Starting phenix.real_space_refine on Fri Mar 22 19:36:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyf_0542/03_2024/6nyf_0542.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyf_0542/03_2024/6nyf_0542.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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyf_0542/03_2024/6nyf_0542.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyf_0542/03_2024/6nyf_0542.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyf_0542/03_2024/6nyf_0542.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyf_0542/03_2024/6nyf_0542.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 sd= 0.078 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 72 5.16 5 C 21474 2.51 5 N 6030 2.21 5 O 6756 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 34332 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5722 Classifications: {'peptide': 750} Link IDs: {'PTRANS': 16, 'TRANS': 733} Chain breaks: 1 Chain: "B" Number of atoms: 5722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5722 Classifications: {'peptide': 750} Link IDs: {'PTRANS': 16, 'TRANS': 733} Chain breaks: 1 Chain: "C" Number of atoms: 5722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5722 Classifications: {'peptide': 750} Link IDs: {'PTRANS': 16, 'TRANS': 733} Chain breaks: 1 Chain: "D" Number of atoms: 5722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5722 Classifications: {'peptide': 750} Link IDs: {'PTRANS': 16, 'TRANS': 733} Chain breaks: 1 Chain: "E" Number of atoms: 5722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5722 Classifications: {'peptide': 750} Link IDs: {'PTRANS': 16, 'TRANS': 733} Chain breaks: 1 Chain: "F" Number of atoms: 5722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5722 Classifications: {'peptide': 750} Link IDs: {'PTRANS': 16, 'TRANS': 733} Chain breaks: 1 Time building chain proxies: 18.89, per 1000 atoms: 0.55 Number of scatterers: 34332 At special positions: 0 Unit cell: (283.02, 308.46, 69.96, 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 72 16.00 O 6756 8.00 N 6030 7.00 C 21474 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 749 " distance=2.03 Simple disulfide: pdb=" SG CYS F 738 " - pdb=" SG CYS F 749 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.85 Conformation dependent library (CDL) restraints added in 6.4 seconds 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8040 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 90 sheets defined 5.1% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.68 Creating SS restraints... Processing helix chain 'A' and resid 29 through 39 removed outlier: 4.303A pdb=" N ASN A 39 " --> pdb=" O ALA A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 60 removed outlier: 4.098A pdb=" N GLU A 59 " --> pdb=" O GLY A 56 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N PHE A 60 " --> pdb=" O PHE A 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 56 through 60' Processing helix chain 'A' and resid 71 through 75 removed outlier: 3.759A pdb=" N SER A 74 " --> pdb=" O LEU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 726 removed outlier: 3.530A pdb=" N ARG A 725 " --> pdb=" O GLN A 721 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU A 726 " --> pdb=" O PHE A 722 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 721 through 726' Processing helix chain 'A' and resid 744 through 754 removed outlier: 4.162A pdb=" N ALA A 748 " --> pdb=" O ASP A 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 39 removed outlier: 4.302A pdb=" N ASN B 39 " --> pdb=" O ALA B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 60 removed outlier: 4.099A pdb=" N GLU B 59 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N PHE B 60 " --> pdb=" O PHE B 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 56 through 60' Processing helix chain 'B' and resid 71 through 75 removed outlier: 3.760A pdb=" N SER B 74 " --> pdb=" O LEU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 726 removed outlier: 3.530A pdb=" N ARG B 725 " --> pdb=" O GLN B 721 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU B 726 " --> pdb=" O PHE B 722 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 721 through 726' Processing helix chain 'B' and resid 744 through 754 removed outlier: 4.162A pdb=" N ALA B 748 " --> pdb=" O ASP B 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 39 removed outlier: 4.302A pdb=" N ASN C 39 " --> pdb=" O ALA C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 60 removed outlier: 4.099A pdb=" N GLU C 59 " --> pdb=" O GLY C 56 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N PHE C 60 " --> pdb=" O PHE C 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 56 through 60' Processing helix chain 'C' and resid 71 through 75 removed outlier: 3.759A pdb=" N SER C 74 " --> pdb=" O LEU C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 721 through 726 removed outlier: 3.530A pdb=" N ARG C 725 " --> pdb=" O GLN C 721 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU C 726 " --> pdb=" O PHE C 722 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 721 through 726' Processing helix chain 'C' and resid 744 through 754 removed outlier: 4.162A pdb=" N ALA C 748 " --> pdb=" O ASP C 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 39 removed outlier: 4.301A pdb=" N ASN D 39 " --> pdb=" O ALA D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 60 removed outlier: 4.098A pdb=" N GLU D 59 " --> pdb=" O GLY D 56 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N PHE D 60 " --> pdb=" O PHE D 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 56 through 60' Processing helix chain 'D' and resid 71 through 75 removed outlier: 3.759A pdb=" N SER D 74 " --> pdb=" O LEU D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 721 through 726 removed outlier: 3.531A pdb=" N ARG D 725 " --> pdb=" O GLN D 721 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU D 726 " --> pdb=" O PHE D 722 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 721 through 726' Processing helix chain 'D' and resid 744 through 754 removed outlier: 4.162A pdb=" N ALA D 748 " --> pdb=" O ASP D 744 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 39 removed outlier: 4.302A pdb=" N ASN E 39 " --> pdb=" O ALA E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 60 removed outlier: 4.099A pdb=" N GLU E 59 " --> pdb=" O GLY E 56 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N PHE E 60 " --> pdb=" O PHE E 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 56 through 60' Processing helix chain 'E' and resid 71 through 75 removed outlier: 3.760A pdb=" N SER E 74 " --> pdb=" O LEU E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 721 through 726 removed outlier: 3.530A pdb=" N ARG E 725 " --> pdb=" O GLN E 721 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU E 726 " --> pdb=" O PHE E 722 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 721 through 726' Processing helix chain 'E' and resid 744 through 754 removed outlier: 4.163A pdb=" N ALA E 748 " --> pdb=" O ASP E 744 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 39 removed outlier: 4.302A pdb=" N ASN F 39 " --> pdb=" O ALA F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 60 removed outlier: 4.099A pdb=" N GLU F 59 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N PHE F 60 " --> pdb=" O PHE F 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 56 through 60' Processing helix chain 'F' and resid 71 through 75 removed outlier: 3.759A pdb=" N SER F 74 " --> pdb=" O LEU F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 721 through 726 removed outlier: 3.531A pdb=" N ARG F 725 " --> pdb=" O GLN F 721 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU F 726 " --> pdb=" O PHE F 722 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 721 through 726' Processing helix chain 'F' and resid 744 through 754 removed outlier: 4.162A pdb=" N ALA F 748 " --> pdb=" O ASP F 744 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 123 through 126 removed outlier: 7.483A pdb=" N LEU A 99 " --> pdb=" O ASP A 124 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N ASN A 126 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL A 101 " --> pdb=" O ASN A 126 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N TRP A 49 " --> pdb=" O GLU A 100 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N ASP A 102 " --> pdb=" O TRP A 49 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE A 51 " --> pdb=" O ASP A 102 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ARG A 50 " --> pdb=" O GLN F 343 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ILE F 345 " --> pdb=" O ARG A 50 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N GLN A 52 " --> pdb=" O ILE F 345 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 140 through 142 removed outlier: 6.625A pdb=" N LEU A 168 " --> pdb=" O SER A 204 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE A 203 " --> pdb=" O TRP A 225 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL A 224 " --> pdb=" O THR A 258 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N LEU A 257 " --> pdb=" O ASP A 281 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU A 280 " --> pdb=" O ASN A 363 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 155 through 157 removed outlier: 6.726A pdb=" N VAL A 155 " --> pdb=" O THR A 188 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N THR A 185 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N ASN A 212 " --> pdb=" O THR A 185 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU A 187 " --> pdb=" O ASN A 212 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 195 through 196 removed outlier: 6.535A pdb=" N ILE A 195 " --> pdb=" O LYS A 219 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 252 through 253 removed outlier: 6.531A pdb=" N VAL A 252 " --> pdb=" O HIS A 276 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR A 275 " --> pdb=" O ASN A 358 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 269 through 270 removed outlier: 6.715A pdb=" N ILE A 269 " --> pdb=" O ILE A 291 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N ASP A 467 " --> pdb=" O PHE A 437 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N PHE A 439 " --> pdb=" O ASP A 467 