Starting phenix.real_space_refine on Fri Mar 6 20:59:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6nyf_0542/03_2026/6nyf_0542.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nyf_0542/03_2026/6nyf_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 { model { file = "/net/cci-nas-00/data/ceres_data/6nyf_0542/03_2026/6nyf_0542.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nyf_0542/03_2026/6nyf_0542.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6nyf_0542/03_2026/6nyf_0542.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nyf_0542/03_2026/6nyf_0542.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 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 Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34332 Number of models: 1 Model: "" Number of chains: 1 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 Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 6.62, per 1000 atoms: 0.19 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.29 Conformation dependent library (CDL) restraints added in 1.3 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: 1.65 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: 8.26 Time building geometry restraints manager: 3.21 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: 0.00 - 2.31: 45470 2.31 - 4.61: 1595 4.61 - 6.92: 178 6.92 - 9.22: 37 9.22 - 11.53: 12 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 3.040 nonbonded pdb=" OG1 THR B 153 " pdb=" OG1 THR B 185 " model vdw 2.263 3.040 nonbonded pdb=" OG1 THR E 153 " pdb=" OG1 THR E 185 " model vdw 2.264 3.040 nonbonded pdb=" OG1 THR F 153 " pdb=" OG1 THR F 185 " model vdw 2.264 3.040 nonbonded pdb=" OG1 THR C 153 " pdb=" OG1 THR C 185 " model vdw 2.264 3.040 ... (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 Time spend for trying shortcut: 0.06 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: 3.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.530 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 29.900 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.440 ------------------------------------------------------------------------------- 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 34926 Z= 0.340 Angle : 0.993 11.526 47304 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 : 6.05 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.007 0.001 ARG E 402 TYR 0.035 0.003 TYR D 574 PHE 0.022 0.003 PHE E 532 TRP 0.050 0.004 TRP A 225 HIS 0.007 0.002 HIS C 385 Details of bonding type rmsd covalent geometry : bond 0.00747 (34920) covalent geometry : angle 0.99319 (47292) SS BOND : bond 0.00440 ( 6) SS BOND : angle 0.71040 ( 12) hydrogen bonds : bond 0.24585 ( 297) hydrogen bonds : angle 10.49756 ( 786) *********************** 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 to be fit. rotamer outliers: 12 poor density : 282 time to evaluate : 1.121 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: 0.2060 time to fit residues: 99.5595 Evaluate side-chains 133 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 127 time to evaluate : 1.216 ------------------------------------------------------------------------------- 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 432 optimal weight: 0.8980 chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 1.9990 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 0.8980 chunk 424 optimal weight: 10.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 A 256 HIS A 387 ASN ** A 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 ASN A 755 ASN ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 ASN B 256 HIS B 387 ASN ** B 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 705 ASN B 755 ASN ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 ASN C 256 HIS C 387 ASN ** C 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 705 ASN C 755 ASN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 ASN D 256 HIS D 387 ASN ** D 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 705 ASN D 755 ASN ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 ASN E 256 HIS E 387 ASN ** E 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 705 ASN E 755 ASN ** F 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 97 ASN F 256 HIS 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: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.167565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.094991 restraints weight = 58302.294| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 3.61 r_work: 0.3414 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 34926 Z= 0.130 Angle : 0.582 7.342 47304 Z= 0.318 Chirality : 0.047 0.174 5310 Planarity : 0.003 0.039 6198 Dihedral : 6.017 26.752 4770 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 1.05 % Allowed : 5.70 % Favored : 93.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.57 (0.11), residues: 4476 helix: -1.55 (0.40), residues: 120 sheet: -3.50 (0.12), residues: 1368 loop : -3.02 (0.09), residues: 2988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 541 TYR 0.013 0.001 TYR A 574 PHE 0.016 0.001 PHE C 664 TRP 0.018 0.002 TRP F 773 HIS 0.004 0.001 HIS D 693 Details of bonding type rmsd covalent geometry : bond 0.00285 (34920) covalent geometry : angle 0.58248 (47292) SS BOND : bond 0.00299 ( 6) SS BOND : angle 0.27355 ( 12) hydrogen bonds : bond 0.03034 ( 297) hydrogen bonds : angle 7.45533 ( 786) *********************** 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 216 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 177 time to evaluate : 1.250 Fit side-chains revert: symmetry clash REVERT: A 47 LYS cc_start: 0.7830 (mttm) cc_final: 0.7326 (mmmm) REVERT: A 165 ASP cc_start: 0.8293 (m-30) cc_final: 0.8072 (m-30) REVERT: A 407 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7481 (tm-30) REVERT: A 634 ASP cc_start: 0.7032 (p0) cc_final: 0.6709 (p0) REVERT: B 47 LYS