 179 " --> pdb=" O CYS C 94 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N TRP C 96 " --> pdb=" O ALA C 179 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 42 through 43 removed outlier: 4.378A pdb=" N ILE C 168 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 118 through 120 Processing sheet with id=AB9, first strand: chain 'C' and resid 298 through 301 removed outlier: 3.825A pdb=" N THR C 298 " --> pdb=" O ALA C 311 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 315 through 316 removed outlier: 3.540A pdb=" N HIS C 358 " --> pdb=" O GLU C 229 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 430 through 431 Processing sheet with id=AC3, first strand: chain 'C' and resid 455 through 458 Processing sheet with id=AC4, first strand: chain 'D' and resid 42 through 43 removed outlier: 4.296A pdb=" N ILE D 168 " --> pdb=" O PHE D 43 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL D 92 " --> pdb=" O VAL D 175 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ILE D 177 " --> pdb=" O VAL D 92 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N CYS D 94 " --> pdb=" O ILE D 177 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ALA D 179 " --> pdb=" O CYS D 94 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N TRP D 96 " --> pdb=" O ALA D 179 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 42 through 43 removed outlier: 4.296A pdb=" N ILE D 168 " --> pdb=" O PHE D 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 118 through 120 Processing sheet with id=AC7, first strand: chain 'D' and resid 298 through 301 removed outlier: 3.808A pdb=" N THR D 298 " --> pdb=" O ALA D 311 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 315 through 316 removed outlier: 3.529A pdb=" N HIS D 358 " --> pdb=" O GLU D 229 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 430 through 431 Processing sheet with id=AD1, first strand: chain 'D' and resid 455 through 458 Processing sheet with id=AD2, first strand: chain 'E' and resid 42 through 43 removed outlier: 4.358A pdb=" N ILE E 168 " --> pdb=" O PHE E 43 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL E 92 " --> pdb=" O VAL E 175 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N ILE E 177 " --> pdb=" O VAL E 92 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N CYS E 94 " --> pdb=" O ILE E 177 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ALA E 179 " --> pdb=" O CYS E 94 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N TRP E 96 " --> pdb=" O ALA E 179 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 42 through 43 removed outlier: 4.358A pdb=" N ILE E 168 " --> pdb=" O PHE E 43 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 118 through 120 Processing sheet with id=AD5, first strand: chain 'E' and resid 298 through 301 removed outlier: 3.810A pdb=" N THR E 298 " --> pdb=" O ALA E 311 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 315 through 316 removed outlier: 3.522A pdb=" N HIS E 358 " --> pdb=" O GLU E 229 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 430 through 431 Processing sheet with id=AD8, first strand: chain 'E' and resid 455 through 458 Processing sheet with id=AD9, first strand: chain 'F' and resid 42 through 43 removed outlier: 4.256A pdb=" N ILE F 168 " --> pdb=" O PHE F 43 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL F 92 " --> pdb=" O VAL F 175 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N ILE F 177 " --> pdb=" O VAL F 92 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N CYS F 94 " --> pdb=" O ILE F 177 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ALA F 179 " --> pdb=" O CYS F 94 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N TRP F 96 " --> pdb=" O ALA F 179 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 42 through 43 removed outlier: 4.256A pdb=" N ILE F 168 " --> pdb=" O PHE F 43 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 118 through 120 Processing sheet with id=AE3, first strand: chain 'F' and resid 298 through 301 removed outlier: 3.891A pdb=" N THR F 298 " --> pdb=" O ALA F 311 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 315 through 316 removed outlier: 3.546A pdb=" N HIS F 358 " --> pdb=" O GLU F 229 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 430 through 431 Processing sheet with id=AE6, first strand: chain 'F' and resid 455 through 458 1726 hydrogen bonds defined for protein. 5016 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: 7.03 Time building geometry restraints manager: 3.12 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: 9722 1.34 - 1.46: 4449 1.46 - 1.58: 15595 1.58 - 1.69: 0 1.69 - 1.81: 294 Bond restraints: 30060 Sorted by residual: bond pdb=" CG1 ILE B 620 " pdb=" CD1 ILE B 620 " ideal model delta sigma weight residual 1.513 1.452 0.061 3.90e-02 6.57e+02 2.42e+00 bond pdb=" CG1 ILE E 620 " pdb=" CD1 ILE E 620 " ideal model delta sigma weight residual 1.513 1.452 0.061 3.90e-02 6.57e+02 2.42e+00 bond pdb=" CG1 ILE D 620 " pdb=" CD1 ILE D 620 " ideal model delta sigma weight residual 1.513 1.453 0.060 3.90e-02 6.57e+02 2.38e+00 bond pdb=" CG1 ILE A 620 " pdb=" CD1 ILE A 620 " ideal model delta sigma weight residual 1.513 1.454 0.059 3.90e-02 6.57e+02 2.32e+00 bond pdb=" CB CYS C 94 " pdb=" SG CYS C 94 " ideal model delta sigma weight residual 1.808 1.771 0.037 3.30e-02 9.18e+02 1.27e+00 ... (remaining 30055 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 39820 1.66 - 3.32: 682 3.32 - 4.98: 148 4.98 - 6.65: 24 6.65 - 8.31: 6 Bond angle restraints: 40680 Sorted by residual: angle pdb=" C VAL C 86 " pdb=" N GLU C 87 " pdb=" CA GLU C 87 " ideal model delta sigma weight residual 122.06 113.75 8.31 1.86e+00 2.89e-01 1.99e+01 angle pdb=" C VAL F 86 " pdb=" N GLU F 87 " pdb=" CA GLU F 87 " ideal model delta sigma weight residual 122.06 114.37 7.69 1.86e+00 2.89e-01 1.71e+01 angle pdb=" N GLU C 87 " pdb=" CA GLU C 87 " pdb=" CB GLU C 87 " ideal model delta sigma weight residual 110.46 115.78 -5.32 1.57e+00 4.06e-01 1.15e+01 angle pdb=" CA MET E 292 " pdb=" CB MET E 292 " pdb=" CG MET E 292 " ideal model delta sigma weight residual 114.10 120.53 -6.43 2.00e+00 2.50e-01 1.03e+01 angle pdb=" CA MET B 292 " pdb=" CB MET B 292 " pdb=" CG MET B 292 " ideal model delta sigma weight residual 114.10 120.48 -6.38 2.00e+00 2.50e-01 1.02e+01 ... (remaining 40675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.70: 16154 16.70 - 33.41: 1522 33.41 - 50.11: 317 50.11 - 66.82: 53 66.82 - 83.52: 26 Dihedral angle restraints: 18072 sinusoidal: 7140 harmonic: 10932 Sorted by residual: dihedral pdb=" CA ILE B 226 " pdb=" C ILE B 226 " pdb=" N GLY B 227 " pdb=" CA GLY B 227 " ideal model delta harmonic sigma weight residual 180.00 160.81 19.19 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA ILE E 226 " pdb=" C ILE E 226 " pdb=" N GLY E 227 " pdb=" CA GLY E 227 " ideal model delta harmonic sigma weight residual 180.00 161.44 18.56 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA PHE F 589 " pdb=" C PHE F 589 " pdb=" N THR F 590 " pdb=" CA THR F 590 " ideal model delta harmonic sigma weight residual 180.00 162.97 17.03 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 18069 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 3364 0.043 - 0.086: 851 0.086 - 0.130: 214 0.130 - 0.173: 10 0.173 - 0.216: 7 Chirality restraints: 4446 Sorted by residual: chirality pdb=" CA GLU C 87 " pdb=" N GLU C 87 " pdb=" C GLU C 87 " pdb=" CB GLU C 87 