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 343 through 345 removed outlier: 6.578A pdb=" N TRP B 49 " --> pdb=" O GLU B 100 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ASP B 102 " --> pdb=" O TRP B 49 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ILE B 51 " --> pdb=" O ASP B 102 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N LEU B 99 " --> pdb=" O ASP B 124 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N ASN B 126 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL B 101 " --> pdb=" O ASN B 126 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 456 through 457 removed outlier: 7.796A pdb=" N ILE A 456 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILE A 476 " --> pdb=" O ILE A 501 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N LEU A 500 " --> pdb=" O ILE A 518 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU A 517 " --> pdb=" O ARG A 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 530 through 531 Processing sheet with id=AB1, first strand: chain 'A' and resid 541 through 542 removed outlier: 6.943A pdb=" N ASN A 587 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE A 569 " --> pdb=" O ASN A 587 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLU A 589 " --> pdb=" O ILE A 569 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR A 614 " --> pdb=" O VAL A 588 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE A 636 " --> pdb=" O LEU A 613 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 572 through 574 removed outlier: 3.732A pdb=" N ALA A 595 " --> pdb=" O PHE A 572 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 621 through 623 removed outlier: 5.779A pdb=" N MET A 621 " --> pdb=" O ASN A 643 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE A 642 " --> pdb=" O LYS A 680 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 662 through 663 removed outlier: 7.190A pdb=" N MET A 662 " --> pdb=" O GLY A 704 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 691 through 697 removed outlier: 3.945A pdb=" N THR A 691 " --> pdb=" O TYR A 791 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N TYR A 791 " --> pdb=" O THR A 691 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ILE A 787 " --> pdb=" O LEU A 695 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 729 through 730 Processing sheet with id=AB7, first strand: chain 'A' and resid 771 through 773 Processing sheet with id=AB8, first strand: chain 'B' and resid 140 through 142 removed outlier: 6.625A pdb=" N LEU B 168 " --> pdb=" O SER B 204 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE B 203 " --> pdb=" O TRP B 225 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL B 224 " --> pdb=" O THR B 258 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N LEU B 257 " --> pdb=" O ASP B 281 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU B 280 " --> pdb=" O ASN B 363 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 155 through 157 removed outlier: 6.727A pdb=" N VAL B 155 " --> pdb=" O THR B 188 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR B 185 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N ASN B 212 " --> pdb=" O THR B 185 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU B 187 " --> pdb=" O ASN B 212 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 195 through 196 removed outlier: 6.535A pdb=" N ILE B 195 " --> pdb=" O LYS B 219 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'B' and resid 252 through 253 removed outlier: 6.530A pdb=" N VAL B 252 " --> pdb=" O HIS B 276 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR B 275 " --> pdb=" O ASN B 358 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 269 through 270 removed outlier: 6.715A pdb=" N ILE B 269 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N ASP B 467 " --> pdb=" O PHE B 437 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N PHE B 439 " --> pdb=" O ASP B 467 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 343 through 345 removed outlier: 6.577A pdb=" N TRP C 49 " --> pdb=" O GLU C 100 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ASP C 102 " --> pdb=" O TRP C 49 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE C 51 " --> pdb=" O ASP C 102 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N LEU C 99 " --> pdb=" O ASP C 124 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N ASN C 126 " --> pdb=" O LEU C 99 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL C 101 " --> pdb=" O ASN C 126 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 456 through 457 removed outlier: 7.797A pdb=" N ILE B 456 " --> pdb=" O ASP B 477 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE B 476 " --> pdb=" O ILE B 501 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N LEU B 500 " --> pdb=" O ILE B 518 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU B 517 " --> pdb=" O ARG B 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 530 through 531 Processing sheet with id=AC7, first strand: chain 'B' and resid 541 through 542 removed outlier: 6.943A pdb=" N ASN B 587 " --> pdb=" O LEU B 567 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE B 569 " --> pdb=" O ASN B 587 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLU B 589 " --> pdb=" O ILE B 569 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR B 614 " --> pdb=" O VAL B 588 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE B 636 " --> pdb=" O LEU B 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 572 through 574 removed outlier: 3.732A pdb=" N ALA B 595 " --> pdb=" O PHE B 572 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 621 through 623 removed outlier: 5.779A pdb=" N MET B 621 " --> pdb=" O ASN B 643 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE B 642 " --> pdb=" O LYS B 680 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 662 through 663 removed outlier: 7.190A pdb=" N MET B 662 " --> pdb=" O GLY B 704 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 691 through 697 removed outlier: 3.945A pdb=" N THR B 691 " --> pdb=" O TYR B 791 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N TYR B 791 " --> pdb=" O THR B 691 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ILE B 787 " --> pdb=" O LEU B 695 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 729 through 730 Processing sheet with id=AD4, first strand: chain 'B' and resid 771 through 773 Processing sheet with id=AD5, first strand: chain 'C' and resid 140 through 142 removed outlier: 6.625A pdb=" N LEU C 168 " --> pdb=" O SER C 204 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE C 203 " --> pdb=" O TRP C 225 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL C 224 " --> pdb=" O THR C 258 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N LEU C 257 " --> pdb=" O ASP C 281 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU C 280 " --> pdb=" O ASN C 363 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 155 through 157 removed outlier: 6.726A pdb=" N VAL C 155 " --> pdb=" O THR C 188 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR C 185 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N ASN C 212 " --> pdb=" O THR C 185 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU C 187 " --> pdb=" O ASN C 212 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'C' and resid 195 through 196 removed outlier: 6.534A pdb=" N ILE C 195 " --> pdb=" O LYS C 219 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'C' and resid 252 through 253 removed outlier: 6.531A pdb=" N VAL C 252 " --> pdb=" O HIS C 276 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N THR C 275 " --> pdb=" O ASN C 358 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 269 through 270 removed outlier: 6.714A pdb=" N ILE C 269 " --> pdb=" O ILE C 291 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N ASP C 467 " --> pdb=" O PHE C 437 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N PHE C 439 " --> pdb=" O ASP C 467 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 343 through 345 removed outlier: 6.578A pdb=" N TRP D 49 " --> pdb=" O GLU D 100 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ASP D 102 " --> pdb=" O TRP D 49 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ILE D 51 " --> pdb=" O ASP D 102 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N LEU D 99 " --> pdb=" O ASP D 124 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N ASN D 126 " --> pdb=" O LEU D 99 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL D 101 " --> pdb=" O ASN D 126 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 456 through 457 removed outlier: 7.796A pdb=" N ILE C 456 " --> pdb=" O ASP C 477 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILE C 476 " --> pdb=" O ILE C 501 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N LEU C 500 " --> pdb=" O ILE C 518 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU C 517 " --> pdb=" O ARG C 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 530 through 531 Processing sheet with id=AE4, first strand: chain 'C' and resid 541 through 542 removed outlier: 6.943A pdb=" N ASN C 587 " --> pdb=" O LEU C 567 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE C 569 " --> pdb=" O ASN C 587 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLU C 589 " --> pdb=" O ILE C 569 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR C 614 " --> pdb=" O VAL C 588 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE C 636 " --> pdb=" O LEU C 613 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 572 through 574 removed outlier: 3.733A pdb=" N ALA C 595 " --> pdb=" O PHE C 572 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 621 through 623 removed outlier: 5.779A pdb=" N MET C 621 " --> pdb=" O ASN C 643 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE C 642 " --> pdb=" O LYS C 680 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'C' and resid 662 through 663 removed outlier: 7.189A pdb=" N MET C 662 " --> pdb=" O GLY C 704 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'C' and resid 691 through 697 removed outlier: 3.946A pdb=" N THR C 691 " --> pdb=" O TYR C 791 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N TYR C 791 " --> pdb=" O THR C 691 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ILE C 787 " --> pdb=" O LEU C 695 