cc_start: 0.7752 (mttm) cc_final: 0.7219 (mmmm) REVERT: B 407 GLU cc_start: 0.7933 (tm-30) cc_final: 0.7628 (tm-30) REVERT: B 609 MET cc_start: 0.7362 (ttt) cc_final: 0.6960 (ttt) REVERT: B 634 ASP cc_start: 0.6908 (p0) cc_final: 0.6532 (p0) REVERT: B 658 ASN cc_start: 0.7830 (t0) cc_final: 0.7568 (t0) REVERT: B 693 HIS cc_start: 0.7245 (m-70) cc_final: 0.6720 (m170) REVERT: C 47 LYS cc_start: 0.7777 (mttm) cc_final: 0.7182 (mmmm) REVERT: C 123 LEU cc_start: 0.7385 (mt) cc_final: 0.7135 (tp) REVERT: C 407 GLU cc_start: 0.7893 (tm-30) cc_final: 0.7581 (tm-30) REVERT: C 586 LYS cc_start: 0.7027 (mmpt) cc_final: 0.6794 (mmmt) REVERT: C 609 MET cc_start: 0.7246 (ttt) cc_final: 0.6996 (ttt) REVERT: C 634 ASP cc_start: 0.7123 (p0) cc_final: 0.6739 (p0) REVERT: C 658 ASN cc_start: 0.7789 (t0) cc_final: 0.7538 (t0) REVERT: D 47 LYS cc_start: 0.7737 (mttm) cc_final: 0.7142 (mmmm) REVERT: D 407 GLU cc_start: 0.7784 (tm-30) cc_final: 0.7478 (tm-30) REVERT: D 486 LEU cc_start: 0.8689 (tp) cc_final: 0.8488 (tp) REVERT: D 634 ASP cc_start: 0.7000 (p0) cc_final: 0.6568 (p0) REVERT: E 47 LYS cc_start: 0.7672 (mttm) cc_final: 0.7178 (mmmm) REVERT: E 407 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7610 (tm-30) REVERT: E 609 MET cc_start: 0.7330 (ttt) cc_final: 0.6915 (ttt) REVERT: E 634 ASP cc_start: 0.6904 (p0) cc_final: 0.6622 (p0) REVERT: E 658 ASN cc_start: 0.7803 (t0) cc_final: 0.7549 (t0) REVERT: E 662 MET cc_start: 0.7321 (mtp) cc_final: 0.7013 (ttm) REVERT: E 693 HIS cc_start: 0.7261 (m-70) cc_final: 0.6832 (m170) REVERT: F 47 LYS cc_start: 0.7770 (mttm) cc_final: 0.7191 (mmmm) REVERT: F 407 GLU cc_start: 0.7843 (tm-30) cc_final: 0.7534 (tm-30) REVERT: F 634 ASP cc_start: 0.7045 (p0) cc_final: 0.6763 (p0) REVERT: F 658 ASN cc_start: 0.7797 (t0) cc_final: 0.7558 (t0) outliers start: 39 outliers final: 16 residues processed: 211 average time/residue: 0.1902 time to fit residues: 69.0877 Evaluate side-chains 143 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 509 VAL Chi-restraints excluded: chain E residue 41 THR Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 509 VAL Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 509 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 295 optimal weight: 0.6980 chunk 71 optimal weight: 30.0000 chunk 70 optimal weight: 3.9990 chunk 48 optimal weight: 10.0000 chunk 321 optimal weight: 1.9990 chunk 208 optimal weight: 20.0000 chunk 118 optimal weight: 4.9990 chunk 373 optimal weight: 40.0000 chunk 389 optimal weight: 3.9990 chunk 196 optimal weight: 2.9990 chunk 158 optimal weight: 0.9980 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 469 HIS A 685 GLN ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 685 GLN ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 469 HIS C 685 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 469 HIS D 685 GLN ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 685 GLN ** F 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 469 HIS F 685 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.149018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.088528 restraints weight = 58335.626| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 3.63 r_work: 0.3324 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 34926 Z= 0.207 Angle : 0.630 8.535 47304 Z= 0.342 Chirality : 0.048 0.163 5310 Planarity : 0.003 0.032 6198 Dihedral : 5.955 25.416 4758 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.89 % Favored : 87.11 % Rotamer: Outliers : 1.35 % Allowed : 7.73 % Favored : 90.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.48 (0.11), residues: 4476 helix: -0.96 (0.37), residues: 156 sheet: -3.44 (0.12), residues: 1392 loop : -2.99 (0.10), residues: 2928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 50 TYR 0.014 0.001 TYR D 574 PHE 0.024 0.002 PHE F 635 TRP 0.023 0.002 TRP E 225 HIS 0.003 0.001 HIS E 385 Details of bonding type rmsd covalent geometry : bond 0.00467 (34920) covalent geometry : angle 0.63026 (47292) SS BOND : bond 0.00145 ( 6) SS BOND : angle 0.26224 ( 12) hydrogen bonds : bond 0.03160 ( 297) hydrogen bonds : angle 6.80129 ( 786) *********************** 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 193 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 143 time to evaluate : 1.220 Fit side-chains REVERT: A 43 ASP cc_start: 0.8634 (OUTLIER) cc_final: 0.8376 (m-30) REVERT: A 47 LYS cc_start: 0.8035 (mttm) cc_final: 0.7631 (mmmm) REVERT: A 407 GLU cc_start: 0.8011 (tm-30) cc_final: 0.7587 (tm-30) REVERT: A 635 PHE cc_start: 0.7275 (t80) cc_final: 0.6866 (t80) REVERT: B 47 LYS cc_start: 0.7995 (mttm) cc_final: 0.7505 (mmmm) REVERT: B 407 GLU cc_start: 0.8039 (tm-30) cc_final: 0.7594 (tm-30) REVERT: B 609 MET cc_start: 0.7467 (ttt) cc_final: 0.7128 (ttt) REVERT: B 658 ASN cc_start: 0.7796 (t0) cc_final: 0.7596 (t0) REVERT: C 47 LYS cc_start: 0.7998 (mttm) cc_final: 0.7435 (mmmm) REVERT: C 407 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7545 (tm-30) REVERT: C 586 LYS cc_start: 0.7147 (mmpt) cc_final: 0.6848 (mmmt) REVERT: C 609 MET cc_start: 0.7284 (ttt) cc_final: 0.7036 (ttt) REVERT: C 634 ASP cc_start: 0.6994 (p0) cc_final: 0.6664 (p0) REVERT: C 658 ASN cc_start: 0.7852 (t0) cc_final: 0.7606 (t0) REVERT: D 43 ASP cc_start: 0.8627 (OUTLIER) cc_final: 0.8380 (m-30) REVERT: D 47 LYS cc_start: 0.8006 (mttm) cc_final: 0.7596 (mmmm) REVERT: D 165 ASP cc_start: 0.8444 (m-30) cc_final: 0.8042 (m-30) REVERT: D 407 GLU cc_start: 0.8001 (tm-30) cc_final: 0.7605 (tm-30) REVERT: E 47 LYS cc_start: 0.8007 (mttm) cc_final: 0.7527 (mmmm) REVERT: E 407 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7585 (tm-30) REVERT: E 609 MET cc_start: 0.7421 (ttt) cc_final: 0.7064 (ttt) REVERT: E 658 ASN cc_start: 0.7790 (t0) cc_final: 0.7580 (t0) REVERT: E 662 MET cc_start: 0.7238 (mtp) cc_final: 0.6883 (mtp) REVERT: F 47 LYS cc_start: 0.8008 (mttm) cc_final: 0.7442 (mmmm) REVERT: F 407 GLU cc_start: 0.7940 (tm-30) cc_final: 0.7547 (tm-30) REVERT: F 634 ASP cc_start: 0.7032 (p0) cc_final: 0.6674 (p0) REVERT: F 658 ASN cc_start: 0.7846 (t0) cc_final: 0.7600 (t0) outliers start: 50 outliers final: 33 residues processed: 187 average time/residue: 0.1764 time to fit residues: 56.7941 Evaluate side-chains 151 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 116 time to evaluate : 1.263 ------------------------------------------------------------------------------- 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 277 ILE Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 613 LEU 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 789 VAL Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 277 ILE 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 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 421 VAL 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 421 VAL Chi-restraints excluded: chain E residue 509 VAL Chi-restraints excluded: chain E residue 613 LEU Chi-restraints excluded: chain E residue 789 VAL 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 613 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 255 optimal weight: 0.9980 chunk 215 optimal weight: 0.5980 chunk 378 optimal weight: 2.9990 chunk 298 optimal weight: 50.0000 chunk 160 optimal weight: 0.9990 chunk 214 optimal weight: 7.9990 chunk 112 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 136 optimal weight: 8.9990 chunk 422 optimal weight: 5.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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** ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 693 HIS ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 GLN ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 340 GLN ** F 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 693 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.126393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.071994 restraints weight = 54212.872| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 3.76 r_work: 0.3343 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34926 Z= 0.153 Angle : 0.571 7.815 47304 Z= 0.308 Chirality : 0.047 0.162 5310 Planarity : 0.003 0.032 6198 Dihedral : 5.588 21.777 4758 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer: Outliers : 1.84 % Allowed : 8.05 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.22 (0.11), residues: 4476 helix: -0.46 (0.40), residues: 156 sheet: -3.28 (0.13), residues: 1368 loop : -2.82 (0.10), residues: 2952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 50 TYR 0.011 0.001 TYR C 574 PHE 0.022 0.001 PHE B 635 TRP 0.016 0.002 TRP E 225 HIS 0.002 0.001 HIS D 385 Details of bonding type rmsd covalent geometry : bond 0.00346 (34920) covalent geometry : angle 0.57058 (47292) SS BOND : bond 0.00189 ( 6) SS BOND : angle 0.25750 ( 12) hydrogen bonds : bond 0.02629 ( 297) hydrogen bonds : angle 6.44585 ( 786) *********************** 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 205 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 137 time to evaluate : 1.246 Fit side-chains REVERT: A 43 ASP cc_start: 0.8660 (OUTLIER) cc_final: 0.8379 (m-30) REVERT: A 47 LYS cc_start: 0.7864 (mttm) cc_final: 0.7478 (mmmm) REVERT: A 407 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7412 (tm-30) REVERT: A 635 PHE cc_start: 0.7277 (t80) cc_final: 0.6927 (t80) REVERT: A 680 LYS cc_start: 0.8166 (mtpp) cc_final: 0.7929 (mtmm) REVERT: A 735 MET cc_start: 0.7159 (OUTLIER) cc_final: 0.6798 (mpp) REVERT: B 47 LYS cc_start: 0.7708 (mttm) cc_final: 0.7278 (mmmm) REVERT: B 407 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7434 (tm-30) REVERT: B 609 MET cc_start: 0.7430 (ttt) cc_final: 0.7050 (ttt) REVERT: B 658 ASN cc_start: 0.7644 (t0) cc_final: 0.7438 (t0) REVERT: B 662 MET cc_start: 0.7139 (mtp) cc_final: 0.6676 (mtp) REVERT: C 47 LYS cc_start: 0.7653 (mttm) cc_final: 0.7085 (mmmm) REVERT: C 407 GLU cc_start: 0.7886 (tm-30) cc_final: 0.7411 (tm-30) REVERT: C 609 MET cc_start: 0.7245 (ttt) cc_final: 0.6991 (ttt) REVERT: C 634 ASP cc_start: 0.6962 (p0) cc_final: 0.6677 (p0) REVERT: D 43 ASP cc_start: 0.8635 (OUTLIER) cc_final: 0.8358 (m-30) REVERT: D 47 LYS cc_start: 0.7730 (mttm) cc_final: 0.7269 (mmmm) REVERT: D 165 ASP cc_start: 0.8428 (m-30) cc_final: 0.8055 (m-30) REVERT: D 407 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7426 (tm-30) REVERT: D 735 MET cc_start: 0.7064 (OUTLIER) cc_final: 0.6737 (mpp) REVERT: E 47 LYS cc_start: 0.7711 (mttm) cc_final: 0.7186 (mmmm) REVERT: E 407 GLU cc_start: 0.7909 (tm-30) cc_final: 0.7439 (tm-30) REVERT: E 609 MET cc_start: 0.7439 (ttt) cc_final: 0.7049 (ttt) REVERT: F 47 LYS cc_start: 0.7671 (mttm) cc_final: 0.7033 (mmmm) REVERT: F 407 GLU cc_start: 0.7876 (tm-30) cc_final: 0.7398 (tm-30) REVERT: F 634 ASP cc_start: 0.6975 (p0) cc_final: 0.6688 (p0) outliers start: 68 outliers final: 50 residues processed: 193 average time/residue: 0.1981 time to fit residues: 65.7377 Evaluate side-chains 174 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 120 time to evaluate : 1.214 ------------------------------------------------------------------------------- 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 185 THR Chi-restraints excluded: chain A residue 205 LEU 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 509 VAL Chi-restraints excluded: chain A residue 613 LEU 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 205 LEU 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 C residue 43 ASP Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 509 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 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 509 VAL Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain D residue 735 MET 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 