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA GLU F 87 " pdb=" N GLU F 87 " pdb=" C GLU F 87 " pdb=" CB GLU F 87 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA GLU D 87 " pdb=" N GLU D 87 " pdb=" C GLU D 87 " pdb=" CB GLU D 87 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 4443 not shown) Planarity restraints: 5346 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP D 83 " 0.013 2.00e-02 2.50e+03 2.53e-02 6.39e+00 pdb=" C ASP D 83 " -0.044 2.00e-02 2.50e+03 pdb=" O ASP D 83 " 0.016 2.00e-02 2.50e+03 pdb=" N TRP D 84 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 83 " 0.012 2.00e-02 2.50e+03 2.30e-02 5.28e+00 pdb=" C ASP A 83 " -0.040 2.00e-02 2.50e+03 pdb=" O ASP A 83 " 0.015 2.00e-02 2.50e+03 pdb=" N TRP A 84 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP E 83 " 0.011 2.00e-02 2.50e+03 2.18e-02 4.74e+00 pdb=" C ASP E 83 " -0.038 2.00e-02 2.50e+03 pdb=" O ASP E 83 " 0.014 2.00e-02 2.50e+03 pdb=" N TRP E 84 " 0.013 2.00e-02 2.50e+03 ... (remaining 5343 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 1080 2.70 - 3.25: 32470 3.25 - 3.80: 53503 3.80 - 4.35: 67127 4.35 - 4.90: 109842 Nonbonded interactions: 264022 Sorted by model distance: nonbonded pdb=" OG1 THR F 365 " pdb=" OD1 ASP F 367 " model vdw 2.152 3.040 nonbonded pdb=" OG1 THR C 365 " pdb=" OD1 ASP C 367 " model vdw 2.152 3.040 nonbonded pdb=" OG1 THR A 365 " pdb=" OD1 ASP A 367 " model vdw 2.153 3.040 nonbonded pdb=" OG1 THR E 365 " pdb=" OD1 ASP E 367 " model vdw 2.155 3.040 nonbonded pdb=" OG1 THR D 365 " pdb=" OD1 ASP D 367 " model vdw 2.156 3.040 ... (remaining 264017 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.520 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: 0.030 Extract box with map and model: 0.390 Check model and map are aligned: 0.050 Set scattering table: 0.090 Process input model: 26.450 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 30060 Z= 0.144 Angle : 0.576 8.307 40680 Z= 0.308 Chirality : 0.041 0.216 4446 Planarity : 0.004 0.037 5346 Dihedral : 13.726 83.522 11040 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 17.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.06 % Allowed : 0.03 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.14), residues: 3768 helix: 0.74 (0.12), residues: 1962 sheet: 0.24 (0.28), residues: 402 loop : -0.80 (0.17), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 487 TYR 0.017 0.001 TYR A 128 PHE 0.028 0.001 PHE B 169 TRP 0.009 0.001 TRP C 84 HIS 0.004 0.001 HIS E 338 Details of bonding type rmsd covalent geometry : bond 0.00318 (30060) covalent geometry : angle 0.57566 (40680) hydrogen bonds : bond 0.12267 ( 1696) hydrogen bonds : angle 6.67593 ( 5016) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 366 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASN cc_start: 0.9282 (m-40) cc_final: 0.8951 (m-40) REVERT: A 169 PHE cc_start: 0.8203 (p90) cc_final: 0.7888 (p90) REVERT: A 290 PHE cc_start: 0.8016 (m-10) cc_final: 0.7307 (m-10) REVERT: A 333 GLU cc_start: 0.8345 (mp0) cc_final: 0.8024 (pm20) REVERT: A 514 PHE cc_start: 0.9274 (m-10) cc_final: 0.9065 (m-10) REVERT: B 119 ASN cc_start: 0.9096 (m-40) cc_final: 0.8776 (m110) REVERT: B 290 PHE cc_start: 0.8207 (m-10) cc_final: 0.7480 (m-10) REVERT: B 514 PHE cc_start: 0.9164 (m-10) cc_final: 0.8852 (m-10) REVERT: C 119 ASN cc_start: 0.8873 (m-40) cc_final: 0.8417 (m110) REVERT: C 290 PHE cc_start: 0.7475 (m-10) cc_final: 0.6893 (m-10) REVERT: D 119 ASN cc_start: 0.9173 (m-40) cc_final: 0.8823 (m110) REVERT: D 169 PHE cc_start: 0.8197 (p90) cc_final: 0.7879 (p90) REVERT: D 290 PHE cc_start: 0.8068 (m-10) cc_final: 0.7351 (m-10) REVERT: D 333 GLU cc_start: 0.8361 (mp0) cc_final: 0.8006 (mp0) REVERT: E 100 MET cc_start: 0.7994 (mmm) cc_final: 0.7700 (mmt) REVERT: E 119 ASN cc_start: 0.9223 (m-40) cc_final: 0.8952 (m-40) REVERT: E 210 LEU cc_start: 0.9554 (mt) cc_final: 0.9234 (mt) REVERT: E 290 PHE cc_start: 0.8112 (m-10) cc_final: 0.7468 (m-10) REVERT: E 340 LEU cc_start: 0.8731 (mt) cc_final: 0.8509 (mt) REVERT: E 498 ASN cc_start: 0.8622 (OUTLIER) cc_final: 0.8410 (p0) REVERT: F 119 ASN cc_start: 0.8963 (m-40) cc_final: 0.8496 (m110) REVERT: F 169 PHE cc_start: 0.8238 (p90) cc_final: 0.7398 (p90) REVERT: F 290 PHE cc_start: 0.7826 (m-10) cc_final: 0.7219 (m-10) REVERT: F 332 GLU cc_start: 0.8623 (tp30) cc_final: 0.8382 (tp30) REVERT: F 499 VAL cc_start: 0.9343 (m) cc_final: 0.9025 (p) outliers start: 2 outliers final: 0 residues processed: 368 average time/residue: 0.1711 time to fit residues: 103.1990 Evaluate side-chains 308 residues out of total 3114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 307 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 498 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.0980 chunk 183 optimal weight: 0.5980 chunk 298 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 ASN A 498 ASN ** A 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 GLN B 306 ASN ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 ASN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 GLN ** C 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 ASN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 306 ASN ** D 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 ASN ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 287 GLN E 306 ASN E 498 ASN ** E 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 88 ASN ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 306 ASN F 345 GLN F 503 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.097868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.077997 restraints weight = 99466.879| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 4.19 r_work: 0.3473 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 30060 Z= 0.136 Angle : 0.596 7.230 40680 Z= 0.311 Chirality : 0.041 0.193 4446 Planarity : 0.004 0.036 5346 Dihedral : 4.076 19.731 4058 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.74 % Allowed : 7.48 % Favored : 91.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.14), residues: 3768 helix: 1.15 (0.11), residues: 1986 sheet: 0.13 (0.29), residues: 318 loop : -0.90 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 487 TYR 0.011 0.001 TYR A 128 PHE 0.029 0.001 PHE F 118 TRP 0.015 0.001 TRP B 84 HIS 0.004 0.001 HIS F 538 Details of bonding type rmsd covalent geometry : bond 0.00300 (30060) covalent geometry : angle 0.59620 (40680) hydrogen bonds : bond 0.03713 ( 1696) hydrogen bonds : angle 5.35703 ( 5016) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 3114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 365 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASN cc_start: 0.9392 (m-40) cc_final: 0.9103 (m-40) REVERT: A 289 CYS cc_start: 0.8789 (m) cc_final: 0.8233 (m) REVERT: A 290 PHE cc_start: 0.8327 (m-10) cc_final: 0.7906 (m-10) REVERT: A 438 GLU cc_start: 0.9480 (OUTLIER) cc_final: 0.9264 (mp0) REVERT: A 514 PHE cc_start: 0.9369 (m-10) cc_final: 0.9050 (m-10) REVERT: B 119 ASN cc_start: 0.9414 (m-40) cc_final: 0.9111 (m110) REVERT: B 289 CYS cc_start: 0.8269 (m) cc_final: 0.7921 (m) REVERT: B 290 PHE cc_start: 0.8272 (m-10) cc_final: 0.7947 (m-10) REVERT: B 514 PHE cc_start: 0.9396 (m-10) cc_final: 0.9139 (m-10) REVERT: C 119 ASN cc_start: 0.9217 (m-40) cc_final: 0.8750 (m110) REVERT: C 169 PHE cc_start: 0.8427 (p90) cc_final: 0.8197 (p90) REVERT: C 290 PHE cc_start: 0.7980 (m-10) cc_final: 0.7568 (m-10) REVERT: C 487 ARG cc_start: 0.7837 (ptm160) cc_final: 0.7536 (ptm160) REVERT: D 119 ASN cc_start: 0.9399 (m-40) cc_final: 0.9121 (m110) REVERT: D 213 MET cc_start: 0.8729 (ppp) cc_final: 0.8508 (ppp) REVERT: D 289 CYS cc_start: 0.8520 (m) cc_final: 0.8033 (m) REVERT: D 290 PHE cc_start: 0.8362 (m-10) cc_final: 0.7936 (m-10) REVERT: D 314 PHE cc_start: 0.8257 (p90) cc_final: 0.7906 (p90) REVERT: D 394 MET cc_start: 0.9157 (mpp) cc_final: 0.8718 (mpp) REVERT: E 119 ASN cc_start: 0.9474 (m-40) cc_final: 0.9234 (m110) REVERT: E 289 CYS cc_start: 0.8268 (m) cc_final: 0.7933 (m) REVERT: E 290 PHE cc_start: 0.8258 (m-10) cc_final: 0.7936 (m-10) REVERT: F 169 PHE cc_start: 0.8437 (p90) cc_final: 0.7613 (p90) REVERT: F 289 CYS cc_start: 0.8656 (m) cc_final: 0.8240 (m) REVERT: F 290 PHE cc_start: 0.7974 (m-10) cc_final: 0.7569 (m-10) REVERT: F 332 GLU cc_start: 0.8793 (tp30) cc_final: 0.8527 (tp30) REVERT: F 459 GLU cc_start: 0.8782 (pm20) cc_final: 0.8540 (pm20) REVERT: F 499 VAL cc_start: 0.9442 (m) cc_final: 0.9144 (p) outliers start: 23 outliers final: 13 residues processed: 377 average time/residue: 0.1676 time to fit residues: 104.5568 Evaluate side-chains 344 residues out of total 3114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 330 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 438 GLU Chi-restraints excluded: chain B residue 674 MET Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 279 PHE Chi-restraints excluded: chain C residue 326 MET Chi-restraints excluded: chain C residue 438 GLU Chi-restraints excluded: chain D residue 281 CYS Chi-restraints excluded: chain D residue 700 GLU Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 438 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 146 optimal weight: 2.9990 chunk 282 optimal weight: 0.9980 chunk 235 optimal weight: 9.9990 chunk 154 optimal weight: 0.9990 chunk 314 optimal weight: 4.9990 chunk 322 optimal weight: 5.9990 chunk 155 optimal weight: 0.9990 chunk 162 optimal weight: 6.9990 chunk 260 optimal weight: 10.0000 chunk 201 optimal weight: 9.9990 chunk 43 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 ASN B 98 GLN B 225 ASN ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 306 ASN D 98 GLN ** D 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 287 GLN ** D 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN ** E 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 225 ASN F 287 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.097308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.077555 restraints weight = 99332.645| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 4.15 r_work: 0.3468 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 30060 Z= 0.127 Angle : 0.566 7.438 40680 Z= 0.292 Chirality : 0.040 0.181 4446 Planarity : 0.004 0.038 5346 Dihedral : 3.938 17.065 4056 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.28 % Allowed : 10.28 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.14), residues: 3768 helix: 1.42 (0.11), residues: 1974 sheet: 0.00 (0.29), residues: 318 loop : -0.89 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 487 TYR 0.008 0.001 TYR A 128 PHE 0.029 0.001 PHE A 118 TRP 0.010 0.001 TRP B 84 HIS 0.004 0.001 HIS B 623 Details of bonding type rmsd covalent geometry : bond 0.00285 (30060) covalent geometry : angle 0.56598 (40680) hydrogen bonds : bond 0.03439 ( 1696) hydrogen bonds : angle 5.08688 ( 5016) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 3114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 358 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASN cc_start: 0.9394 (m-40) cc_final: 0.9113 (m-40) REVERT: A 289 CYS cc_start: 0.8445 (m) cc_final: 0.7870 (m) REVERT: A 290 PHE cc_start: 0.8221 (m-10) cc_final: 0.7743 (m-10) REVERT: A 333 GLU cc_start: 0.8554 (mp0) cc_final: 0.8244 (mp0) REVERT: A 394 MET cc_start: 0.9154 (mpp) cc_final: 0.8732 (mpp) REVERT: B 100 MET cc_start: 0.7806 (mmt) cc_final: 0.7522 (mmt) REVERT: B 119 ASN cc_start: 0.9416 (m-40) cc_final: 0.9085 (m110) REVERT: B 289 CYS cc_start: 0.8284 (m) cc_final: 0.7924 (m) REVERT: B 290 PHE cc_start: 0.8217 (m-10) cc_final: 0.7667 (m-10) REVERT: B 487 ARG cc_start: 0.7848 (ptp90) cc_final: 0.7292 (ptt-90) REVERT: C 87 GLU cc_start: 0.9326 (OUTLIER) cc_final: 0.9043 (pp20) REVERT: C 119 ASN cc_start: 0.9213 (m-40) cc_final: 0.8746 (m110) REVERT: C 169 PHE cc_start: 0.8486 (p90) cc_final: 0.8253 (p90) REVERT: C 290 PHE cc_start: 0.7994 (m-10) cc_final: 0.7563 (m-10) REVERT: D 119 ASN cc_start: 0.9394 (m-40) cc_final: 0.9106 (m110) REVERT: D 287 GLN cc_start: 0.9261 (OUTLIER) cc_final: 0.8675 (pp30) REVERT: D 289 CYS cc_start: 0.8534 (m) cc_final: 0.7912 (m) REVERT: D 290 PHE cc_start: 0.8329 (m-10) cc_final: 0.7897 (m-10) REVERT: D 332 GLU cc_start: 0.8815 (tp30) cc_final: 0.8577 (tp30) REVERT: D 333 GLU cc_start: 0.8598 (mp0) cc_final: 0.8300 (mp0) REVERT: D 394 MET cc_start: 0.9155 (mpp) cc_final: 0.8799 (mpp) REVERT: E 100 MET cc_start: 0.7980 (mmt) cc_final: 0.7704 (mmt) REVERT: E 119 ASN cc_start: 0.9478 (m-40) cc_final: 0.9252 (m110) REVERT: E 289 CYS cc_start: 0.8305 (m) cc_final: 0.7899 (m) REVERT: E 290 PHE cc_start: 0.8233 (m-10) cc_final: 0.7671 (m-10) REVERT: E 487 ARG cc_start: 0.7617 (ptt-90) cc_final: 0.7315 (ptt-90) REVERT: F 87 GLU cc_start: 0.9329 (OUTLIER) cc_final: 0.9095 (pp20) REVERT: F 169 PHE cc_start: 0.8498 (p90) cc_final: 0.7785 (p90) REVERT: F 285 ILE cc_start: 0.9251 (mm) cc_final: 0.8955 (mm) REVERT: F 287 GLN cc_start: 0.9129 (OUTLIER) cc_final: 0.8807 (pp30) REVERT: F 289 CYS cc_start: 0.8657 (m) cc_final: 0.8136 (m) REVERT: F 290 PHE cc_start: 0.7991 (m-10) cc_final: 0.7406 (m-10) REVERT: F 292 MET cc_start: 0.5790 (tpp) cc_final: 0.5173 (tpp) REVERT: F 332 GLU cc_start: 0.8831 (tp30) cc_final: 0.8480 (tp30) REVERT: F 499 VAL cc_start: 0.9481 (m) cc_final: 0.9091 (p) REVERT: F 503 ASN cc_start: 0.9288 (m-40) cc_final: 0.9087 (m110) outliers start: 40 outliers final: 14 residues processed: 386 average time/residue: 0.1590 time to fit residues: 101.6496 Evaluate side-chains 356 residues out of total 3114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 338 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 674 MET Chi-restraints excluded: chain B residue 438 GLU Chi-restraints excluded: chain B residue 674 MET Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 279 PHE Chi-restraints excluded: chain C residue 301 ARG Chi-restraints excluded: chain C residue 333 GLU Chi-restraints excluded: chain C residue 438 GLU Chi-restraints excluded: chain D residue 281 CYS Chi-restraints excluded: chain D residue 287 GLN Chi-restraints excluded: chain D residue 438 GLU Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 438 GLU Chi-restraints excluded: chain E residue 674 MET Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 287 GLN Chi-restraints excluded: chain F residue 438 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 375 optimal weight: 2.9990 chunk 111 optimal weight: 8.9990 chunk 149 optimal weight: 9.9990 chunk 58 optimal weight: 0.2980 chunk 234 optimal weight: 6.9990 chunk 82 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 chunk 97 optimal weight: 1.9990 chunk 345 optimal weight: 1.9990 chunk 171 optimal weight: 5.9990 chunk 181 optimal weight: 2.