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 729 through 730 Processing sheet with id=AF1, first strand: chain 'C' and resid 771 through 773 Processing sheet with id=AF2, first strand: chain 'D' and resid 140 through 142 removed outlier: 6.624A pdb=" N LEU D 168 " --> pdb=" O SER D 204 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE D 203 " --> pdb=" O TRP D 225 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL D 224 " --> pdb=" O THR D 258 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N LEU D 257 " --> pdb=" O ASP D 281 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU D 280 " --> pdb=" O ASN D 363 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 155 through 157 removed outlier: 6.726A pdb=" N VAL D 155 " --> pdb=" O THR D 188 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR D 185 " --> pdb=" O THR D 210 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N ASN D 212 " --> pdb=" O THR D 185 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU D 187 " --> pdb=" O ASN D 212 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'D' and resid 195 through 196 removed outlier: 6.535A pdb=" N ILE D 195 " --> pdb=" O LYS D 219 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'D' and resid 252 through 253 removed outlier: 6.531A pdb=" N VAL D 252 " --> pdb=" O HIS D 276 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N THR D 275 " --> pdb=" O ASN D 358 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 269 through 270 removed outlier: 6.715A pdb=" N ILE D 269 " --> pdb=" O ILE D 291 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N ASP D 467 " --> pdb=" O PHE D 437 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N PHE D 439 " --> pdb=" O ASP D 467 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 343 through 345 removed outlier: 6.577A pdb=" N TRP E 49 " --> pdb=" O GLU E 100 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ASP E 102 " --> pdb=" O TRP E 49 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ILE E 51 " --> pdb=" O ASP E 102 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N LEU E 99 " --> pdb=" O ASP E 124 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N ASN E 126 " --> pdb=" O LEU E 99 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL E 101 " --> pdb=" O ASN E 126 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 456 through 457 removed outlier: 7.796A pdb=" N ILE D 456 " --> pdb=" O ASP D 477 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE D 476 " --> pdb=" O ILE D 501 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N LEU D 500 " --> pdb=" O ILE D 518 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU D 517 " --> pdb=" O ARG D 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'D' and resid 530 through 531 Processing sheet with id=AG1, first strand: chain 'D' and resid 541 through 542 removed outlier: 6.943A pdb=" N ASN D 587 " --> pdb=" O LEU D 567 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE D 569 " --> pdb=" O ASN D 587 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLU D 589 " --> pdb=" O ILE D 569 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR D 614 " --> pdb=" O VAL D 588 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE D 636 " --> pdb=" O LEU D 613 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 572 through 574 removed outlier: 3.732A pdb=" N ALA D 595 " --> pdb=" O PHE D 572 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'D' and resid 621 through 623 removed outlier: 5.781A pdb=" N MET D 621 " --> pdb=" O ASN D 643 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE D 642 " --> pdb=" O LYS D 680 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'D' and resid 662 through 663 removed outlier: 7.189A pdb=" N MET D 662 " --> pdb=" O GLY D 704 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'D' and resid 691 through 697 removed outlier: 3.946A pdb=" N THR D 691 " --> pdb=" O TYR D 791 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N TYR D 791 " --> pdb=" O THR D 691 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ILE D 787 " --> pdb=" O LEU D 695 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'D' and resid 729 through 730 Processing sheet with id=AG7, first strand: chain 'D' and resid 771 through 773 Processing sheet with id=AG8, first strand: chain 'E' and resid 140 through 142 removed outlier: 6.625A pdb=" N LEU E 168 " --> pdb=" O SER E 204 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE E 203 " --> pdb=" O TRP E 225 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL E 224 " --> pdb=" O THR E 258 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N LEU E 257 " --> pdb=" O ASP E 281 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU E 280 " --> pdb=" O ASN E 363 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'E' and resid 155 through 157 removed outlier: 6.726A pdb=" N VAL E 155 " --> pdb=" O THR E 188 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR E 185 " --> pdb=" O THR E 210 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N ASN E 212 " --> pdb=" O THR E 185 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU E 187 " --> pdb=" O ASN E 212 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG9 Processing sheet with id=AH1, first strand: chain 'E' and resid 195 through 196 removed outlier: 6.535A pdb=" N ILE E 195 " --> pdb=" O LYS E 219 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH1 Processing sheet with id=AH2, first strand: chain 'E' and resid 252 through 253 removed outlier: 6.530A pdb=" N VAL E 252 " --> pdb=" O HIS E 276 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N THR E 275 " --> pdb=" O ASN E 358 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'E' and resid 269 through 270 removed outlier: 6.714A pdb=" N ILE E 269 " --> pdb=" O ILE E 291 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N ASP E 467 " --> pdb=" O PHE E 437 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N PHE E 439 " --> pdb=" O ASP E 467 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'E' and resid 343 through 345 removed outlier: 6.577A pdb=" N TRP F 49 " --> pdb=" O GLU F 100 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ASP F 102 " --> pdb=" O TRP F 49 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ILE F 51 " --> pdb=" O ASP F 102 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N LEU F 99 " --> pdb=" O ASP F 124 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N ASN F 126 " --> pdb=" O LEU F 99 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL F 101 " --> pdb=" O ASN F 126 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'E' and resid 456 through 457 removed outlier: 7.796A pdb=" N ILE E 456 " --> pdb=" O ASP E 477 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE E 476 " --> pdb=" O ILE E 501 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N LEU E 500 " --> pdb=" O ILE E 518 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU E 517 " --> pdb=" O ARG E 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH5 Processing sheet with id=AH6, first strand: chain 'E' and resid 530 through 531 Processing sheet with id=AH7, first strand: chain 'E' and resid 541 through 542 removed outlier: 6.943A pdb=" N ASN E 587 " --> pdb=" O LEU E 567 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE E 569 " --> pdb=" O ASN E 587 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLU E 589 " --> pdb=" O ILE E 569 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR E 614 " --> pdb=" O VAL E 588 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE E 636 " --> pdb=" O LEU E 613 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'E' and resid 572 through 574 removed outlier: 3.732A pdb=" N ALA E 595 " --> pdb=" O PHE E 572 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'E' and resid 621 through 623 removed outlier: 5.779A pdb=" N MET E 621 " --> pdb=" O ASN E 643 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE E 642 " --> pdb=" O LYS E 680 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH9 Processing sheet with id=AI1, first strand: chain 'E' and resid 662 through 663 removed outlier: 7.189A pdb=" N MET E 662 " --> pdb=" O GLY E 704 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI1 Processing sheet with id=AI2, first strand: chain 'E' and resid 691 through 697 removed outlier: 3.945A pdb=" N THR E 691 " --> pdb=" O TYR E 791 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N TYR E 791 " --> pdb=" O THR E 691 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ILE E 787 " --> pdb=" O LEU E 695 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'E' and resid 729 through 730 Processing sheet with id=AI4, first strand: chain 'E' and resid 771 through 773 Processing sheet with id=AI5, first strand: chain 'F' and resid 140 through 142 removed outlier: 6.625A pdb=" N LEU F 168 " --> pdb=" O SER F 204 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE F 203 " --> pdb=" O TRP F 225 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL F 224 " --> pdb=" O THR F 258 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N LEU F 257 " --> pdb=" O ASP F 281 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU F 280 " --> pdb=" O ASN F 363 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'F' and resid 155 through 157 removed outlier: 6.726A pdb=" N VAL F 155 " --> pdb=" O THR F 188 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR F 185 " --> pdb=" O THR F 210 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N ASN F 212 " --> pdb=" O THR F 185 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU F 187 " --> pdb=" O ASN F 212 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI6 Processing sheet with id=AI7, first strand: chain 'F' and resid 195 through 196 removed outlier: 6.535A pdb=" N ILE F 195 " --> pdb=" O LYS F 219 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI7 Processing sheet with id=AI8, first strand: chain 'F' and resid 252 through 253 removed outlier: 6.530A pdb=" N VAL F 252 " --> pdb=" O HIS F 276 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR F 275 " --> pdb=" O ASN F 358 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'F' and resid 269 through 270 removed outlier: 6.715A pdb=" N ILE F 269 " --> pdb=" O ILE F 291 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N