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 613 LEU Chi-restraints excluded: chain F residue 185 THR Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 345 ILE Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 509 VAL 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 246 optimal weight: 2.9990 chunk 144 optimal weight: 0.9980 chunk 371 optimal weight: 10.0000 chunk 323 optimal weight: 7.9990 chunk 59 optimal weight: 0.0020 chunk 62 optimal weight: 0.0770 chunk 190 optimal weight: 6.9990 chunk 253 optimal weight: 0.9990 chunk 301 optimal weight: 2.9990 chunk 157 optimal weight: 0.0270 chunk 177 optimal weight: 5.9990 overall best weight: 0.4206 ------------------------------------------------------------------------------- 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 340 GLN A 398 GLN ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 GLN ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 693 HIS ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 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 = 0.4392 r_free = 0.4392 target = 0.154351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.093994 restraints weight = 57174.557| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 3.77 r_work: 0.3423 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 34926 Z= 0.087 Angle : 0.517 9.298 47304 Z= 0.276 Chirality : 0.046 0.160 5310 Planarity : 0.002 0.029 6198 Dihedral : 5.006 18.049 4758 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 1.70 % Allowed : 8.21 % Favored : 90.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.82 (0.11), residues: 4476 helix: -0.36 (0.40), residues: 156 sheet: -2.94 (0.13), residues: 1332 loop : -2.58 (0.10), residues: 2988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 50 TYR 0.009 0.001 TYR A 574 PHE 0.022 0.001 PHE C 635 TRP 0.028 0.001 TRP E 773 HIS 0.002 0.000 HIS F 531 Details of bonding type rmsd covalent geometry : bond 0.00185 (34920) covalent geometry : angle 0.51744 (47292) SS BOND : bond 0.00262 ( 6) SS BOND : angle 0.57020 ( 12) hydrogen bonds : bond 0.02057 ( 297) hydrogen bonds : angle 6.10705 ( 786) *********************** 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 224 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 161 time to evaluate : 1.326 Fit side-chains revert: symmetry clash REVERT: A 47 LYS cc_start: 0.7632 (mttm) cc_final: 0.7229 (mmmm) REVERT: A 345 ILE cc_start: 0.7929 (OUTLIER) cc_final: 0.7704 (mt) REVERT: A 735 MET cc_start: 0.7159 (OUTLIER) cc_final: 0.6806 (mpp) REVERT: B 47 LYS cc_start: 0.7535 (mttm) cc_final: 0.7018 (mmmm) REVERT: B 407 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7427 (tm-30) REVERT: B 609 MET cc_start: 0.7371 (ttt) cc_final: 0.7072 (ttt) REVERT: B 658 ASN cc_start: 0.7631 (t0) cc_final: 0.7397 (t0) REVERT: C 47 LYS cc_start: 0.7583 (mttm) cc_final: 0.7061 (mmmm) REVERT: C 125 VAL cc_start: 0.8483 (t) cc_final: 0.8212 (t) REVERT: C 407 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7335 (tm-30) REVERT: C 609 MET cc_start: 0.7259 (ttt) cc_final: 0.6999 (ttt) REVERT: C 634 ASP cc_start: 0.6885 (p0) cc_final: 0.6620 (p0) REVERT: D 47 LYS cc_start: 0.7555 (mttm) cc_final: 0.7046 (mmmm) REVERT: D 165 ASP cc_start: 0.8370 (m-30) cc_final: 0.7996 (m-30) REVERT: D 345 ILE cc_start: 0.7947 (OUTLIER) cc_final: 0.7712 (mt) REVERT: D 634 ASP cc_start: 0.7046 (p0) cc_final: 0.6746 (p0) REVERT: D 635 PHE cc_start: 0.6806 (t80) cc_final: 0.6238 (t80) REVERT: D 654 LEU cc_start: 0.8273 (mt) cc_final: 0.8062 (mt) REVERT: D 680 LYS cc_start: 0.8167 (mtpp) cc_final: 0.7951 (mtmm) REVERT: D 735 MET cc_start: 0.7182 (OUTLIER) cc_final: 0.6790 (mpp) REVERT: E 47 LYS cc_start: 0.7528 (mttm) cc_final: 0.7010 (mmmm) REVERT: E 407 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7408 (tm-30) REVERT: E 609 MET cc_start: 0.7375 (ttt) cc_final: 0.7065 (ttt) REVERT: E 662 MET cc_start: 0.7437 (mtt) cc_final: 0.7215 (mtp) REVERT: F 47 LYS cc_start: 0.7584 (mttm) cc_final: 0.7066 (mmmm) REVERT: F 407 GLU cc_start: 0.7819 (tm-30) cc_final: 0.7338 (tm-30) REVERT: F 634 ASP cc_start: 0.6888 (p0) cc_final: 0.6619 (p0) outliers start: 63 outliers final: 36 residues processed: 209 average time/residue: 0.1958 time to fit residues: 69.6666 Evaluate side-chains 163 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 123 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 613 LEU 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 379 LEU Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain C residue 127 MET 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 613 LEU Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 509 VAL Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain D residue 735 MET Chi-restraints excluded: chain D residue 773 TRP Chi-restraints excluded: chain E residue 41 THR Chi-restraints excluded: chain E residue 127 MET 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 F residue 226 MET Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 509 VAL Chi-restraints excluded: chain F residue 613 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 89 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 74 optimal weight: 30.0000 chunk 404 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 255 optimal weight: 9.9990 chunk 57 optimal weight: 5.9990 chunk 142 optimal weight: 9.9990 chunk 150 optimal weight: 5.9990 chunk 444 optimal weight: 0.6980 chunk 206 optimal weight: 9.9990 overall best weight: 3.4786 ------------------------------------------------------------------------------- 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** ** B 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 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** ** F 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 693 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.142906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.083247 