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN ** C 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 503 ASN ** D 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 98 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.097105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.077547 restraints weight = 98701.131| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 4.11 r_work: 0.3462 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 30060 Z= 0.133 Angle : 0.563 8.113 40680 Z= 0.291 Chirality : 0.040 0.186 4446 Planarity : 0.004 0.034 5346 Dihedral : 3.902 16.664 4056 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.06 % Allowed : 11.24 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.14), residues: 3768 helix: 1.45 (0.11), residues: 1986 sheet: 0.49 (0.29), residues: 294 loop : -0.99 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 487 TYR 0.009 0.001 TYR A 51 PHE 0.030 0.001 PHE C 118 TRP 0.010 0.001 TRP B 84 HIS 0.004 0.001 HIS A 401 Details of bonding type rmsd covalent geometry : bond 0.00298 (30060) covalent geometry : angle 0.56316 (40680) hydrogen bonds : bond 0.03336 ( 1696) hydrogen bonds : angle 4.98631 ( 5016) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 3114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 349 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASN cc_start: 0.9407 (m-40) cc_final: 0.9121 (m-40) REVERT: A 289 CYS cc_start: 0.8585 (m) cc_final: 0.7995 (m) REVERT: A 290 PHE cc_start: 0.8136 (m-10) cc_final: 0.7810 (m-10) REVERT: A 332 GLU cc_start: 0.8771 (tp30) cc_final: 0.8518 (tp30) REVERT: A 394 MET cc_start: 0.9111 (mpp) cc_final: 0.8781 (mpp) REVERT: B 100 MET cc_start: 0.7851 (mmt) cc_final: 0.7559 (mmt) REVERT: B 119 ASN cc_start: 0.9424 (m-40) cc_final: 0.9146 (m110) REVERT: B 289 CYS cc_start: 0.8371 (m) cc_final: 0.8014 (m) REVERT: B 290 PHE cc_start: 0.8282 (m-10) cc_final: 0.7946 (m-10) REVERT: B 459 GLU cc_start: 0.7963 (mp0) cc_final: 0.7737 (mp0) REVERT: B 487 ARG cc_start: 0.7805 (ptp90) cc_final: 0.7432 (ptt-90) REVERT: C 87 GLU cc_start: 0.9305 (OUTLIER) cc_final: 0.9054 (pp20) REVERT: C 119 ASN cc_start: 0.9211 (m-40) cc_final: 0.8730 (m110) REVERT: C 169 PHE cc_start: 0.8495 (p90) cc_final: 0.8214 (p90) REVERT: C 290 PHE cc_start: 0.8004 (m-10) cc_final: 0.7427 (m-10) REVERT: C 616 MET cc_start: 0.9031 (ttm) cc_final: 0.8757 (ttm) REVERT: D 119 ASN cc_start: 0.9402 (m-40) cc_final: 0.9108 (m110) REVERT: D 289 CYS cc_start: 0.8605 (m) cc_final: 0.8135 (m) REVERT: D 290 PHE cc_start: 0.8257 (m-10) cc_final: 0.7890 (m-10) REVERT: D 332 GLU cc_start: 0.8786 (tp30) cc_final: 0.8547 (tp30) REVERT: D 394 MET cc_start: 0.9156 (mpp) cc_final: 0.8784 (mpp) REVERT: E 100 MET cc_start: 0.7968 (mmt) cc_final: 0.7699 (mmt) REVERT: E 119 ASN cc_start: 0.9491 (m-40) cc_final: 0.9266 (m110) REVERT: E 289 CYS cc_start: 0.8458 (m) cc_final: 0.8063 (m) REVERT: E 290 PHE cc_start: 0.8357 (m-10) cc_final: 0.8027 (m-10) REVERT: E 459 GLU cc_start: 0.8109 (mp0) cc_final: 0.7900 (mp0) REVERT: F 87 GLU cc_start: 0.9310 (OUTLIER) cc_final: 0.9091 (pp20) REVERT: F 169 PHE cc_start: 0.8433 (p90) cc_final: 0.7878 (p90) REVERT: F 285 ILE cc_start: 0.9248 (mm) cc_final: 0.8992 (mm) REVERT: F 289 CYS cc_start: 0.8926 (m) cc_final: 0.8370 (m) REVERT: F 290 PHE cc_start: 0.8294 (m-10) cc_final: 0.7856 (m-10) REVERT: F 332 GLU cc_start: 0.8860 (tp30) cc_final: 0.8518 (tp30) REVERT: F 499 VAL cc_start: 0.9493 (m) cc_final: 0.9097 (p) REVERT: F 503 ASN cc_start: 0.9333 (m-40) cc_final: 0.9111 (m110) REVERT: F 616 MET cc_start: 0.8885 (ttm) cc_final: 0.8473 (ttm) outliers start: 33 outliers final: 17 residues processed: 367 average time/residue: 0.1658 time to fit residues: 100.5145 Evaluate side-chains 351 residues out of total 3114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 332 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain B residue 38 PHE Chi-restraints excluded: chain B residue 438 GLU Chi-restraints excluded: chain B residue 674 MET Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 279 PHE Chi-restraints excluded: chain C residue 301 ARG Chi-restraints excluded: chain C residue 333 GLU Chi-restraints excluded: chain C residue 438 GLU Chi-restraints excluded: chain C residue 700 GLU Chi-restraints excluded: chain D residue 38 PHE Chi-restraints excluded: chain D residue 586 MET Chi-restraints excluded: chain D residue 674 MET Chi-restraints excluded: chain E residue 38 PHE Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 674 MET Chi-restraints excluded: chain F residue 38 PHE Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 438 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 124 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 13 optimal weight: 20.0000 chunk 2 optimal weight: 8.9990 chunk 211 optimal weight: 1.9990 chunk 274 optimal weight: 9.9990 chunk 240 optimal weight: 0.9990 chunk 263 optimal weight: 0.9980 chunk 326 optimal weight: 5.9990 chunk 375 optimal weight: 3.9990 chunk 217 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.096516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.076860 restraints weight = 99980.587| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 4.11 r_work: 0.3449 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 30060 Z= 0.144 Angle : 0.571 8.561 40680 Z= 0.293 Chirality : 0.040 0.196 4446 Planarity : 0.004 0.036 5346 Dihedral : 3.873 16.345 4056 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.06 % Allowed : 12.14 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.14), residues: 3768 helix: 1.55 (0.11), residues: 1974 sheet: 0.31 (0.28), residues: 348 loop : -0.93 (0.16), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 487 TYR 0.010 0.001 TYR B 51 PHE 0.032 0.001 PHE C 118 TRP 0.015 0.001 TRP B 84 HIS 0.004 0.001 HIS A 401 Details of bonding type rmsd covalent geometry : bond 0.00322 (30060) covalent geometry : angle 0.57142 (40680) hydrogen bonds : bond 0.03282 ( 1696) hydrogen bonds : angle 4.91441 ( 5016) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 3114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 355 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASN cc_start: 0.9418 (m-40) cc_final: 0.9123 (m-40) REVERT: A 289 CYS cc_start: 0.8580 (m) cc_final: 0.7983 (m) REVERT: A 290 PHE cc_start: 0.8057 (m-10) cc_final: 0.7739 (m-10) REVERT: A 314 PHE cc_start: 0.8205 (m-10) cc_final: 0.7992 (m-10) REVERT: B 100 MET cc_start: 0.7943 (mmt) cc_final: 0.7669 (mmt) REVERT: B 119 ASN cc_start: 0.9438 (m-40) cc_final: 0.9147 (m110) REVERT: B 289 CYS cc_start: 0.8372 (m) cc_final: 0.8020 (m) REVERT: B 290 PHE cc_start: 0.8242 (m-10) cc_final: 0.7941 (m-10) REVERT: B 459 GLU cc_start: 0.8011 (mp0) cc_final: 0.7737 (mp0) REVERT: B 487 ARG cc_start: 0.7826 (ptp90) cc_final: 0.7466 (ptt-90) REVERT: C 87 GLU cc_start: 0.9175 (OUTLIER) cc_final: 0.8911 (pp20) REVERT: C 119 ASN cc_start: 0.9212 (m-40) cc_final: 0.8734 (m110) REVERT: C 169 PHE cc_start: 0.8453 (p90) cc_final: 0.8100 (p90) REVERT: C 289 CYS cc_start: 0.9018 (m) cc_final: 0.8445 (m) REVERT: C 290 PHE cc_start: 0.8175 (m-10) cc_final: 0.7834 (m-10) REVERT: C 326 MET cc_start: 0.8739 (ptt) cc_final: 0.8526 (ptp) REVERT: C 616 MET cc_start: 0.9045 (ttm) cc_final: 0.8776 (ttm) REVERT: D 119 ASN cc_start: 0.9427 (m-40) cc_final: 0.9132 (m110) REVERT: D 289 CYS cc_start: 0.8614 (m) cc_final: 0.8135 (m) REVERT: D 290 PHE cc_start: 0.8170 (m-10) cc_final: 0.7843 (m-10) REVERT: D 394 MET cc_start: 0.9168 (mpp) cc_final: 0.8806 (mpp) REVERT: E 100 MET cc_start: 0.8112 (mmt) cc_final: 0.7877 (mmt) REVERT: E 119 ASN cc_start: 0.9463 (m-40) cc_final: 0.9214 (m110) REVERT: E 171 ARG cc_start: 0.8412 (mmm-85) cc_final: 0.7690 (tpp-160) REVERT: E 