ASP F 467 " --> pdb=" O PHE F 437 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N PHE F 439 " --> pdb=" O ASP F 467 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'F' and resid 456 through 457 removed outlier: 7.797A pdb=" N ILE F 456 " --> pdb=" O ASP F 477 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE F 476 " --> pdb=" O ILE F 501 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N LEU F 500 " --> pdb=" O ILE F 518 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU F 517 " --> pdb=" O ARG F 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ1 Processing sheet with id=AJ2, first strand: chain 'F' and resid 530 through 531 Processing sheet with id=AJ3, first strand: chain 'F' and resid 541 through 542 removed outlier: 6.943A pdb=" N ASN F 587 " --> pdb=" O LEU F 567 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE F 569 " --> pdb=" O ASN F 587 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N GLU F 589 " --> pdb=" O ILE F 569 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR F 614 " --> pdb=" O VAL F 588 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE F 636 " --> pdb=" O LEU F 613 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'F' and resid 572 through 574 removed outlier: 3.732A pdb=" N ALA F 595 " --> pdb=" O PHE F 572 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'F' and resid 621 through 623 removed outlier: 5.780A pdb=" N MET F 621 " --> pdb=" O ASN F 643 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE F 642 " --> pdb=" O LYS F 680 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ5 Processing sheet with id=AJ6, first strand: chain 'F' and resid 662 through 663 removed outlier: 7.190A pdb=" N MET F 662 " --> pdb=" O GLY F 704 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ6 Processing sheet with id=AJ7, first strand: chain 'F' and resid 691 through 697 removed outlier: 3.945A pdb=" N THR F 691 " --> pdb=" O TYR F 791 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N TYR F 791 " --> pdb=" O THR F 691 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ILE F 787 " --> pdb=" O LEU F 695 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'F' and resid 729 through 730 Processing sheet with id=AJ9, first strand: chain 'F' and resid 771 through 773 297 hydrogen bonds defined for protein. 786 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: 14.19 Time building geometry restraints manager: 13.97 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: 11237 1.34 - 1.45: 5030 1.45 - 1.57: 18521 1.57 - 1.69: 0 1.69 - 1.80: 132 Bond restraints: 34920 Sorted by residual: bond pdb=" CB THR B 185 " pdb=" CG2 THR B 185 " ideal model delta sigma weight residual 1.521 1.453 0.068 3.30e-02 9.18e+02 4.26e+00 bond pdb=" CB THR F 185 " pdb=" CG2 THR F 185 " ideal model delta sigma weight residual 1.521 1.453 0.068 3.30e-02 9.18e+02 4.26e+00 bond pdb=" CB THR D 185 " pdb=" CG2 THR D 185 " ideal model delta sigma weight residual 1.521 1.453 0.068 3.30e-02 9.18e+02 4.20e+00 bond pdb=" CB THR A 185 " pdb=" CG2 THR A 185 " ideal model delta sigma weight residual 1.521 1.453 0.068 3.30e-02 9.18e+02 4.20e+00 bond pdb=" CB THR C 185 " pdb=" CG2 THR C 185 " ideal model delta sigma weight residual 1.521 1.453 0.068 3.30e-02 9.18e+02 4.20e+00 ... (remaining 34915 not shown) Histogram of bond angle deviations from ideal: 98.17 - 105.33: 378 105.33 - 112.50: 17504 112.50 - 119.66: 11611 119.66 - 126.83: 17430 126.83 - 133.99: 369 Bond angle restraints: 47292 Sorted by residual: angle pdb=" C GLY C 83 " pdb=" N ASN C 84 " pdb=" CA ASN C 84 " ideal model delta sigma weight residual 122.82 130.44 -7.62 1.42e+00 4.96e-01 2.88e+01 angle pdb=" C GLY B 83 " pdb=" N ASN B 84 " pdb=" CA ASN B 84 " ideal model delta sigma weight residual 122.82 130.43 -7.61 1.42e+00 4.96e-01 2.87e+01 angle pdb=" C GLY E 83 " pdb=" N ASN E 84 " pdb=" CA ASN E 84 " ideal model delta sigma weight residual 122.82 130.43 -7.61 1.42e+00 4.96e-01 2.87e+01 angle pdb=" C GLY F 83 " pdb=" N ASN F 84 " pdb=" CA ASN F 84 " ideal model delta sigma weight residual 122.82 130.41 -7.59 1.42e+00 4.96e-01 2.86e+01 angle pdb=" C GLY D 83 " pdb=" N ASN D 84 " pdb=" CA ASN D 84 " ideal model delta sigma weight residual 122.82 130.41 -7.59 1.42e+00 4.96e-01 2.86e+01 ... (remaining 47287 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.68: 19259 15.68 - 31.36: 1093 31.36 - 47.05: 204 47.05 - 62.73: 12 62.73 - 78.41: 18 Dihedral angle restraints: 20586 sinusoidal: 7914 harmonic: 12672 Sorted by residual: dihedral pdb=" CB CYS F 738 " pdb=" SG CYS F 738 " pdb=" SG CYS F 749 " pdb=" CB CYS F 749 " ideal model delta sinusoidal sigma weight residual -86.00 -164.41 78.41 1 1.00e+01 1.00e-02 7.67e+01 dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 749 " pdb=" CB CYS A 749 " ideal model delta sinusoidal sigma weight residual -86.00 -164.40 78.40 1 1.00e+01 1.00e-02 7.67e+01 dihedral pdb=" CB CYS E 738 " pdb=" SG CYS E 738 " pdb=" SG CYS E 749 " pdb=" CB CYS E 749 " ideal model delta sinusoidal sigma weight residual -86.00 -164.39 78.39 1 1.00e+01 1.00e-02 7.67e+01 ... (remaining 20583 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 3568 0.056 - 0.111: 1344 0.111 - 0.167: 355 0.167 - 0.222: 25 0.222 - 0.278: 18 Chirality restraints: 5310 Sorted by residual: chirality pdb=" CA ASN A 84 " pdb=" N ASN A 84 " pdb=" C ASN A 84 " pdb=" CB ASN A 84 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA ASN F 84 " pdb=" N ASN F 84 " pdb=" C ASN F 84 " pdb=" CB ASN F 84 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CA ASN D 84 " pdb=" N ASN D 84 " pdb=" C ASN D 84 " pdb=" CB ASN D 84 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 5307 not shown) Planarity restraints: 6198 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 225 " 0.020 2.00e-02 2.50e+03 1.93e-02 9.28e+00 pdb=" CG TRP C 225 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP C 225 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP C 225 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C 225 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 225 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP C 225 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 225 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 225 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP C 225 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 225 " -0.020 2.00e-02 2.50e+03 1.93e-02 9.28e+00 pdb=" CG TRP A 225 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP A 225 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP A 225 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 225 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 225 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 225 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 225 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 225 " -0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP A 225 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 225 " 0.020 2.00e-02 2.50e+03 1.92e-02 9.26e+00 pdb=" CG TRP E 225 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP E 225 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP E 225 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP E 225 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP E 225 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP E 225 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 225 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 225 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP E 225 " 0.003 2.00e-02 2.50e+03 ... (remaining 6195 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 8610 2.79 - 3.32: 31281 3.32 - 3.85: 57321 3.85 - 4.37: 66662 4.37 - 4.90: 117461 Nonbonded interactions: 281335 Sorted by model distance: nonbonded pdb=" OG1 THR A 153 " pdb=" OG1 THR A 185 " model vdw 2.263 2.440 nonbonded pdb=" OG1 THR B 153 " pdb=" OG1 THR B 185 " model vdw 2.263 2.440 nonbonded pdb=" OG1 THR E 153 " pdb=" OG1 THR E 185 " model vdw 2.264 2.440 nonbonded pdb=" OG1 THR F 153 " pdb=" OG1 THR F 185 " model vdw 2.264 2.440 nonbonded pdb=" OG1 THR C 153 " pdb=" OG1 THR C 185 " model vdw 2.264 2.440 ... (remaining 281330 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' 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: 2.330 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: 13.590 Check model and map are aligned: 0.500 Set scattering table: 0.320 Process input model: 91.280 Find NCS groups from input model: 2.210 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 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 : 0.007 0.068 34920 Z= 0.498 Angle : 0.993 11.526 47292 Z= 0.566 Chirality : 0.062 0.278 5310 Planarity : 0.005 0.054 6198 Dihedral : 10.445 72.090 12528 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.94 % Favored : 87.06 % Rotamer: Outliers : 0.32 % Allowed : 2.43 % Favored : 97.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.20 (0.10), residues: 4476 helix: -4.54 (0.13), residues: 150 sheet: -3.80 (0.11), residues: 1476 loop : -3.33 (0.09), residues: 2850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.004 TRP A 225 HIS 0.007 0.002 HIS C 385 PHE 0.022 0.003 PHE E 532 TYR 0.035 0.003 TYR D 574 ARG 0.007 0.001 ARG E 402 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 3702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 282 time to evaluate : 3.230 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 LYS cc_start: 0.8140 (mttm) cc_final: 0.7727 (mmmm) REVERT: A 513 ASN cc_start: 0.7473 (OUTLIER) cc_final: 0.7124 (p0) REVERT: A 634 ASP cc_start: 0.6853 (p0) cc_final: 0.6323 (p0) REVERT: A 658 ASN cc_start: 0.8003 (t0) cc_final: 0.7641 (t0) REVERT: B 513 ASN cc_start: 0.7380 (OUTLIER) cc_final: 0.7060 (p0) REVERT: B 609 MET cc_start: 0.7431 (ttt) cc_final: 0.7032 (ttt) REVERT: B 634 ASP cc_start: 0.6920 (p0) cc_final: 0.6373 (p0) REVERT: B 658 ASN cc_start: 0.7999 (t0) cc_final: 0.7776 (t0) REVERT: C 513 ASN cc_start: 0.7339 (OUTLIER) cc_final: 0.7101 (p0) REVERT: C 586 LYS cc_start: 0.7014 (mmpt) cc_final: 0.6719 (mmmt) REVERT: C 609 MET cc_start: 0.7322 (ttt) cc_final: 0.7118 (ttt) REVERT: C 634 ASP cc_start: 0.6863 (p0) cc_final: 0.6372 (p0) REVERT: C 658 ASN cc_start: 0.8031 (t0) cc_final: 0.7641 (t0) REVERT: D 47 LYS cc_start: 0.8141 (mttm) cc_final: 0.7689 (mmmm) REVERT: D 513 ASN cc_start: 0.7480 (OUTLIER) cc_final: 0.7160 (p0) REVERT: D 634 ASP cc_start: 0.6785 (p0) cc_final: 0.6247 (p0) REVERT: D 658 ASN cc_start: 0.8007 (t0) cc_final: 0.7632 (t0) REVERT: E 47 LYS cc_start: 0.8104 (mttm) cc_final: 0.7710 (mmmm) REVERT: E 513 ASN cc_start: 0.7326 (OUTLIER) cc_final: 0.7098 (p0) REVERT: E 609 MET cc_start: 0.7382 (ttt) cc_final: 0.7148 (ttt) REVERT: E 634 ASP cc_start: 0.6744 (p0) cc_final: 0.6224 (p0) REVERT: E 658 ASN cc_start: 0.8020 (t0) cc_final: 0.7799 (t0) REVERT: F 47 LYS cc_start: 0.8281 (mttm) cc_final: 0.7777 (mmmm) REVERT: F 513 ASN cc_start: 0.7296 (OUTLIER) cc_final: 0.7043 (p0) REVERT: F 634 ASP cc_start: 0.6864 (p0) cc_final: 0.6380 (p0) REVERT: F 658 ASN cc_start: 0.8012 (t0) cc_final: 0.7621 (t0) outliers start: 12 outliers final: 0 residues processed: 294 average time/residue: 0.4490 time to fit residues: 215.9687 Evaluate side-chains 133 residues out of total 3702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 127 time to evaluate : 3.