restraints weight = 58470.597| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 3.63 r_work: 0.3264 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 34926 Z= 0.310 Angle : 0.694 9.344 47304 Z= 0.377 Chirality : 0.051 0.194 5310 Planarity : 0.003 0.030 6198 Dihedral : 6.000 28.653 4758 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.43 % Favored : 85.57 % Rotamer: Outliers : 2.38 % Allowed : 8.64 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.01 (0.11), residues: 4476 helix: -0.43 (0.40), residues: 156 sheet: -2.97 (0.14), residues: 1284 loop : -2.79 (0.10), residues: 3036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 402 TYR 0.010 0.001 TYR D 574 PHE 0.017 0.002 PHE E 561 TRP 0.021 0.002 TRP E 225 HIS 0.003 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00701 (34920) covalent geometry : angle 0.69365 (47292) SS BOND : bond 0.00039 ( 6) SS BOND : angle 0.30874 ( 12) hydrogen bonds : bond 0.03033 ( 297) hydrogen bonds : angle 6.25288 ( 786) *********************** 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 206 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 118 time to evaluate : 1.179 Fit side-chains REVERT: A 43 ASP cc_start: 0.8709 (OUTLIER) cc_final: 0.8384 (m-30) REVERT: A 485 THR cc_start: 0.8605 (m) cc_final: 0.8400 (t) REVERT: A 622 ASP cc_start: 0.8011 (m-30) cc_final: 0.7809 (m-30) REVERT: A 735 MET cc_start: 0.7289 (ptp) cc_final: 0.6921 (mpp) REVERT: B 47 LYS cc_start: 0.8290 (mttm) cc_final: 0.7812 (mmmm) REVERT: B 407 GLU cc_start: 0.7950 (tm-30) cc_final: 0.7430 (tm-30) REVERT: B 609 MET cc_start: 0.7594 (ttt) cc_final: 0.7208 (ttt) REVERT: B 662 MET cc_start: 0.7315 (mtp) cc_final: 0.6967 (mtp) REVERT: C 47 LYS cc_start: 0.7995 (mttm) cc_final: 0.7363 (mmmm) REVERT: C 407 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7379 (tm-30) REVERT: C 609 MET cc_start: 0.7169 (ttt) cc_final: 0.6822 (ttt) REVERT: C 634 ASP cc_start: 0.7086 (p0) cc_final: 0.6821 (p0) REVERT: D 43 ASP cc_start: 0.8700 (OUTLIER) cc_final: 0.8375 (m-30) REVERT: D 485 THR cc_start: 0.8560 (m) cc_final: 0.8356 (t) REVERT: D 680 LYS cc_start: 0.8193 (mtpp) cc_final: 0.7979 (mtmm) REVERT: D 735 MET cc_start: 0.7327 (ptp) cc_final: 0.6895 (mpp) REVERT: E 47 LYS cc_start: 0.8282 (mttm) cc_final: 0.7791 (mmmm) REVERT: E 407 GLU cc_start: 0.7942 (tm-30) cc_final: 0.7427 (tm-30) REVERT: E 609 MET cc_start: 0.7603 (ttt) cc_final: 0.7209 (ttt) REVERT: F 47 LYS cc_start: 0.8030 (mttm) cc_final: 0.7418 (mmmm) REVERT: F 407 GLU cc_start: 0.7923 (tm-30) cc_final: 0.7390 (tm-30) REVERT: F 634 ASP cc_start: 0.7089 (p0) cc_final: 0.6816 (p0) outliers start: 88 outliers final: 62 residues processed: 194 average time/residue: 0.1827 time to fit residues: 61.5968 Evaluate side-chains 178 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 114 time to evaluate : 1.072 ------------------------------------------------------------------------------- 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 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 509 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 185 THR 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 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 345 ILE 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 613 LEU Chi-restraints excluded: chain C residue 635 PHE Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 103 MET 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 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 773 TRP Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 185 THR 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 567 LEU Chi-restraints excluded: chain E residue 613 LEU Chi-restraints excluded: chain F residue 185 THR Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 226 MET Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 345 ILE Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 509 VAL Chi-restraints excluded: chain F residue 613 LEU Chi-restraints excluded: chain F residue 635 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 393 optimal weight: 0.7980 chunk 436 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 119 optimal weight: 0.7980 chunk 261 optimal weight: 4.9990 chunk 156 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 146 optimal weight: 7.9990 chunk 337 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 398 GLN ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 GLN C 693 HIS ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 693 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.151238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.090963 restraints weight = 56774.490| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 3.55 r_work: 0.3382 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 34926 Z= 0.112 Angle : 0.555 10.995 47304 Z= 0.293 Chirality : 0.047 0.160 5310 Planarity : 0.002 0.030 6198 Dihedral : 5.297 20.284 4758 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 1.81 % Allowed : 9.40 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.79 (0.12), residues: 4476 helix: -0.58 (0.39), residues: 156 sheet: -2.84 (0.14), residues: 1338 loop : -2.59 (0.10), residues: 2982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 50 TYR 0.010 0.001 TYR C 145 PHE 0.032 0.001 PHE A 635 TRP 0.015 0.002 TRP D 577 HIS 0.002 0.001 HIS B 385 Details of bonding type rmsd covalent geometry : bond 0.00247 (34920) covalent geometry : angle 0.55476 (47292) SS BOND : bond 0.00131 ( 6) SS BOND : angle 0.55784 ( 12) hydrogen bonds : bond 0.02202 ( 297) hydrogen bonds : angle 6.06136 ( 786) *********************** 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 202 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 135 time to evaluate : 1.254 Fit side-chains REVERT: A 43 ASP cc_start: 0.8517 (OUTLIER) cc_final: 0.8259 (m-30) REVERT: A 47 LYS cc_start: 0.7899 (mttm) cc_final: 