289 CYS cc_start: 0.8452 (m) cc_final: 0.8061 (m) REVERT: E 290 PHE cc_start: 0.8278 (m-10) cc_final: 0.7954 (m-10) REVERT: E 333 GLU cc_start: 0.9312 (pm20) cc_final: 0.8867 (pm20) REVERT: E 459 GLU cc_start: 0.8138 (mp0) cc_final: 0.7870 (mp0) REVERT: F 87 GLU cc_start: 0.9244 (OUTLIER) cc_final: 0.9035 (pp20) REVERT: F 169 PHE cc_start: 0.8440 (p90) cc_final: 0.8010 (p90) REVERT: F 285 ILE cc_start: 0.9229 (mm) cc_final: 0.8978 (mm) REVERT: F 289 CYS cc_start: 0.8895 (m) cc_final: 0.8317 (m) REVERT: F 290 PHE cc_start: 0.8245 (m-10) cc_final: 0.7832 (m-10) REVERT: F 292 MET cc_start: 0.5976 (tpp) cc_final: 0.5237 (tpp) REVERT: F 332 GLU cc_start: 0.8870 (tp30) cc_final: 0.8527 (tp30) REVERT: F 499 VAL cc_start: 0.9509 (m) cc_final: 0.9101 (p) REVERT: F 503 ASN cc_start: 0.9352 (m-40) cc_final: 0.9092 (m110) outliers start: 33 outliers final: 18 residues processed: 371 average time/residue: 0.1744 time to fit residues: 107.7867 Evaluate side-chains 358 residues out of total 3114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 338 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain B residue 38 PHE Chi-restraints excluded: chain B residue 438 GLU Chi-restraints excluded: chain B residue 674 MET Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 301 ARG Chi-restraints excluded: chain C residue 333 GLU Chi-restraints excluded: chain C residue 438 GLU Chi-restraints excluded: chain C residue 700 GLU Chi-restraints excluded: chain D residue 281 CYS Chi-restraints excluded: chain D residue 586 MET Chi-restraints excluded: chain E residue 38 PHE Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 438 GLU Chi-restraints excluded: chain E residue 643 VAL Chi-restraints excluded: chain E residue 674 MET Chi-restraints excluded: chain F residue 38 PHE Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 438 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 269 optimal weight: 6.9990 chunk 140 optimal weight: 0.9990 chunk 321 optimal weight: 10.0000 chunk 108 optimal weight: 8.9990 chunk 355 optimal weight: 0.5980 chunk 345 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 306 optimal weight: 0.9980 chunk 273 optimal weight: 5.9990 chunk 87 optimal weight: 0.0870 chunk 309 optimal weight: 4.9990 overall best weight: 1.5362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 329 GLN ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 ASN ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.097153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.077593 restraints weight = 99049.911| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 4.14 r_work: 0.3456 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 30060 Z= 0.131 Angle : 0.587 8.949 40680 Z= 0.296 Chirality : 0.040 0.198 4446 Planarity : 0.004 0.035 5346 Dihedral : 3.865 18.729 4056 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.80 % Allowed : 12.85 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.14), residues: 3768 helix: 1.54 (0.11), residues: 1986 sheet: 0.27 (0.28), residues: 348 loop : -0.90 (0.17), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 487 TYR 0.010 0.001 TYR E 51 PHE 0.032 0.001 PHE C 118 TRP 0.014 0.001 TRP B 84 HIS 0.004 0.001 HIS B 623 Details of bonding type rmsd covalent geometry : bond 0.00292 (30060) covalent geometry : angle 0.58720 (40680) hydrogen bonds : bond 0.03222 ( 1696) hydrogen bonds : angle 4.87943 ( 5016) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 3114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 357 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASN cc_start: 0.9433 (m-40) cc_final: 0.9159 (m-40) REVERT: A 289 CYS cc_start: 0.8533 (m) cc_final: 0.7936 (m) REVERT: A 290 PHE cc_start: 0.8008 (m-10) cc_final: 0.7649 (m-10) REVERT: A 314 PHE cc_start: 0.8361 (m-10) cc_final: 0.8032 (m-10) REVERT: A 487 ARG cc_start: 0.8135 (ptt-90) cc_final: 0.7860 (ttp80) REVERT: A 503 ASN cc_start: 0.9004 (m-40) cc_final: 0.8599 (m110) REVERT: B 100 MET cc_start: 0.8032 (mmt) cc_final: 0.7768 (mmt) REVERT: B 119 ASN cc_start: 0.9452 (m-40) cc_final: 0.9169 (m110) REVERT: B 289 CYS cc_start: 0.8352 (m) cc_final: 0.7985 (m) REVERT: B 290 PHE cc_start: 0.8198 (m-10) cc_final: 0.7908 (m-10) REVERT: B 459 GLU cc_start: 0.8059 (mp0) cc_final: 0.7793 (mp0) REVERT: B 487 ARG cc_start: 0.7740 (ptp90) cc_final: 0.7346 (ptt-90) REVERT: B 514 PHE cc_start: 0.9429 (m-80) cc_final: 0.9188 (m-80) REVERT: C 87 GLU cc_start: 0.9203 (OUTLIER) cc_final: 0.8912 (pp20) REVERT: C 119 ASN cc_start: 0.9239 (m-40) cc_final: 0.8764 (m110) REVERT: C 169 PHE cc_start: 0.8362 (p90) cc_final: 0.8125 (p90) REVERT: C 289 CYS cc_start: 0.8996 (m) cc_final: 0.8452 (m) REVERT: C 290 PHE cc_start: 0.8105 (m-10) cc_final: 0.7776 (m-10) REVERT: C 326 MET cc_start: 0.8723 (ptt) cc_final: 0.8327 (ptm) REVERT: C 416 PHE cc_start: 0.8556 (m-10) cc_final: 0.8310 (m-10) REVERT: C 459 GLU cc_start: 0.8900 (mp0) cc_final: 0.8625 (pm20) REVERT: D 119 ASN cc_start: 0.9442 (m-40) cc_final: 0.9156 (m110) REVERT: D 289 CYS cc_start: 0.8706 (m) cc_final: 0.8149 (m) REVERT: D 290 PHE cc_start: 0.8101 (m-10) cc_final: 0.7797 (m-10) REVERT: D 394 MET cc_start: 0.9226 (mpp) cc_final: 0.8885 (mpp) REVERT: D 438 GLU cc_start: 0.9517 (pm20) cc_final: 0.9240 (pm20) REVERT: D 487 ARG cc_start: 0.8261 (ptt-90) cc_final: 0.8043 (ptt-90) REVERT: E 119 ASN cc_start: 0.9463 (m-40) cc_final: 0.9222 (m110) REVERT: E 170 LEU cc_start: 0.9331 (tt) cc_final: 0.8882 (pp) REVERT: E 171 ARG cc_start: 0.8503 (mmm-85) cc_final: 0.7660 (tpp-160) REVERT: E 289 CYS cc_start: 0.8452 (m) cc_final: 0.8084 (m) REVERT: E 290 PHE cc_start: 0.8274 (m-10) cc_final: 0.7957 (m-10) REVERT: E 454 LYS cc_start: 0.8748 (mptt) cc_final: 0.8520 (mmtm) REVERT: E 459 GLU cc_start: 0.8156 (mp0) cc_final: 0.7845 (mp0) REVERT: F 87 GLU cc_start: 0.9242 (OUTLIER) cc_final: 0.9025 (pp20) REVERT: F 169 PHE cc_start: 0.8354 (p90) cc_final: 0.7895 (p90) REVERT: F 289 CYS cc_start: 0.8862 (m) cc_final: 0.8270 (m) REVERT: F 290 PHE cc_start: 0.8008 (m-10) cc_final: 0.7626 (m-10) REVERT: F 292 MET cc_start: 0.5720 (tpp) cc_final: 0.4965 (tpp) REVERT: F 332 GLU cc_start: 0.8844 (tp30) cc_final: 0.8548 (tp30) REVERT: F 499 VAL cc_start: 0.9513 (m) cc_final: 0.9092 (p) REVERT: F 503 ASN cc_start: 0.9348 (m-40) cc_final: 0.9061 (m110) outliers start: 25 outliers final: 16 residues processed: 369 average time/residue: 0.1653 time to fit residues: 100.4295 Evaluate side-chains 356 residues out of total 3114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 338 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 438 GLU Chi-restraints excluded: chain B residue 674 MET Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 301 ARG Chi-restraints excluded: chain C residue 333 GLU Chi-restraints excluded: chain C residue 438 GLU Chi-restraints excluded: chain C residue 700 GLU Chi-restraints excluded: chain D residue 281 CYS Chi-restraints excluded: chain D residue 586 MET Chi-restraints excluded: chain E residue 38 PHE Chi-restraints excluded: chain E residue 438 GLU Chi-restraints excluded: chain E residue 586 MET Chi-restraints excluded: chain E residue 643 VAL Chi-restraints excluded: chain E residue 674 MET Chi-restraints excluded: chain F residue 38 PHE Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 438 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 212 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 51 optimal weight: 10.0000 chunk 85 optimal weight: 6.9990 chunk 331 optimal weight: 20.0000 chunk 134 optimal weight: 7.9990 chunk 180 optimal weight: 0.8980 chunk 291 optimal weight: 0.0040 chunk 84 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 overall best weight: 0.