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 513 ASN Chi-restraints excluded: chain B residue 513 ASN Chi-restraints excluded: chain C residue 513 ASN Chi-restraints excluded: chain D residue 513 ASN Chi-restraints excluded: chain E residue 513 ASN Chi-restraints excluded: chain F residue 513 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 379 optimal weight: 0.5980 chunk 341 optimal weight: 1.9990 chunk 189 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 230 optimal weight: 10.0000 chunk 182 optimal weight: 2.9990 chunk 352 optimal weight: 7.9990 chunk 136 optimal weight: 6.9990 chunk 214 optimal weight: 20.0000 chunk 262 optimal weight: 2.9990 chunk 408 optimal weight: 4.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 HIS A 387 ASN ** A 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 ASN ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 HIS B 387 ASN ** B 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 ASN ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 ASN ** C 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 705 ASN C 755 ASN ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 256 HIS D 387 ASN ** D 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 755 ASN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 HIS E 387 ASN ** E 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 755 ASN ** F 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 387 ASN ** F 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 705 ASN F 755 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 34920 Z= 0.309 Angle : 0.632 7.817 47292 Z= 0.344 Chirality : 0.048 0.167 5310 Planarity : 0.003 0.039 6198 Dihedral : 6.453 42.766 4770 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.38 % Favored : 87.62 % Rotamer: Outliers : 1.57 % Allowed : 5.59 % Favored : 92.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.75 (0.11), residues: 4476 helix: -1.52 (0.41), residues: 120 sheet: -3.58 (0.12), residues: 1380 loop : -3.17 (0.09), residues: 2976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 225 HIS 0.005 0.001 HIS F 693 PHE 0.017 0.002 PHE C 664 TYR 0.015 0.001 TYR B 574 ARG 0.008 0.000 ARG A 541 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 3702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 173 time to evaluate : 3.892 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.8558 (OUTLIER) cc_final: 0.8336 (m-30) REVERT: A 47 LYS cc_start: 0.8224 (mttm) cc_final: 0.7850 (mmmm) REVERT: A 634 ASP cc_start: 0.7226 (p0) cc_final: 0.6665 (p0) REVERT: B 47 LYS cc_start: 0.8216 (mttm) cc_final: 0.7786 (mmmm) REVERT: B 407 GLU cc_start: 0.7693 (tm-30) cc_final: 0.7460 (tm-30) REVERT: B 609 MET cc_start: 0.7752 (ttt) cc_final: 0.7329 (ttt) REVERT: B 634 ASP cc_start: 0.7111 (p0) cc_final: 0.6558 (p0) REVERT: B 658 ASN cc_start: 0.7974 (t0) cc_final: 0.7755 (t0) REVERT: B 662 MET cc_start: 0.7348 (mtp) cc_final: 0.7091 (mtp) REVERT: B 693 HIS cc_start: 0.7190 (m-70) cc_final: 0.6671 (m170) REVERT: C 47 LYS cc_start: 0.8324 (mttm) cc_final: 0.7779 (mmmm) REVERT: C 407 GLU cc_start: 0.7533 (tm-30) cc_final: 0.7311 (tm-30) REVERT: C 609 MET cc_start: 0.7547 (ttt) cc_final: 0.7330 (ttt) REVERT: C 634 ASP cc_start: 0.7341 (p0) cc_final: 0.6763 (p0) REVERT: C 658 ASN cc_start: 0.8016 (t0) cc_final: 0.7665 (t0) REVERT: D 43 ASP cc_start: 0.8587 (OUTLIER) cc_final: 0.8378 (m-30) REVERT: D 47 LYS cc_start: 0.8240 (mttm) cc_final: 0.7788 (mmmm) REVERT: D 634 ASP cc_start: 0.7200 (p0) cc_final: 0.6634 (p0) REVERT: E 47 LYS cc_start: 0.8225 (mttm) cc_final: 0.7805 (mmmm) REVERT: E 407 GLU cc_start: 0.7688 (tm-30) cc_final: 0.7455 (tm-30) REVERT: E 609 MET cc_start: 0.7737 (ttt) cc_final: 0.7305 (ttt) REVERT: E 634 ASP cc_start: 0.7144 (p0) cc_final: 0.6593 (p0) REVERT: E 658 ASN cc_start: 0.7953 (t0) cc_final: 0.7723 (t0) REVERT: F 47 LYS cc_start: 0.8345 (mttm) cc_final: 0.7816 (mmmm) REVERT: F 407 GLU cc_start: 0.7533 (tm-30) cc_final: 0.7309 (tm-30) REVERT: F 634 ASP cc_start: 0.7446 (p0) cc_final: 0.6833 (p0) REVERT: F 658 ASN cc_start: 0.7994 (t0) cc_final: 0.7731 (t0) outliers start: 58 outliers final: 27 residues processed: 229 average time/residue: 0.4236 time to fit residues: 164.8445 Evaluate side-chains 158 residues out of total 3702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 129 time to evaluate : 4.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 513 ASN Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 789 VAL Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 513 ASN Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 513 ASN Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 505 THR Chi-restraints excluded: chain E residue 789 VAL Chi-restraints excluded: chain F residue 43 ASP Chi-restraints excluded: chain F residue 369 THR Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 505 THR Chi-restraints excluded: chain F residue 513 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 227 optimal weight: 3.9990 chunk 126 optimal weight: 9.9990 chunk 340 optimal weight: 1.9990 chunk 278 optimal weight: 9.9990 chunk 112 optimal weight: 5.9990 chunk 409 optimal weight: 2.9990 chunk 442 optimal weight: 9.9990 chunk 364 optimal weight: 20.0000 chunk 405 optimal weight: 0.9980 chunk 139 optimal weight: 20.0000 chunk 328 optimal weight: 0.9980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 HIS ** C 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 705 ASN ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 256 HIS ** F 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 34920 Z= 0.316 Angle : 0.623 8.718 47292 Z= 0.337 Chirality : 0.048 0.173 5310 Planarity : 0.003 0.032 6198 Dihedral : 6.191 50.909 4766 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.61 % Favored : 86.39 % Rotamer: Outliers : 1.73 % Allowed : 7.97 % Favored : 90.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.57 (0.11), residues: 4476 helix: 0.06 (0.43), residues: 120 sheet: -3.54 (0.12), residues: 1458 loop : -3.03 (0.10), residues: 2898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 773 HIS 0.003 0.001 HIS B 385 PHE 0.026 0.002 PHE F 635 TYR 0.014 0.001 TYR B 574 ARG 0.003 0.000 ARG D 402 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 3702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 141 time to evaluate : 3.745 Fit side-chains REVERT: A 43 ASP cc_start: 0.8656 (OUTLIER) cc_final: 0.8364 (m-30) REVERT: A 47 LYS cc_start: 0.8285 (mttm) cc_final: 0.7975 (mmmm) REVERT: B 47 LYS cc_start: 0.8215 (mttm) cc_final: 0.7774 (mmmm) REVERT: B 407 GLU cc_start: 0.7617 (tm-30) cc_final: 0.7273 (tm-30) REVERT: B 609 MET cc_start: 0.7855 (ttt) cc_final: 0.7520 (ttt) REVERT: B 662 MET cc_start: 0.7509 (mtp) cc_final: 0.7271 (mtp) REVERT: C 47 LYS cc_start: 0.8298 (mttm) cc_final: 0.7784 (mmmm) REVERT: C 407 GLU cc_start: 0.7492 (tm-30) cc_final: 0.7206 (tm-30) REVERT: C 609 MET cc_start: 0.7643 (ttt) cc_final: 0.7376 (ttt) REVERT: C 634 ASP cc_start: 0.7286 (p0) cc_final: 0.6622 (p0) REVERT: C 658 ASN cc_start: 0.8004 (t0) cc_final: 0.7751 (t0) REVERT: D 43 ASP cc_start: 0.8688 (OUTLIER) cc_final: 0.8386 (m-30) REVERT: D 47 LYS cc_start: 0.8268 (mttm) cc_final: 0.7844 (mmmm) REVERT: E 47 LYS cc_start: 0.8222 (mttm) cc_final: 0.7792 (mmmm) REVERT: E 407 GLU cc_start: 0.7617 (tm-30) cc_final: 0.7279 (tm-30) REVERT: E 609 MET cc_start: 0.7843 (ttt) cc_final: 0.7492 (ttt) REVERT: F 47 LYS cc_start: 0.8293 (mttm) cc_final: 0.7782 (mmmm) REVERT: F 407 GLU cc_start: 0.7496 (tm-30) cc_final: 0.7209 (tm-30) REVERT: F 634 ASP cc_start: 0.7277 (p0) cc_final: 0.6614 (p0) REVERT: F 658 ASN cc_start: 0.7988 (t0) cc_final: 0.7736 (t0) outliers start: 64 outliers final: 53 residues processed: 197 average time/residue: 0.4175 time to fit residues: 141.1896 Evaluate side-chains 169 residues out of total 3702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 114 time to evaluate : 3.