0.7516 (mmmm) REVERT: A 407 GLU cc_start: 0.8276 (tt0) cc_final: 0.7603 (tm-30) REVERT: A 735 MET cc_start: 0.7316 (OUTLIER) cc_final: 0.6813 (mpp) REVERT: B 47 LYS cc_start: 0.7733 (mttm) cc_final: 0.7166 (mmmm) REVERT: B 407 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7371 (tm-30) REVERT: B 609 MET cc_start: 0.7468 (ttt) cc_final: 0.7125 (ttt) REVERT: B 676 LYS cc_start: 0.8063 (OUTLIER) cc_final: 0.7855 (pttm) REVERT: C 47 LYS cc_start: 0.7742 (mttm) cc_final: 0.7163 (mmmm) REVERT: C 407 GLU cc_start: 0.7818 (tm-30) cc_final: 0.7319 (tm-30) REVERT: C 609 MET cc_start: 0.7329 (ttt) cc_final: 0.7050 (ttt) REVERT: C 634 ASP cc_start: 0.7115 (p0) cc_final: 0.6798 (p0) REVERT: D 43 ASP cc_start: 0.8540 (OUTLIER) cc_final: 0.8278 (m-30) REVERT: D 47 LYS cc_start: 0.7821 (mttm) cc_final: 0.7283 (mmmm) REVERT: D 407 GLU cc_start: 0.8283 (tt0) cc_final: 0.7605 (tm-30) REVERT: D 735 MET cc_start: 0.7354 (OUTLIER) cc_final: 0.6894 (mpp) REVERT: E 47 LYS cc_start: 0.7735 (mttm) cc_final: 0.7175 (mmmm) REVERT: E 407 GLU cc_start: 0.7879 (tm-30) cc_final: 0.7360 (tm-30) REVERT: E 609 MET cc_start: 0.7459 (ttt) cc_final: 0.7097 (ttt) REVERT: F 47 LYS cc_start: 0.7763 (mttm) cc_final: 0.7195 (mmmm) REVERT: F 407 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7328 (tm-30) REVERT: F 634 ASP cc_start: 0.7044 (p0) cc_final: 0.6739 (p0) outliers start: 67 outliers final: 49 residues processed: 187 average time/residue: 0.1838 time to fit residues: 59.5389 Evaluate side-chains 173 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 119 time to evaluate : 1.210 ------------------------------------------------------------------------------- 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 103 MET 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 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 735 MET 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 185 THR Chi-restraints excluded: chain B residue 205 LEU 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 676 LYS Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 185 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 613 LEU Chi-restraints excluded: chain C residue 735 MET Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 103 MET 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 277 ILE 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 735 MET Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 145 TYR Chi-restraints excluded: chain E residue 185 THR Chi-restraints excluded: chain E residue 205 LEU 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 567 LEU Chi-restraints excluded: chain E residue 613 LEU Chi-restraints excluded: chain F residue 185 THR Chi-restraints excluded: chain F residue 226 MET Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 509 VAL 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 325 optimal weight: 2.9990 chunk 233 optimal weight: 0.4980 chunk 122 optimal weight: 4.9990 chunk 424 optimal weight: 9.9990 chunk 310 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 chunk 90 optimal weight: 4.9990 chunk 174 optimal weight: 6.9990 chunk 330 optimal weight: 1.9990 chunk 226 optimal weight: 0.4980 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** ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 GLN C 693 HIS ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 693 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.145828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.085935 restraints weight = 58173.781| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 3.74 r_work: 0.3297 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 34926 Z= 0.206 Angle : 0.615 10.888 47304 Z= 0.328 Chirality : 0.048 0.157 5310 Planarity : 0.003 0.027 6198 Dihedral : 5.591 26.761 4758 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.94 % Favored : 87.06 % Rotamer: Outliers : 1.92 % Allowed : 9.70 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.92 (0.12), residues: 4476 helix: -0.72 (0.39), residues: 156 sheet: -3.02 (0.13), residues: 1446 loop : -2.57 (0.11), residues: 2874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 50 TYR 0.008 0.001 TYR D 574 PHE 0.026 0.002 PHE A 635 TRP 0.047 0.002 TRP D 773 HIS 0.002 0.001 HIS D 385 Details of bonding type rmsd covalent geometry : bond 0.00468 (34920) covalent geometry : angle 0.61543 (47292) SS BOND : bond 0.00028 ( 6) SS BOND : angle 0.36806 ( 12) hydrogen bonds : bond 0.02685 ( 297) hydrogen bonds : angle 5.95725 ( 786) *********************** 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 196 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 125 time to evaluate : 1.287 Fit side-chains REVERT: A 43 ASP cc_start: 0.8702 (OUTLIER) cc_final: 0.8375 (m-30) REVERT: A 47 LYS cc_start: 0.8057 (mttm) cc_final: 0.7622 (mmmm) REVERT: A 226 MET cc_start: 0.8830 (OUTLIER) cc_final: 0.7884 (ttp) REVERT: A 407 GLU cc_start: 0.8360 (tt0) cc_final: 0.7636 (tm-30) REVERT: A 485 THR cc_start: 0.8595 (m) cc_final: 0.8388 (t) REVERT: A 735 MET cc_start: 0.7312 (OUTLIER) cc_final: 0.6790 (mpp) REVERT: B 47 LYS cc_start: 0.8002 (mttm) cc_final: 0.7412 (mmmm) REVERT: B 407 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7364 (tm-30) REVERT: B 609 MET cc_start: 0.7465 (ttt) cc_final: 0.7065 (ttt) REVERT: C 47 LYS cc_start: 0.7975 (mttm) cc_final: 0.7407 (mmmm) REVERT: C 407 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7266 (tm-30) REVERT: C 609 MET cc_start: 0.7139 (ttt) cc_final: 0.6731 (ttt) REVERT: C 634 ASP cc_start: 0.7144 (p0) cc_final: 0.6823 (p0) REVERT: D 43 ASP cc_start: 0.8716 (OUTLIER) cc_final: 0.8376 (m-30) REVERT: D 47 LYS cc_start: 0.8041 (mttm) cc_final: 0.7572 (mmmm) REVERT: D 127 MET cc_start: 0.8928 (ptm) cc_final: 0.8650 (ptm) REVERT: D 226 MET cc_start: 0.8827 (OUTLIER) cc_final: 0.7878 (ttp) REVERT: D 407 GLU cc_start: 0.8362 (tt0) cc_final: 0.7635 (tm-30) REVERT: D 485 THR cc_start: 0.8601 (m) cc_final: 0.8398 (t) REVERT: D 735 MET cc_start: 0.7342 (OUTLIER) cc_final: 0.6878 (mpp) REVERT: E 47 LYS cc_start: 0.7999 (mttm) cc_final: 0.7414 (mmmm) REVERT: E 407 GLU cc_start: 0.7931 (tm-30) cc_final: 0.7354 (tm-30) REVERT: E 609 MET cc_start: 0.7466 (ttt) cc_final: 0.7057 (ttt) REVERT: F 47 LYS cc_start: 0.8003 (mttm) cc_final: 0.7420 (mmmm) REVERT: F 407 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7273 (tm-30) REVERT: F 634 ASP cc_start: 0.7101 (p0) cc_final: 0.6794 (p0) outliers start: 71 outliers final: 56 residues processed: 182 average time/residue: 0.1861 time to fit residues: 58.8440 Evaluate side-chains 181 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 119 time to evaluate : 1.040 ------------------------------------------------------------------------------- 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 103 MET 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 226 MET 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 613 LEU 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 185 THR Chi-restraints excluded: chain B residue 205 LEU 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 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 379 LEU Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 735 MET Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 103 MET 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 226 MET 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 613 LEU Chi-restraints excluded: chain D residue 735 MET Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 145 TYR Chi-restraints excluded: chain E residue 185 THR Chi-restraints excluded: chain E residue 205 LEU 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 567 LEU Chi-restraints excluded: chain E residue 613 LEU Chi-restraints excluded: chain F residue 185 THR Chi-restraints excluded: chain F residue 205 LEU 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 509 VAL 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 442 optimal weight: 3.9990 chunk 381 optimal weight: 2.9990 chunk 395 optimal weight: 3.9990 chunk 387 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 chunk 146 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 54 optimal weight: 6.9990 chunk 118 optimal weight: 3.9990 chunk 344 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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** ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 ASN C 340 GLN C 693 HIS ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 693 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.146909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.086916 restraints weight = 58660.173| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 3.62 r_work: 0.3300 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 34926 Z= 0.220 Angle : 0.634 12.015 47304 Z= 0.338 Chirality : 0.049 0.157 5310 Planarity : 0.003 0.027 6198 Dihedral : 5.733 27.774 4758 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.42 % Favored : 87.58 % Rotamer: Outliers : 1.94 % Allowed : 9.62 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.90 (0.12), residues: 4476 helix: -0.91 (0.38), residues: 156 sheet: -2.93 (0.13), residues: 1404 loop : -2.61 (0.11), residues: 2916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 50 TYR 0.009 0.001 TYR D 574 PHE 0.024 0.002 PHE A 635 TRP 0.037 0.002 TRP D 773 HIS 0.003 0.001 HIS D 385 Details of bonding type rmsd covalent geometry : bond 0.00500 (34920) covalent geometry : angle 0.63424 (47292) SS BOND : bond 0.00029 ( 6) SS BOND : angle 0.37744 ( 12) hydrogen bonds : bond 0.02758 ( 297) hydrogen bonds : angle 5.91529 ( 786) *********************** 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 193 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 121 time to evaluate : 1.303 Fit side-chains REVERT: A 43 ASP cc_start: 0.8765 (OUTLIER) cc_final: 0.8408 (m-30) REVERT: A 47 LYS cc_start: 0.8061 (mttm) cc_final: 0.7632 (mmmm) REVERT: A 226 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.7923 (ttp) REVERT: A 407 GLU cc_start: 0.8371 (tt0) cc_final: 0.7632 (tm-30) REVERT: A 735 MET cc_start: 0.7350 (OUTLIER) cc_final: 0.6821 (mpp) REVERT: B 47 LYS cc_start: 0.7975 (mttm) cc_final: 0.7404 (mmmm) REVERT: B 407 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7377 (tm-30) REVERT: B 609 MET cc_start: 0.7595 (ttt) cc_final: 0.7203 (ttt) REVERT: C 47 LYS cc_start: 0.7875 (mttm) cc_final: 0.7249 (mmmm) REVERT: C 407 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7296 (tm-30) REVERT: C 609 MET cc_start: 0.7179 (ttt) cc_final: 0.6768 (ttt) REVERT: C 634 ASP cc_start: 0.7176 (p0) cc_final: 0.6826 (p0) REVERT: D 43 ASP cc_start: 0.8848 (OUTLIER) cc_final: 0.8473 (m-30) REVERT: D 47 LYS cc_start: 0.8004 (mttm) cc_final: 0.7539 (mmmm) REVERT: D 226 MET cc_start: 0.8846 (OUTLIER) cc_final: 0.7945 (ttp) REVERT: D 407 GLU cc_start: 0.8367 (tt0) cc_final: 0.7616 (tm-30) REVERT: D 735 MET cc_start: 0.7477 (OUTLIER) cc_final: 0.7000 (mpp) REVERT: E 47 LYS cc_start: 0.7977 (mttm) cc_final: 0.7408 (mmmm) REVERT: E 407 GLU cc_start: 0.7958 (tm-30) cc_final: 0.7382 (tm-30) REVERT: E 609 MET cc_start: 0.7519 (ttt) cc_final: 0.7097 (ttt) REVERT: E 662 MET cc_start: 0.7831 (mtt) cc_final: 0.7524 (mtp) REVERT: F 47 LYS cc_start: 0.7855 (mttm) cc_final: 0.7232 (mmmm) REVERT: F 407 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7299 (tm-30) REVERT: F 634 ASP cc_start: 0.7191 (p0) cc_final: 0.6853 (p0) outliers start: 72 outliers final: 61 residues processed: 179 average time/residue: 0.1785 time to fit residues: 55.7318 Evaluate side-chains 182 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 115 time to evaluate : 1.193 ------------------------------------------------------------------------------- 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 103 MET 