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 ASN ** A 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 ASN D 306 ASN ** D 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 329 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.096962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.077430 restraints weight = 99567.843| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 4.14 r_work: 0.3471 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30060 Z= 0.115 Angle : 0.594 10.128 40680 Z= 0.299 Chirality : 0.040 0.202 4446 Planarity : 0.004 0.036 5346 Dihedral : 3.844 18.854 4056 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.93 % Allowed : 13.33 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.14), residues: 3768 helix: 1.59 (0.11), residues: 1974 sheet: 0.27 (0.28), residues: 348 loop : -0.87 (0.16), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 487 TYR 0.009 0.001 TYR E 51 PHE 0.033 0.001 PHE C 118 TRP 0.013 0.001 TRP B 84 HIS 0.005 0.001 HIS B 623 Details of bonding type rmsd covalent geometry : bond 0.00257 (30060) covalent geometry : angle 0.59400 (40680) hydrogen bonds : bond 0.03172 ( 1696) hydrogen bonds : angle 4.85405 ( 5016) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 3114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 363 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASN cc_start: 0.9432 (m-40) cc_final: 0.9174 (m110) REVERT: A 289 CYS cc_start: 0.8434 (m) cc_final: 0.8080 (m) REVERT: A 290 PHE cc_start: 0.7904 (m-10) cc_final: 0.7554 (m-10) REVERT: A 314 PHE cc_start: 0.8356 (m-10) cc_final: 0.7777 (m-10) REVERT: A 332 GLU cc_start: 0.8767 (tp30) cc_final: 0.8509 (tp30) REVERT: A 503 ASN cc_start: 0.9031 (m-40) cc_final: 0.8656 (m110) REVERT: B 100 MET cc_start: 0.8004 (mmt) cc_final: 0.7741 (mmt) REVERT: B 119 ASN cc_start: 0.9458 (m-40) cc_final: 0.9181 (m110) REVERT: B 211 LYS cc_start: 0.9617 (tttt) cc_final: 0.9414 (mmtm) REVERT: B 289 CYS cc_start: 0.8336 (m) cc_final: 0.7987 (m) REVERT: B 290 PHE cc_start: 0.8127 (m-10) cc_final: 0.7849 (m-10) REVERT: B 459 GLU cc_start: 0.8056 (mp0) cc_final: 0.7769 (mp0) REVERT: B 514 PHE cc_start: 0.9363 (m-80) cc_final: 0.9144 (m-80) REVERT: C 87 GLU cc_start: 0.9200 (OUTLIER) cc_final: 0.8914 (pp20) REVERT: C 119 ASN cc_start: 0.9246 (m-40) cc_final: 0.8775 (m110) REVERT: C 289 CYS cc_start: 0.8984 (m) cc_final: 0.8446 (m) REVERT: C 290 PHE cc_start: 0.7939 (m-10) cc_final: 0.7612 (m-10) REVERT: C 416 PHE cc_start: 0.8462 (m-10) cc_final: 0.8204 (m-10) REVERT: C 459 GLU cc_start: 0.8911 (mp0) cc_final: 0.8635 (pm20) REVERT: D 119 ASN cc_start: 0.9455 (m-40) cc_final: 0.9181 (m110) REVERT: D 225 ASN cc_start: 0.8633 (OUTLIER) cc_final: 0.7916 (m110) REVERT: D 289 CYS cc_start: 0.8641 (m) cc_final: 0.8008 (m) REVERT: D 290 PHE cc_start: 0.8083 (m-10) cc_final: 0.7761 (m-10) REVERT: D 332 GLU cc_start: 0.8847 (tp30) cc_final: 0.8624 (tp30) REVERT: D 394 MET cc_start: 0.9210 (mpp) cc_final: 0.8850 (mpp) REVERT: D 487 ARG cc_start: 0.8223 (ptt-90) cc_final: 0.7981 (ptt-90) REVERT: E 289 CYS cc_start: 0.8394 (m) cc_final: 0.7999 (m) REVERT: E 290 PHE cc_start: 0.8201 (m-10) cc_final: 0.7894 (m-10) REVERT: E 454 LYS cc_start: 0.8737 (mptt) cc_final: 0.8491 (mmtm) REVERT: E 459 GLU cc_start: 0.8184 (mp0) cc_final: 0.7864 (mp0) REVERT: F 87 GLU cc_start: 0.9256 (OUTLIER) cc_final: 0.9054 (pp20) REVERT: F 169 PHE cc_start: 0.8324 (p90) cc_final: 0.7869 (p90) REVERT: F 209 MET cc_start: 0.9493 (ppp) cc_final: 0.8814 (ppp) REVERT: F 289 CYS cc_start: 0.8823 (m) cc_final: 0.8112 (m) REVERT: F 290 PHE cc_start: 0.7999 (m-10) cc_final: 0.7626 (m-10) REVERT: F 292 MET cc_start: 0.5474 (tpp) cc_final: 0.4618 (tpp) REVERT: F 332 GLU cc_start: 0.8878 (tp30) cc_final: 0.8517 (tp30) REVERT: F 416 PHE cc_start: 0.8530 (m-10) cc_final: 0.8244 (m-10) REVERT: F 503 ASN cc_start: 0.9299 (m-40) cc_final: 0.9018 (m110) REVERT: F 514 PHE cc_start: 0.9357 (m-80) cc_final: 0.8558 (m-80) REVERT: F 611 MET cc_start: 0.8468 (mtt) cc_final: 0.8225 (ttm) outliers start: 29 outliers final: 16 residues processed: 379 average time/residue: 0.1681 time to fit residues: 104.7791 Evaluate side-chains 354 residues out of total 3114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 335 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 438 GLU Chi-restraints excluded: chain B residue 674 MET Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 301 ARG Chi-restraints excluded: chain C residue 333 GLU Chi-restraints excluded: chain C residue 438 GLU Chi-restraints excluded: chain D residue 225 ASN Chi-restraints excluded: chain D residue 438 GLU Chi-restraints excluded: chain D residue 586 MET Chi-restraints excluded: chain E residue 38 PHE Chi-restraints excluded: chain E residue 292 MET Chi-restraints excluded: chain E residue 438 GLU Chi-restraints excluded: chain E residue 586 MET Chi-restraints excluded: chain E residue 643 VAL Chi-restraints excluded: chain E residue 674 MET Chi-restraints excluded: chain F residue 38 PHE Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 438 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 151 optimal weight: 6.9990 chunk 116 optimal weight: 0.9980 chunk 272 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 200 optimal weight: 5.9990 chunk 355 optimal weight: 10.0000 chunk 213 optimal weight: 0.7980 chunk 362 optimal weight: 2.9990 chunk 161 optimal weight: 20.0000 chunk 288 optimal weight: 4.9990 chunk 175 optimal weight: 7.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 ASN ** D 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.097011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.077674 restraints weight = 98120.261| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 4.11 r_work: 0.3457 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30060 Z= 0.135 Angle : 0.609 11.138 40680 Z= 0.305 Chirality : 0.040 0.235 4446 Planarity : 0.004 0.036 5346 Dihedral : 3.826 18.333 4056 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.96 % Allowed : 13.97 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.14), residues: 3768 helix: 1.59 (0.11), residues: 1980 sheet: 0.27 (0.28), residues: 348 loop : -0.83 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 487 TYR 0.009 0.001 TYR E 51 PHE 0.033 0.001 PHE C 118 TRP 0.013 0.001 TRP B 84 HIS 0.004 0.001 HIS B 623 Details of bonding type rmsd covalent geometry : bond 0.00305 (30060) covalent geometry : angle 0.60893 (40680) hydrogen bonds : bond 0.03222 ( 1696) hydrogen bonds : angle 4.84761 ( 5016) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 3114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 343 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASN cc_start: 0.9433 (m-40) cc_final: 0.9173 (m110) REVERT: A 289 CYS cc_start: 0.8656 (m) cc_final: 0.8270 (m) REVERT: A 290 PHE cc_start: 0.7923 (m-10) cc_final: 0.7597 (m-10) REVERT: A 332 GLU cc_start: 0.8738 (tp30) cc_final: 0.8443 (tp30) REVERT: A 503 ASN cc_start: 0.9082 (m-40) cc_final: 0.8663 (m110) REVERT: B 119 ASN cc_start: 0.9462 (m-40) cc_final: 0.9201 (m110) REVERT: B 211 LYS cc_start: 0.9617 (tttt) cc_final: 0.9416 (mmtm) REVERT: B 289 CYS cc_start: 0.8381 (m) cc_final: 0.8026 (m) REVERT: B 290 PHE cc_start: 0.8132 (m-10) cc_final: 0.7839 (m-10) REVERT: B 459 GLU cc_start: 0.8084 (mp0) cc_final: 0.7787 (mp0) REVERT: B 514 PHE cc_start: 0.9369 (m-80) cc_final: 0.9159 (m-80) REVERT: C 87 GLU cc_start: 0.9151 (OUTLIER) cc_final: 0.8890 (pp20) REVERT: C 119 ASN cc_start: 0.9244 (m-40) cc_final: 0.8781 (m110) REVERT: C 285 ILE cc_start: 0.9228 (mm) cc_final: 0.8943 (mm) REVERT: C 289 CYS cc_start: 0.8955 (m) cc_final: 0.8483 (m) REVERT: C 290 PHE cc_start: 0.8082 (m-10) cc_final: 0.7748 (m-10) REVERT: C 416 PHE cc_start: 0.8491 (m-10) cc_final: 0.8202 (m-10) REVERT: C 459 GLU cc_start: 0.8893 (mp0) cc_final: 0.8609 (pm20) REVERT: C 616 MET cc_start: 0.9009 (ttm) cc_final: 0.8637 (ttm) REVERT: D 119 ASN cc_start: 0.9452 (m-40) cc_final: 0.9177 (m110) REVERT: D 289 CYS cc_start: 0.8603 (m) cc_final: 0.8143 (m) REVERT: D 290 PHE cc_start: 0.8125 (m-10) cc_final: 0.7849 (m-10) REVERT: D 314 PHE cc_start: 0.8441 (m-10) cc_final: 0.8227 (m-10) REVERT: D 394 MET cc_start: 0.9213 (mpp) cc_final: 0.8975 (mpp) REVERT: D 438 GLU cc_start: 0.9518 (OUTLIER) cc_final: 0.9270 (pm20) REVERT: D 487 ARG cc_start: 0.8202 (ptt-90) cc_final: 0.7991 (ptt-90) REVERT: E 171 ARG cc_start: 0.8558 (mmm-85) cc_final: 0.8017 (tpp-160) REVERT: E 289 CYS cc_start: 0.8425 (m) cc_final: 0.8057 (m) REVERT: E 290 PHE cc_start: 0.8194 (m-10) cc_final: 0.7891 (m-10) REVERT: E 454 LYS cc_start: 0.8741 (mptt) cc_final: 0.8534 (mmtm) REVERT: E 459 GLU cc_start: 0.8231 (mp0) cc_final: 0.7893 (mp0) REVERT: F 87 GLU cc_start: 0.9228 (OUTLIER) cc_final: 0.9000 (pp20) REVERT: F 169 PHE cc_start: 0.8343 (p90) cc_final: 0.7834 (p90) REVERT: F 289 CYS cc_start: 0.8801 (m) cc_final: 0.8175 (m) REVERT: F 290 PHE cc_start: 0.7956 (m-10) cc_final: 0.7608 (m-10) REVERT: F 332 GLU cc_start: 0.8890 (tp30) cc_final: 0.8532 (tp30) REVERT: F 416 PHE cc_start: 0.8536 (m-10) cc_final: 0.8221 (m-10) REVERT: F 459 GLU cc_start: 0.8804 (mp0) cc_final: 0.8563 (pm20) outliers start: 30 outliers final: 17 residues processed: 360 average time/residue: 0.1672 time to fit residues: 99.3853 Evaluate side-chains 358 residues out of total 3114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 338 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 HIS Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain B residue 438 GLU Chi-restraints excluded: chain B residue 674 MET Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 301 ARG Chi-restraints excluded: chain C residue 333 GLU Chi-restraints excluded: chain C residue 438 GLU Chi-restraints excluded: chain C residue 700 GLU Chi-restraints excluded: chain D residue 95 HIS Chi-restraints excluded: chain D residue 438 GLU Chi-restraints excluded: chain D residue 586 MET Chi-restraints excluded: chain E residue 292 MET Chi-restraints excluded: chain E residue 438 GLU Chi-restraints excluded: chain E residue 643 VAL Chi-restraints excluded: chain E residue 674 MET Chi-restraints excluded: chain F residue 38 PHE Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 438 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 38 optimal weight: 6.9990 chunk 295 optimal weight: 6.9990 chunk 306 optimal weight: 0.9980 chunk 22 optimal weight: 0.0040 chunk 325 optimal weight: 8.9990 chunk 233 optimal weight: 0.9990 chunk 122 optimal weight: 4.9990 chunk 310 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 90 optimal weight: 0.9980 chunk 174 optimal weight: 2.9990 overall best weight: 1.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 286 GLN ** F 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.096922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.077679 restraints weight = 97536.389| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 4.14 r_work: 0.3465 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30060 Z= 0.122 Angle : 0.623 11.777 40680 Z= 0.310 Chirality : 0.040 0.239 4446 Planarity : 0.004 0.049 5346 Dihedral : 3.837 18.502 4056 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.80 % Allowed : 14.29 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.14), residues: 3768 helix: 1.62 (0.11), residues: 1986 sheet: 0.26 (0.28), residues: 348 loop : -0.84 (0.17), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 487 TYR 0.008 0.001 TYR E 51 PHE 0.038 0.001 PHE C 169 TRP 0.012 0.001 TRP B 84 HIS 0.004 0.001 HIS B 623 Details of bonding type rmsd covalent geometry : bond 0.00276 (30060) covalent geometry : angle 0.62283 (40680) hydrogen bonds : bond 0.03178 ( 1696) hydrogen bonds : angle 4.83950 ( 5016) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 346 time to evaluate : 1.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASN cc_start: 0.9432 (m-40) cc_final: 0.9182 (m110) REVERT: A 289 CYS cc_start: 0.8501 (m) cc_final: 0.7987 (m) REVERT: A 290 PHE cc_start: 0.7890 (m-10) cc_final: 0.7604 (m-10) REVERT: A 332 GLU cc_start: 0.8753 (tp30) cc_final: 0.8423 (tp30) REVERT: A 503 ASN cc_start: 0.9084 (m-40) cc_final: 0.8691 (m110) REVERT: B 119 ASN cc_start: 0.9473 (m-40) cc_final: 0.9234 (m110) REVERT: B 211 LYS cc_start: 0.9601 (tttt) cc_final: 0.9397 (tppt) REVERT: B 289 CYS cc_start: 0.8403 (m) cc_final: 0.7999 (m) REVERT: B 290 PHE cc_start: 0.8099 (m-10) cc_final: 0.7819 (m-10) REVERT: B 313 MET cc_start: 0.7156 (pmm) cc_final: 0.6381 (pmm) REVERT: B 459 GLU cc_start: 0.8060 (mp0) cc_final: 0.7754 (mp0) REVERT: C 87 GLU cc_start: 0.9162 (OUTLIER) cc_final: 0.8873 (pp20) REVERT: C 117 MET cc_start: 0.6517 (ptp) cc_final: 0.6174 (pmm) REVERT: C 119 ASN cc_start: 0.9276 (m-40) cc_final: 0.8805 (m110) REVERT: C 289 CYS cc_start: 0.8966 (m) cc_final: 0.8416 (m) REVERT: C 290 PHE cc_start: 0.8059 (m-10) cc_final: 0.7725 (m-10) REVERT: C 416 PHE cc_start: 0.8459 (m-10) cc_final: 0.8174 (m-10) REVERT: C 459 GLU cc_start: 0.8892 (mp0) cc_final: 0.8608 (pm20) REVERT: C 616 MET cc_start: 0.8997 (ttm) cc_final: 0.8616 (ttm) REVERT: D 119 ASN cc_start: 0.9457 (m-40) cc_final: 0.9197 (m110) REVERT: D 290 PHE cc_start: 0.8090 (m-10) cc_final: 0.7830 (m-10) REVERT: D 314 PHE cc_start: 0.8435 (m-10) cc_final: 0.8229 (m-10) REVERT: D 394 MET cc_start: 0.9232 (mpp) cc_final: 0.8991 (mpp) REVERT: D 438 GLU cc_start: 0.9523 (OUTLIER) cc_final: 0.9267 (pm20) REVERT: D 487 ARG cc_start: 0.8265 (ptt-90) cc_final: 0.8051 (ptt-90) REVERT: E 289 CYS cc_start: 0.8382 (m) cc_final: 0.8029 (m) REVERT: E 290 PHE cc_start: 0.8162 (m-10) cc_final: 0.7841 (m-10) REVERT: E 454 LYS cc_start: 0.8770 (mptt) cc_final: 0.8554 (mmtm) REVERT: E 459 GLU cc_start: 0.8306 (mp0) cc_final: 0.7982 (mp0) REVERT: F 87 GLU cc_start: 0.9221 (OUTLIER) cc_final: 0.8974 (pp20) REVERT: F 169 PHE cc_start: 0.8300 (p90) cc_final: 0.7974 (p90) REVERT: F 289 CYS cc_start: 0.8773 (m) cc_final: 0.8265 (m) REVERT: F 292 MET cc_start: 0.5300 (tpp) cc_final: 0.4501 (tpp) REVERT: F 332 GLU cc_start: 0.8948 (tp30) cc_final: 0.8594 (tp30) REVERT: F 416 PHE cc_start: 0.8535 (m-10) cc_final: 0.8228 (m-10) REVERT: F 459 GLU cc_start: 0.8777 (mp0) cc_final: 0.8533 (pm20) REVERT: F 611 MET cc_start: 0.8472 (mtt) cc_final: 0.8251 (ttm) REVERT: F 616 MET cc_start: 0.8987 (ttm) cc_final: 0.8671 (ttm) outliers start: 25 outliers final: 17 residues processed: 359 average time/residue: 0.1637 time to fit residues: 97.6233 Evaluate side-chains 355 residues out of total 3114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 335 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 HIS Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain B residue 438 GLU Chi-restraints excluded: chain B residue 674 