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 513 ASN Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 773 TRP Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 773 TRP Chi-restraints excluded: chain B residue 789 VAL Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 513 ASN Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 513 ASN Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 505 THR Chi-restraints excluded: chain E residue 509 VAL Chi-restraints excluded: chain E residue 613 LEU Chi-restraints excluded: chain E residue 773 TRP Chi-restraints excluded: chain E residue 789 VAL Chi-restraints excluded: chain F residue 43 ASP Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 369 THR Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 505 THR Chi-restraints excluded: chain F residue 509 VAL Chi-restraints excluded: chain F residue 513 ASN Chi-restraints excluded: chain F residue 613 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 404 optimal weight: 0.8980 chunk 307 optimal weight: 2.9990 chunk 212 optimal weight: 8.9990 chunk 45 optimal weight: 5.9990 chunk 195 optimal weight: 2.9990 chunk 274 optimal weight: 9.9990 chunk 410 optimal weight: 1.9990 chunk 434 optimal weight: 0.0970 chunk 214 optimal weight: 30.0000 chunk 389 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 GLN A 685 GLN ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 GLN ** B 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 705 ASN ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 685 GLN C 693 HIS ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 GLN D 685 GLN D 705 ASN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 340 GLN E 685 GLN ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 685 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 34920 Z= 0.208 Angle : 0.552 8.078 47292 Z= 0.296 Chirality : 0.046 0.173 5310 Planarity : 0.003 0.030 6198 Dihedral : 5.688 49.882 4766 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.99 % Favored : 89.01 % Rotamer: Outliers : 1.70 % Allowed : 8.81 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.28 (0.11), residues: 4476 helix: 0.49 (0.46), residues: 120 sheet: -3.34 (0.13), residues: 1428 loop : -2.85 (0.10), residues: 2928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 773 HIS 0.002 0.001 HIS A 385 PHE 0.023 0.001 PHE D 635 TYR 0.010 0.001 TYR F 574 ARG 0.002 0.000 ARG D 402 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 3702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 140 time to evaluate : 3.983 Fit side-chains REVERT: A 43 ASP cc_start: 0.8669 (OUTLIER) cc_final: 0.8353 (m-30) REVERT: A 47 LYS cc_start: 0.8203 (mttm) cc_final: 0.7927 (mmmm) REVERT: A 127 MET cc_start: 0.8998 (ptm) cc_final: 0.8712 (ptm) REVERT: A 345 ILE cc_start: 0.8236 (OUTLIER) cc_final: 0.7979 (mt) REVERT: B 47 LYS cc_start: 0.8068 (mttm) cc_final: 0.7622 (mmmm) REVERT: B 407 GLU cc_start: 0.7516 (tm-30) cc_final: 0.7160 (tm-30) REVERT: B 513 ASN cc_start: 0.7485 (OUTLIER) cc_final: 0.7278 (p0) REVERT: B 609 MET cc_start: 0.7856 (ttt) cc_final: 0.7514 (ttt) REVERT: B 662 MET cc_start: 0.7394 (mtp) cc_final: 0.7104 (mtp) REVERT: C 47 LYS cc_start: 0.8118 (mttm) cc_final: 0.7596 (mmmm) REVERT: C 407 GLU cc_start: 0.7386 (tm-30) cc_final: 0.7085 (tm-30) REVERT: C 609 MET cc_start: 0.7726 (ttt) cc_final: 0.7476 (ttt) REVERT: C 634 ASP cc_start: 0.7294 (p0) cc_final: 0.6829 (p0) REVERT: D 43 ASP cc_start: 0.8659 (OUTLIER) cc_final: 0.8347 (m-30) REVERT: D 47 LYS cc_start: 0.8162 (mttm) cc_final: 0.7739 (mmmm) REVERT: D 127 MET cc_start: 0.8991 (ptm) cc_final: 0.8698 (ptm) REVERT: D 345 ILE cc_start: 0.8226 (OUTLIER) cc_final: 0.7968 (mt) REVERT: E 47 LYS cc_start: 0.8068 (mttm) cc_final: 0.7615 (mmmm) REVERT: E 407 GLU cc_start: 0.7512 (tm-30) cc_final: 0.7162 (tm-30) REVERT: E 609 MET cc_start: 0.7882 (ttt) cc_final: 0.7538 (ttt) REVERT: E 662 MET cc_start: 0.7598 (mtp) cc_final: 0.7324 (mtp) REVERT: F 47 LYS cc_start: 0.8110 (mttm) cc_final: 0.7596 (mmmm) REVERT: F 407 GLU cc_start: 0.7390 (tm-30) cc_final: 0.7083 (tm-30) REVERT: F 634 ASP cc_start: 0.7221 (p0) cc_final: 0.6759 (p0) REVERT: F 735 MET cc_start: 0.7347 (ptm) cc_final: 0.7102 (ptp) outliers start: 63 outliers final: 46 residues processed: 194 average time/residue: 0.4296 time to fit residues: 141.8093 Evaluate side-chains 169 residues out of total 3702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 118 time to evaluate : 3.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 513 ASN Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 773 TRP Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 513 ASN Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 773 TRP Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 513 ASN Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 513 ASN Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain D residue 773 TRP Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 509 VAL Chi-restraints excluded: chain E residue 613 LEU Chi-restraints excluded: chain E residue 773 TRP Chi-restraints excluded: chain F residue 43 ASP Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 369 THR Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 509 VAL Chi-restraints excluded: chain F residue 513 ASN Chi-restraints excluded: chain F residue 613 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 362 optimal weight: 20.0000 chunk 246 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 323 optimal weight: 6.9990 chunk 179 optimal weight: 4.9990 chunk 371 optimal weight: 10.0000 chunk 300 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 222 optimal weight: 0.0470 chunk 390 optimal weight: 9.9990 chunk 109 optimal weight: 6.9990 overall best weight: 4.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 693 HIS C 711 ASN C 810 ASN ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 711 ASN F 810 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.070 34920 Z= 0.562 Angle : 0.758 10.442 47292 Z= 0.413 Chirality : 0.053 0.220 5310 Planarity : 0.004 0.034 6198 Dihedral : 6.715 55.079 4766 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.30 % Favored : 80.70 % Rotamer: Outliers : 3.11 % Allowed : 9.08 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.64 (0.11), residues: 4476 helix: -0.41 (0.40), residues: 156 sheet: -3.77 (0.12), residues: 1476 loop : -2.95 (0.10), residues: 2844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 225 HIS 0.004 0.001 HIS C 385 PHE 0.018 0.003 PHE E 561 TYR 0.013 0.002 TYR D 574 ARG 0.004 0.001 ARG A 402 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 3702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 122 time to evaluate : 4.187 Fit side-chains revert: symmetry clash REVERT: A 43 ASP cc_start: 0.8917 (OUTLIER) cc_final: 0.8517 (m-30) REVERT: A 513 ASN cc_start: 0.7556 (OUTLIER) cc_final: 0.7285 (m-40) REVERT: A 680 LYS cc_start: 0.8056 (mtpp) cc_final: 0.7769 (mtmm) REVERT: A 735 MET cc_start: 0.7022 (ptp) cc_final: 0.6681 (mpp) REVERT: B 407 GLU cc_start: 0.7598 (tm-30) cc_final: 0.7168 (tm-30) REVERT: B 513 ASN cc_start: 0.7830 (OUTLIER) cc_final: 0.7359 (p0) REVERT: B 609 MET cc_start: 0.8041 (ttt) cc_final: 0.7661 (ttt) REVERT: B 662 MET cc_start: 0.7493 (mtp) cc_final: 0.7291 (mtp) REVERT: C 407 GLU cc_start: 0.7489 (tm-30) cc_final: 0.7117 (tm-30) REVERT: C 452 PHE cc_start: 0.8506 (OUTLIER) cc_final: 0.7639 (m-80) REVERT: C 462 VAL cc_start: 0.8547 (OUTLIER) cc_final: 0.8323 (m) REVERT: C 609 MET cc_start: 0.7631 (ttt) cc_final: 0.7279 (ttt) REVERT: D 43 ASP cc_start: 0.8920 (OUTLIER) cc_final: 0.8534 (m-30) REVERT: D 513 ASN cc_start: 0.7604 (OUTLIER) cc_final: 0.7372 (m-40) REVERT: D 680 LYS cc_start: 0.8082 (mtpp) cc_final: 0.7878 (mtmm) REVERT: E 407 GLU cc_start: 0.7591 (tm-30) cc_final: 0.7180 (tm-30) REVERT: E 513 ASN cc_start: 0.7883 (OUTLIER) cc_final: 0.7412 (p0) REVERT: E 609 MET cc_start: 0.8057 (ttt) cc_final: 0.7676 (ttt) REVERT: E 662 MET cc_start: 0.7684 (mtp) cc_final: 0.7370 (mtp) REVERT: F 407 GLU cc_start: 0.7527 (tm-30) cc_final: 0.7146 (tm-30) REVERT: F 452 PHE cc_start: 0.8512 (OUTLIER) cc_final: 0.7653 (m-80) REVERT: F 462 VAL cc_start: 0.8548 (OUTLIER) cc_final: 0.8325 (m) REVERT: F 735 MET cc_start: 0.7494 (ptm) cc_final: 0.7174 (ptp) outliers start: 115 outliers final: 78 residues processed: 224 average time/residue: 0.4241 time to fit residues: 166.1616 Evaluate side-chains 192 residues out of total 3702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 104 time to evaluate : 3.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 513 ASN Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 773 TRP Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 513 ASN Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 773 TRP Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 452 PHE Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 513 ASN Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 452 PHE Chi-restraints excluded: chain D residue 456 ILE Chi-restraints excluded: chain D residue 462 VAL Chi-restraints excluded: chain D residue 513 ASN Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain D residue 773 TRP Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 456 ILE Chi-restraints excluded: chain E residue 505 THR Chi-restraints excluded: chain E residue 509 VAL Chi-restraints excluded: chain E residue 513 ASN Chi-restraints excluded: chain E residue 613 LEU Chi-restraints excluded: chain E residue 773 TRP Chi-restraints excluded: chain E residue 789 VAL Chi-restraints excluded: chain F residue 43 ASP Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 345 ILE Chi-restraints excluded: chain F residue 369 THR Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain F residue 452 PHE Chi-restraints excluded: chain F residue 456 ILE Chi-restraints excluded: chain F residue 462 VAL Chi-restraints excluded: chain F residue 505 THR Chi-restraints excluded: chain F residue 513 ASN Chi-restraints excluded: chain F residue 613 LEU Chi-restraints excluded: chain F residue 635 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 146 optimal weight: 20.0000 chunk 391 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 255 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 435 optimal weight: 20.0000 chunk 361 optimal weight: 10.0000 chunk 201 optimal weight: 9.9990 chunk 36 optimal weight: 7.9990 chunk 144 optimal weight: 2.9990 chunk 228 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 ASN A 705 ASN ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 685 GLN ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 GLN C 693 HIS C 711 ASN C 810 ASN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 513 ASN ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 340 GLN F 693 HIS F 711 ASN F 810 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 34920 Z= 0.233 Angle : 0.584 10.484 47292 Z= 0.311 Chirality : 0.048 0.253 5310 Planarity : 0.003 0.031 6198 Dihedral : 5.903 54.924 4766 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.10 % Favored : 88.90 % Rotamer: Outliers : 2.54 % Allowed : 9.86 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.41 (0.11), residues: 4476 helix: -0.50 (0.39), residues: 156 sheet: -3.57 (0.12), residues: 1512 loop : -2.78 (0.10), residues: 2808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 773 HIS 0.002 0.001 HIS F 385 PHE 0.024 0.001 PHE A 635 TYR 0.010 0.001 TYR D 574 ARG 0.002 0.000 ARG B 402 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 3702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 134 time to evaluate : 4.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.8782 (OUTLIER) cc_final: 0.8355 (m-30) REVERT: A 47 LYS cc_start: 0.8267 (mttm) cc_final: 0.7814 (mmmm) REVERT: A 345 ILE cc_start: 0.8313 (OUTLIER) cc_final: 0.8039 (mt) REVERT: A 680 LYS cc_start: 0.8054 (mtpp) cc_final: 0.7804 (mtmm) REVERT: B 47 LYS cc_start: 0.8280 (mttm) cc_final: 0.7827 (mmmm) REVERT: B 407 GLU cc_start: 0.7484 (tm-30) cc_final: 0.7046 (tm-30) REVERT: B 609 MET cc_start: 0.7877 (ttt) cc_final: 0.7468 (ttt) REVERT: C 47 LYS cc_start: 0.8123 (mttm) cc_final: 0.7542 (mmmm) REVERT: C 407 GLU cc_start: 0.7388 (tm-30) cc_final: 0.7007 (tm-30) REVERT: C 462 VAL cc_start: 0.8441 (OUTLIER) cc_final: 0.8230 (m) REVERT: C 609 MET cc_start: 0.7649 (ttt) cc_final: 0.7376 (ttt) REVERT: C 634 ASP cc_start: 0.7369 (p0) cc_final: 0.6779 (p0) REVERT: C 680 LYS cc_start: 0.8262 (mtpp) cc_final: 0.7984 (mtmm) REVERT: D 43 ASP cc_start: 0.8814 (OUTLIER) cc_final: 0.8401 (m-30) REVERT: D 47 LYS cc_start: 0.8256 (mttm) cc_final: 0.7739 (mmmm) REVERT: D 345 ILE cc_start: 0.8309 (OUTLIER) cc_final: 0.8035 (mt) REVERT: D 680 LYS cc_start: 0.8064 (mtpp) cc_final: 0.7851 (mtmm) REVERT: E 47 LYS cc_start: 0.8297 (mttm) cc_final: 0.7826 (mmmm) REVERT: E 407 GLU cc_start: 0.7482 (tm-30) cc_final: 0.7050 (tm-30) REVERT: E 513 ASN cc_start: 0.7497 (OUTLIER) cc_final: 0.7276 (p0) REVERT: E 609 MET cc_start: 0.7944 (ttt) cc_final: 0.7552 (ttt) REVERT: E 662 MET cc_start: 0.7527 (mtp) cc_final: 0.7321 (mtp) REVERT: F 47 LYS cc_start: 0.8123 (mttm) cc_final: 0.7537 (mmmm) REVERT: F 407 GLU cc_start: 0.7395 (tm-30) cc_final: 0.7006 (tm-30) REVERT: F 462 VAL cc_start: 0.8441 (OUTLIER) cc_final: 0.8229 (m) REVERT: F 634 ASP cc_start: 0.7385 (p0) cc_final: 0.6798 (p0) REVERT: F 735 MET cc_start: 0.7400 (ptm) cc_final: 0.7052 (ptp) outliers start: 94 outliers final: 58 residues processed: 216 average time/residue: 0.4156 time to fit residues: 153.6715 Evaluate side-chains 186 residues out of total 3702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 121 time to evaluate : 4.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 773 TRP Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 628 ASN Chi-restraints excluded: chain B residue 773 TRP Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 513 ASN Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain D residue 676 LYS Chi-restraints excluded: chain D residue 773 TRP Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 509 VAL Chi-restraints excluded: chain E residue 513 ASN Chi-restraints excluded: chain E residue 613 LEU Chi-restraints excluded: chain E residue 773 TRP Chi-restraints excluded: chain F residue 43 ASP Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 369 THR Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain F residue 462 VAL Chi-restraints excluded: chain F residue 513 ASN Chi-restraints excluded: chain F residue 613 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 419 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 248 optimal weight: 6.9990 chunk 317 optimal weight: 0.6980 chunk 246 optimal weight: 0.5980 chunk 366 optimal weight: 10.0000 chunk 243 optimal weight: 2.9990 chunk 433 optimal weight: 10.0000 chunk 271 optimal weight: 9.9990 chunk 264 optimal weight: 0.0470 chunk 200 optimal weight: 0.2980 overall best weight: 0.9280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 ASN ** B 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 693 HIS ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 513 ASN D 584 ASN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 693 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 34920 Z= 0.167 Angle : 0.563 11.786 47292 Z= 0.294 Chirality : 0.047 0.223 5310 Planarity : 0.002 0.032 6198 Dihedral : 5.357 47.283 4762 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.44 % Favored : 88.56 % Rotamer: Outliers : 1.97 % Allowed : 10.97 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.14 (0.11), residues: 4476 helix: -0.44 (0.39), residues: 156 sheet: -3.23 (0.13), residues: 1488 loop : -2.69 (0.10), residues: 2832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 773 HIS 0.002 0.000 HIS C 531 PHE 0.023 0.001 PHE D 635 TYR 0.009 0.001 TYR A 623 ARG 0.001 0.000 ARG B 402 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 3702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 140 time to evaluate : 4.295 Fit side-chains REVERT: A 43 ASP cc_start: 0.8684 (OUTLIER) cc_final: 0.8396 (m-30) REVERT: A 47 LYS cc_start: 0.8235 (mttm) cc_final: 0.7873 (mmmm) REVERT: A 680 LYS cc_start: 0.8084 (mtpp) cc_final: 0.7841 (mtmm) REVERT: B 47 LYS cc_start: 0.8200 (mttm) cc_final: 0.7713 (mmmm) REVERT: B 407 GLU cc_start: 0.7444 (tm-30) cc_final: 0.6996 (tm-30) REVERT: B 609 MET cc_start: 0.7860 (ttt) cc_final: 0.7483 (ttt) REVERT: C 47 LYS cc_start: 0.8159 (mttm) cc_final: 0.7620 (mmmm) REVERT: C 407 GLU cc_start: 0.7331 (tm-30) cc_final: 0.6952 (tm-30) REVERT: C 609 MET cc_start: 0.7714 (ttt) cc_final: 0.7454 (ttt) REVERT: C 634 ASP cc_start: 0.7289 (p0) cc_final: 0.6784 (p0) REVERT: C 680 LYS cc_start: 0.8256 (mtpp) cc_final: 0.7999 (mtmm) REVERT: D 43 ASP cc_start: 0.8704 (OUTLIER) cc_final: 0.8421 (m-30) REVERT: D 47 LYS cc_start: 0.8224 (mttm) cc_final: 0.7773 (mmmm) REVERT: D 680 LYS cc_start: 0.8139 (mtpp) cc_final: 0.7916 (mtmm) REVERT: E 47 LYS cc_start: 0.8199 (mttm) cc_final: 0.7714 (mmmm) REVERT: E 407 GLU cc_start: 0.7473 (tm-30) cc_final: 0.7025 (tm-30) REVERT: E 609 MET cc_start: 0.7886 (ttt) cc_final: 0.7512 (ttt) REVERT: E 662 MET cc_start: 0.7349 (mtp) cc_final: 0.7018 (mtp) REVERT: F 47 LYS cc_start: 0.8160 (mttm) cc_final: 0.7622 (mmmm) REVERT: F 407 GLU cc_start: 0.7336 (tm-30) cc_final: 0.6948 (tm-30) REVERT: F 634 ASP cc_start: 0.7265 (p0) cc_final: 0.6748 (p0) REVERT: F 735 MET cc_start: 0.7379 (ptm) cc_final: 0.7072 (ptp) outliers start: 73 outliers final: 55 residues processed: 205 average time/residue: 0.4338 time to fit residues: 152.8493 Evaluate side-chains 181 residues out of total 3702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 124 time to evaluate : 4.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 628 ASN Chi-restraints excluded: chain A residue 773 TRP Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 628 ASN Chi-restraints excluded: chain B residue 664 PHE Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain D residue 628 ASN Chi-restraints excluded: chain D residue 664 PHE Chi-restraints excluded: chain D residue 773 TRP Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 145 TYR Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 509 VAL Chi-restraints excluded: chain E residue 613 LEU Chi-restraints excluded: chain E residue 628 ASN Chi-restraints excluded: chain F residue 43 ASP Chi-restraints excluded: chain F residue 46 ASP Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain F residue 613 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 268 optimal weight: 3.9990 chunk 173 optimal weight: 6.9990 chunk 259 optimal weight: 4.9990 chunk 130 optimal weight: 10.0000 chunk 85 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 275 optimal weight: 8.9990 chunk 295 optimal weight: 0.5980 chunk 214 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 340 optimal weight: 6.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 513 ASN C 693 HIS C 711 ASN C 810 ASN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 711 ASN E 810 ASN ** F 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 513 ASN F 693 HIS F 711 ASN F 810 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 34920 Z= 0.502 Angle : 0.734 9.854 47292 Z= 0.393 Chirality : 0.052 0.254 5310 Planarity : 0.004 0.041 6198 Dihedral : 6.267 30.416 4758 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.87 % Favored : 82.13 % Rotamer: Outliers : 2.38 % Allowed : 11.62 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.28 (0.11), residues: 4476 helix: -0.67 (0.38), residues: 156 sheet: -3.26 (0.13), residues: 1374 loop : -2.89 (0.10), residues: 2946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 773 HIS 0.003 0.001 HIS C 385 PHE 0.018 0.002 PHE B 664 TYR 0.009 0.001 TYR F 579 ARG 0.003 0.001 ARG A 402 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 3702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 125 time to evaluate : 4.394 Fit side-chains REVERT: A 43 ASP cc_start: 0.8924 (OUTLIER) cc_final: 0.8531 (m-30) REVERT: A 662 MET cc_start: 0.7667 (mtp) cc_final: 0.7436 (mtp) REVERT: A 680 LYS cc_start: 0.8083 (mtpp) cc_final: 0.7864 (mtmm) REVERT: B 407 GLU cc_start: 0.7585 (tm-30) cc_final: 0.7113 (tm-30) REVERT: B 513 ASN cc_start: 0.7754 (OUTLIER) cc_final: 0.7471 (p0) REVERT: B 609 MET cc_start: 0.7934 (ttt) cc_final: 0.7500 (ttt) REVERT: C 47 LYS cc_start: 0.8562 (mttm) cc_final: 0.7999 (mmmm) REVERT: C 407 GLU cc_start: 0.7457 (tm-30) cc_final: 0.7063 (tm-30) REVERT: C 609 MET cc_start: 0.7643 (ttt) cc_final: 0.7276 (ttt) REVERT: C 634 ASP cc_start: 0.7423 (p0) cc_final: 0.6783 (p0) REVERT: C 680 LYS cc_start: 0.8231 (mtpp) cc_final: 0.7893 (mtmm) REVERT: D 43 ASP cc_start: 0.8926 (OUTLIER) cc_final: 0.8526 (m-30) REVERT: D 541 ARG cc_start: 0.7367 (OUTLIER) cc_final: 0.7086 (ttp80) REVERT: D 680 LYS cc_start: 0.8175 (mtpp) cc_final: 0.7925 (mtmm) REVERT: E 407 GLU cc_start: 0.7578 (tm-30) cc_final: 0.7118 (tm-30) REVERT: E 513 ASN cc_start: 0.7727 (OUTLIER) cc_final: 0.7429 (p0) REVERT: E 609 MET cc_start: 0.7951 (ttt) cc_final: 0.7520 (ttt) REVERT: E 662 MET cc_start: 0.7564 (mtp) cc_final: 0.7235 (mtp) REVERT: F 47 LYS cc_start: 0.8564 (mttm) cc_final: 0.7999 (mmmm) REVERT: F 407 GLU cc_start: 0.7464 (tm-30) cc_final: 0.7063 (tm-30) REVERT: F 634 ASP cc_start: 0.7382 (p0) cc_final: 0.6765 (p0) REVERT: F 735 MET cc_start: 0.7477 (ptm) cc_final: 0.7142 (ptp) outliers start: 88 outliers final: 68 residues processed: 201 average time/residue: 0.4187 time to fit residues: 146.2929 Evaluate side-chains 191 residues out of total 3702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 118 time to evaluate : 3.