MET Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 301 ARG Chi-restraints excluded: chain C residue 333 GLU Chi-restraints excluded: chain C residue 438 GLU Chi-restraints excluded: chain D residue 95 HIS Chi-restraints excluded: chain D residue 281 CYS Chi-restraints excluded: chain D residue 438 GLU Chi-restraints excluded: chain D residue 586 MET Chi-restraints excluded: chain E residue 292 MET Chi-restraints excluded: chain E residue 438 GLU Chi-restraints excluded: chain E residue 643 VAL Chi-restraints excluded: chain E residue 674 MET Chi-restraints excluded: chain F residue 38 PHE Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 438 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 171 optimal weight: 6.9990 chunk 157 optimal weight: 0.9980 chunk 295 optimal weight: 6.9990 chunk 355 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 340 optimal weight: 0.9980 chunk 252 optimal weight: 10.0000 chunk 216 optimal weight: 5.9990 chunk 352 optimal weight: 10.0000 chunk 19 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 329 GLN ** C 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 225 ASN ** F 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.095656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.076359 restraints weight = 97634.593| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 4.09 r_work: 0.3441 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 30060 Z= 0.159 Angle : 0.650 12.547 40680 Z= 0.323 Chirality : 0.041 0.240 4446 Planarity : 0.004 0.040 5346 Dihedral : 3.873 18.817 4056 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.83 % Allowed : 14.52 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.14), residues: 3768 helix: 1.63 (0.11), residues: 1986 sheet: 0.17 (0.28), residues: 348 loop : -0.84 (0.17), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 487 TYR 0.010 0.001 TYR A 51 PHE 0.056 0.002 PHE C 169 TRP 0.013 0.001 TRP B 84 HIS 0.005 0.001 HIS F 623 Details of bonding type rmsd covalent geometry : bond 0.00356 (30060) covalent geometry : angle 0.64951 (40680) hydrogen bonds : bond 0.03303 ( 1696) hydrogen bonds : angle 4.88597 ( 5016) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 329 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASN cc_start: 0.9424 (m-40) cc_final: 0.9097 (m110) REVERT: A 289 CYS cc_start: 0.8469 (m) cc_final: 0.8052 (m) REVERT: A 290 PHE cc_start: 0.8003 (m-10) cc_final: 0.7721 (m-10) REVERT: A 332 GLU cc_start: 0.8721 (tp30) cc_final: 0.8404 (tp30) REVERT: B 119 ASN cc_start: 0.9466 (m-40) cc_final: 0.9229 (m110) REVERT: B 211 LYS cc_start: 0.9608 (tttt) cc_final: 0.9392 (mmtt) REVERT: B 289 CYS cc_start: 0.8399 (m) cc_final: 0.8039 (m) REVERT: B 290 PHE cc_start: 0.8098 (m-10) cc_final: 0.7741 (m-10) REVERT: B 313 MET cc_start: 0.7235 (pmm) cc_final: 0.6482 (pmm) REVERT: B 459 GLU cc_start: 0.8148 (mp0) cc_final: 0.7839 (mp0) REVERT: C 87 GLU cc_start: 0.9190 (OUTLIER) cc_final: 0.8884 (pp20) REVERT: C 117 MET cc_start: 0.6519 (ptp) cc_final: 0.6153 (pmm) REVERT: C 119 ASN cc_start: 0.9201 (m-40) cc_final: 0.8764 (m110) REVERT: C 169 PHE cc_start: 0.8444 (p90) cc_final: 0.8204 (p90) REVERT: C 283 ARG cc_start: 0.9249 (ppt170) cc_final: 0.8987 (ptm-80) REVERT: C 289 CYS cc_start: 0.9004 (m) cc_final: 0.8441 (m) REVERT: C 290 PHE cc_start: 0.8135 (m-10) cc_final: 0.7782 (m-10) REVERT: C 416 PHE cc_start: 0.8519 (m-10) cc_final: 0.8200 (m-10) REVERT: C 459 GLU cc_start: 0.8926 (mp0) cc_final: 0.8644 (pm20) REVERT: C 616 MET cc_start: 0.9057 (ttm) cc_final: 0.8683 (ttm) REVERT: D 241 TYR cc_start: 0.8871 (m-10) cc_final: 0.8436 (m-80) REVERT: D 289 CYS cc_start: 0.8632 (m) cc_final: 0.8018 (m) REVERT: D 290 PHE cc_start: 0.8089 (m-10) cc_final: 0.7802 (m-10) REVERT: D 394 MET cc_start: 0.9241 (mpp) cc_final: 0.8969 (mpp) REVERT: D 438 GLU cc_start: 0.9526 (OUTLIER) cc_final: 0.9272 (pm20) REVERT: D 487 ARG cc_start: 0.8262 (ptt-90) cc_final: 0.8051 (ptt-90) REVERT: E 117 MET cc_start: 0.7172 (ptp) cc_final: 0.6800 (pmm) REVERT: E 289 CYS cc_start: 0.8367 (m) cc_final: 0.8036 (m) REVERT: E 290 PHE cc_start: 0.8170 (m-10) cc_final: 0.7845 (m-10) REVERT: E 454 LYS cc_start: 0.8883 (mptt) cc_final: 0.8650 (mmtm) REVERT: E 459 GLU cc_start: 0.8374 (mp0) cc_final: 0.8057 (mp0) REVERT: F 87 GLU cc_start: 0.9241 (OUTLIER) cc_final: 0.8994 (pp20) REVERT: F 169 PHE cc_start: 0.8316 (p90) cc_final: 0.7990 (p90) REVERT: F 289 CYS cc_start: 0.8798 (m) cc_final: 0.8281 (m) REVERT: F 292 MET cc_start: 0.5437 (tpp) cc_final: 0.4505 (tpp) REVERT: F 332 GLU cc_start: 0.8947 (tp30) cc_final: 0.8590 (tp30) REVERT: F 416 PHE cc_start: 0.8532 (m-10) cc_final: 0.8181 (m-10) REVERT: F 459 GLU cc_start: 0.8736 (mp0) cc_final: 0.8478 (pm20) REVERT: F 616 MET cc_start: 0.9010 (ttm) cc_final: 0.8671 (ttm) outliers start: 26 outliers final: 16 residues processed: 347 average time/residue: 0.1690 time to fit residues: 96.3756 Evaluate side-chains 345 residues out of total 3114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 326 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 HIS Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain B residue 438 GLU Chi-restraints excluded: chain B residue 674 MET Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 301 ARG Chi-restraints excluded: chain C residue 333 GLU Chi-restraints excluded: chain C residue 438 GLU Chi-restraints excluded: chain D residue 95 HIS Chi-restraints excluded: chain D residue 281 CYS Chi-restraints excluded: chain D residue 438 GLU Chi-restraints excluded: chain D residue 586 MET Chi-restraints excluded: chain E residue 292 MET Chi-restraints excluded: chain E residue 438 GLU Chi-restraints excluded: chain E residue 643 VAL Chi-restraints excluded: chain E residue 674 MET Chi-restraints excluded: chain F residue 38 PHE Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 438 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 214 optimal weight: 0.9990 chunk 194 optimal weight: 6.9990 chunk 171 optimal weight: 8.9990 chunk 253 optimal weight: 9.9990 chunk 35 optimal weight: 0.0170 chunk 1 optimal weight: 9.9990 chunk 376 optimal weight: 6.9990 chunk 297 optimal weight: 4.9990 chunk 293 optimal weight: 0.0670 chunk 37 optimal weight: 5.9990 chunk 286 optimal weight: 2.9990 overall best weight: 1.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 360 ASN ** E 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.095746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.076472 restraints weight = 98552.564| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 4.10 r_work: 0.3447 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30060 Z= 0.141 Angle : 0.650 12.820 40680 Z= 0.322 Chirality : 0.041 0.234 4446 Planarity : 0.004 0.039 5346 Dihedral : 3.895 23.251 4056 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.77 % Allowed : 14.80 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.14), residues: 3768 helix: 1.64 (0.11), residues: 1980 sheet: 0.14 (0.28), residues: 348 loop : -0.87 (0.17), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 487 TYR 0.009 0.001 TYR A 51 PHE 0.049 0.001 PHE C 169 TRP 0.013 0.001 TRP B 84 HIS 0.004 0.001 HIS B 623 Details of bonding type rmsd covalent geometry : bond 0.00321 (30060) covalent geometry : angle 0.64999 (40680) hydrogen bonds : bond 0.03242 ( 1696) hydrogen bonds : angle 4.87795 ( 5016) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6429.53 seconds wall clock time: 111 minutes 33.40 seconds (6693.40 seconds total)