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 628 ASN Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 773 TRP Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 513 ASN Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 628 ASN Chi-restraints excluded: chain B residue 664 PHE Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain D residue 628 ASN Chi-restraints excluded: chain D residue 641 THR Chi-restraints excluded: chain D residue 664 PHE Chi-restraints excluded: chain D residue 676 LYS Chi-restraints excluded: chain D residue 773 TRP Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 145 TYR Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 509 VAL Chi-restraints excluded: chain E residue 513 ASN Chi-restraints excluded: chain E residue 567 LEU Chi-restraints excluded: chain E residue 613 LEU Chi-restraints excluded: chain E residue 628 ASN Chi-restraints excluded: chain F residue 43 ASP Chi-restraints excluded: chain F residue 46 ASP Chi-restraints excluded: chain F residue 185 THR Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain F residue 613 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 394 optimal weight: 0.5980 chunk 415 optimal weight: 3.9990 chunk 379 optimal weight: 0.5980 chunk 404 optimal weight: 1.9990 chunk 243 optimal weight: 0.9980 chunk 176 optimal weight: 0.9990 chunk 317 optimal weight: 0.8980 chunk 124 optimal weight: 6.9990 chunk 365 optimal weight: 0.9990 chunk 382 optimal weight: 0.9980 chunk 402 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 ASN ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 693 HIS C 711 ASN C 810 ASN ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 711 ASN E 810 ASN ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 584 ASN F 693 HIS F 711 ASN F 810 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 34920 Z= 0.151 Angle : 0.569 9.835 47292 Z= 0.296 Chirality : 0.047 0.204 5310 Planarity : 0.003 0.048 6198 Dihedral : 5.290 21.798 4758 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Rotamer: Outliers : 1.65 % Allowed : 12.45 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.04 (0.12), residues: 4476 helix: -0.84 (0.38), residues: 156 sheet: -3.06 (0.13), residues: 1428 loop : -2.69 (0.10), residues: 2892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 773 HIS 0.002 0.001 HIS C 531 PHE 0.022 0.001 PHE D 635 TYR 0.011 0.001 TYR A 623 ARG 0.002 0.000 ARG D 50 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 3702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 135 time to evaluate : 4.038 Fit side-chains revert: symmetry clash REVERT: A 43 ASP cc_start: 0.8692 (OUTLIER) cc_final: 0.8373 (m-30) REVERT: A 47 LYS cc_start: 0.8184 (mttm) cc_final: 0.7797 (mmmm) REVERT: A 680 LYS cc_start: 0.8145 (mtpp) cc_final: 0.7944 (mtmm) REVERT: B 47 LYS cc_start: 0.8146 (mttm) cc_final: 0.7671 (mmmm) REVERT: B 407 GLU cc_start: 0.7414 (tm-30) cc_final: 0.7028 (tm-30) REVERT: B 609 MET cc_start: 0.7863 (ttt) cc_final: 0.7516 (ttt) REVERT: B 634 ASP cc_start: 0.7477 (p0) cc_final: 0.6910 (p0) REVERT: C 47 LYS cc_start: 0.8103 (mttm) cc_final: 0.7555 (mmmm) REVERT: C 609 MET cc_start: 0.7697 (ttt) cc_final: 0.7431 (ttt) REVERT: C 634 ASP cc_start: 0.7309 (p0) cc_final: 0.6766 (p0) REVERT: C 680 LYS cc_start: 0.8243 (mtpp) cc_final: 0.7932 (mtmm) REVERT: D 43 ASP cc_start: 0.8721 (OUTLIER) cc_final: 0.8408 (m-30) REVERT: D 47 LYS cc_start: 0.8176 (mttm) cc_final: 0.7762 (mmmm) REVERT: D 541 ARG cc_start: 0.7205 (OUTLIER) cc_final: 0.6794 (ttp80) REVERT: D 680 LYS cc_start: 0.8145 (mtpp) cc_final: 0.7927 (mtmm) REVERT: E 47 LYS cc_start: 0.8146 (mttm) cc_final: 0.7671 (mmmm) REVERT: E 407 GLU cc_start: 0.7433 (tm-30) cc_final: 0.7055 (tm-30) REVERT: E 609 MET cc_start: 0.7877 (ttt) cc_final: 0.7530 (ttt) REVERT: E 634 ASP cc_start: 0.7400 (p0) cc_final: 0.6802 (p0) REVERT: E 662 MET cc_start: 0.7340 (mtp) cc_final: 0.6995 (mtp) REVERT: F 47 LYS cc_start: 0.8161 (mttm) cc_final: 0.7620 (mmmm) REVERT: F 634 ASP cc_start: 0.7309 (p0) cc_final: 0.6710 (p0) REVERT: F 735 MET cc_start: 0.7386 (ptm) cc_final: 0.7163 (ptp) outliers start: 61 outliers final: 44 residues processed: 184 average time/residue: 0.4437 time to fit residues: 138.4120 Evaluate side-chains 177 residues out of total 3702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 130 time to evaluate : 4.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 735 MET Chi-restraints excluded: chain A residue 773 TRP Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 664 PHE Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain D residue 641 THR Chi-restraints excluded: chain D residue 664 PHE Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 145 TYR Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 509 VAL Chi-restraints excluded: chain E residue 613 LEU Chi-restraints excluded: chain E residue 628 ASN Chi-restraints excluded: chain F residue 43 ASP Chi-restraints excluded: chain F residue 226 MET Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain F residue 641 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 265 optimal weight: 6.9990 chunk 427 optimal weight: 0.5980 chunk 260 optimal weight: 3.9990 chunk 202 optimal weight: 8.9990 chunk 297 optimal weight: 7.9990 chunk 448 optimal weight: 0.9990 chunk 412 optimal weight: 2.9990 chunk 356 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 275 optimal weight: 7.9990 chunk 218 optimal weight: 4.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 693 HIS ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 711 ASN E 810 ASN ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 693 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 34920 Z= 0.297 Angle : 0.618 9.157 47292 Z= 0.325 Chirality : 0.048 0.203 5310 Planarity : 0.003 0.054 6198 Dihedral : 5.556 26.077 4758 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.68 % Favored : 85.32 % Rotamer: Outliers : 1.49 % Allowed : 12.72 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.08 (0.12), residues: 4476 helix: -0.94 (0.38), residues: 156 sheet: -3.14 (0.13), residues: 1500 loop : -2.65 (0.11), residues: 2820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP D 773 HIS 0.002 0.001 HIS C 385 PHE 0.020 0.002 PHE B 664 TYR 0.010 0.001 TYR B 574 ARG 0.002 0.000 ARG F 583 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 3702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 127 time to evaluate : 4.271 Fit side-chains REVERT: A 43 ASP cc_start: 0.8776 (OUTLIER) cc_final: 0.8416 (m-30) REVERT: A 47 LYS cc_start: 0.8410 (mttm) cc_final: 0.8057 (mmmm) REVERT: A 226 MET cc_start: 0.8532 (ttp) cc_final: 0.8193 (mtp) REVERT: A 680 LYS cc_start: 0.8153 (mtpp) cc_final: 0.7931 (mtmm) REVERT: B 47 LYS cc_start: 0.8505 (mttm) cc_final: 0.8218 (mtpp) REVERT: B 407 GLU cc_start: 0.7516 (tm-30) cc_final: 0.7131 (tm-30) REVERT: B 609 MET cc_start: 0.7870 (ttt) cc_final: 0.7428 (ttt) REVERT: B 634 ASP cc_start: 0.7484 (p0) cc_final: 0.6968 (p0) REVERT: C 47 LYS cc_start: 0.8441 (mttm) cc_final: 0.7858 (mmmm) REVERT: C 407 GLU cc_start: 0.7358 (tm-30) cc_final: 0.6967 (tm-30) REVERT: C 609 MET cc_start: 0.7714 (ttt) cc_final: 0.7303 (ttt) REVERT: C 634 ASP cc_start: 0.7341 (p0) cc_final: 0.6755 (p0) REVERT: C 680 LYS cc_start: 0.8255 (mtpp) cc_final: 0.7958 (mtmm) REVERT: D 43 ASP cc_start: 0.8781 (OUTLIER) cc_final: 0.8424 (m-30) REVERT: D 226 MET cc_start: 0.8529 (ttp) cc_final: 0.8186 (mtp) REVERT: D 541 ARG cc_start: 0.7260 (OUTLIER) cc_final: 0.6835 (ttp80) REVERT: E 47 LYS cc_start: 0.8498 (mttm) cc_final: 0.8213 (mtpp) REVERT: E 407 GLU cc_start: 0.7516 (tm-30) cc_final: 0.7054 (tm-30) REVERT: E 609 MET cc_start: 0.7893 (ttt) cc_final: 0.7451 (ttt) REVERT: E 634 ASP cc_start: 0.7429 (p0) cc_final: 0.6960 (p0) REVERT: E 662 MET cc_start: 0.7410 (mtp) cc_final: 0.7043 (mtp) REVERT: F 47 LYS cc_start: 0.8443 (mttm) cc_final: 0.7857 (mmmm) REVERT: F 407 GLU cc_start: 0.7369 (tm-30) cc_final: 0.6969 (tm-30) REVERT: F 634 ASP cc_start: 0.7344 (p0) cc_final: 0.6743 (p0) REVERT: F 735 MET cc_start: 0.7476 (ptm) cc_final: 0.7129 (ptp) outliers start: 55 outliers final: 47 residues processed: 172 average time/residue: 0.4360 time to fit residues: 127.4456 Evaluate side-chains 174 residues out of total 3702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 124 time to evaluate : 4.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 773 TRP Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 145 TYR Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 664 PHE Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain D residue 641 THR Chi-restraints excluded: chain D residue 664 PHE Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 145 TYR Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 509 VAL Chi-restraints excluded: chain E residue 613 LEU Chi-restraints excluded: chain E residue 628 ASN Chi-restraints excluded: chain F residue 43 ASP Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 641 THR Chi-restraints excluded: chain F residue 681 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 283 optimal weight: 0.0770 chunk 380 optimal weight: 0.8980 chunk 109 optimal weight: 4.9990 chunk 329 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 99 optimal weight: 4.9990 chunk 357 optimal weight: 1.9990 chunk 149 optimal weight: 20.0000 chunk 367 optimal weight: 20.0000 chunk 45 optimal weight: 0.0070 chunk 65 optimal weight: 4.9990 overall best weight: 0.9960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 584 ASN C 693 HIS ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 711 ASN E 810 ASN ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 693 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.149971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.090029 restraints weight = 57948.431| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 3.64 r_work: 0.3358 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 34920 Z= 0.170 Angle : 0.566 10.590 47292 Z= 0.294 Chirality : 0.047 0.191 5310 Planarity : 0.003 0.059 6198 Dihedral : 5.186 21.357 4758 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer: Outliers : 1.46 % Allowed : 12.88 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.91 (0.12), residues: 4476 helix: -1.11 (0.38), residues: 156 sheet: -3.06 (0.13), residues: 1374 loop : -2.55 (0.10), residues: 2946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP D 773 HIS 0.002 0.001 HIS C 531 PHE 0.021 0.001 PHE D 635 TYR 0.010 0.001 TYR B 574 ARG 0.002 0.000 ARG E 402 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6284.52 seconds wall clock time: 115 minutes 25.92 seconds (6925.92 seconds total)