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 226 MET 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 456 ILE Chi-restraints excluded: chain A residue 613 LEU 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 145 TYR Chi-restraints excluded: chain B residue 185 THR 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 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 379 LEU Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 735 MET Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 103 MET 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 226 MET 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 456 ILE Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain D residue 735 MET Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 145 TYR Chi-restraints excluded: chain E residue 185 THR 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 567 LEU Chi-restraints excluded: chain E residue 613 LEU Chi-restraints excluded: chain F residue 185 THR Chi-restraints excluded: chain F residue 205 LEU 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 509 VAL Chi-restraints excluded: chain F residue 613 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 330 optimal weight: 3.9990 chunk 405 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 371 optimal weight: 9.9990 chunk 364 optimal weight: 2.9990 chunk 213 optimal weight: 9.9990 chunk 164 optimal weight: 0.9980 chunk 126 optimal weight: 10.0000 chunk 178 optimal weight: 3.9990 chunk 123 optimal weight: 0.7980 chunk 208 optimal weight: 5.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 693 HIS ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 97 ASN F 693 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.146135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.085632 restraints weight = 57840.528| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 3.57 r_work: 0.3288 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 34926 Z= 0.236 Angle : 0.665 11.253 47304 Z= 0.352 Chirality : 0.050 0.291 5310 Planarity : 0.003 0.031 6198 Dihedral : 5.825 28.920 4758 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.49 % Favored : 86.51 % Rotamer: Outliers : 1.94 % Allowed : 9.81 % Favored : 88.25 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.96 (0.12), residues: 4476 helix: -1.52 (0.36), residues: 156 sheet: -2.95 (0.13), residues: 1404 loop : -2.64 (0.11), residues: 2916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 50 TYR 0.009 0.001 TYR D 574 PHE 0.022 0.002 PHE A 635 TRP 0.035 0.002 TRP D 773 HIS 0.003 0.001 HIS D 385 Details of bonding type rmsd covalent geometry : bond 0.00535 (34920) covalent geometry : angle 0.66467 (47292) SS BOND : bond 0.00116 ( 6) SS BOND : angle 0.51610 ( 12) hydrogen bonds : bond 0.03084 ( 297) hydrogen bonds : angle 6.20211 ( 786) ********************** 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 190 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 118 time to evaluate : 1.214 Fit side-chains REVERT: A 43 ASP cc_start: 0.8829 (OUTLIER) cc_final: 0.8433 (m-30) REVERT: A 165 ASP cc_start: 0.8475 (m-30) cc_final: 0.8041 (m-30) REVERT: A 226 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.8243 (ttp) REVERT: A 407 GLU cc_start: 0.8390 (tt0) cc_final: 0.7672 (tm-30) REVERT: A 735 MET cc_start: 0.7392 (OUTLIER) cc_final: 0.7011 (mpp) REVERT: B 47 LYS cc_start: 0.8180 (mttm) cc_final: 0.7636 (mmmm) REVERT: B 407 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7421 (tm-30) REVERT: B 609 MET cc_start: 0.7649 (ttt) cc_final: 0.7248 (ttt) REVERT: C 47 LYS cc_start: 0.8084 (mttm) cc_final: 0.7456 (mmmm) REVERT: C 407 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7379 (tm-30) REVERT: C 609 MET cc_start: 0.7231 (ttt) cc_final: 0.6819 (ttt) REVERT: C 634 ASP cc_start: 0.7218 (p0) cc_final: 0.6862 (p0) REVERT: D 43 ASP cc_start: 0.8895 (OUTLIER) cc_final: 0.8455 (m-30) REVERT: D 47 LYS cc_start: 0.8119 (mttm) cc_final: 0.7647 (mmmm) REVERT: D 226 MET cc_start: 0.8830 (OUTLIER) cc_final: 0.8237 (ttp) REVERT: D 407 GLU cc_start: 0.8389 (tt0) cc_final: 0.7670 (tm-30) REVERT: D 735 MET cc_start: 0.7514 (OUTLIER) cc_final: 0.7043 (mpp) REVERT: E 47 LYS cc_start: 0.8134 (mttm) cc_final: 0.7576 (mmmm) REVERT: E 407 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7428 (tm-30) REVERT: E 609 MET cc_start: 0.7556 (ttt) cc_final: 0.7129 (ttt) REVERT: F 47 LYS cc_start: 0.8073 (mttm) cc_final: 0.7460 (mmmm) REVERT: F 407 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7382 (tm-30) REVERT: F 634 ASP cc_start: 0.7233 (p0) cc_final: 0.6889 (p0) outliers start: 72 outliers final: 61 residues processed: 176 average time/residue: 0.1847 time to fit residues: 56.7822 Evaluate side-chains 182 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 115 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 103 MET 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 226 MET 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 456 ILE Chi-restraints excluded: chain A residue 613 LEU 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 145 TYR Chi-restraints excluded: chain B residue 185 THR 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 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 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 103 MET 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 226 MET 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 456 ILE Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain D residue 735 MET Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 145 TYR Chi-restraints excluded: chain E residue 185 THR 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 567 LEU Chi-restraints excluded: chain E residue 613 LEU Chi-restraints excluded: chain F residue 185 THR Chi-restraints excluded: chain F residue 205 LEU 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 613 LEU Chi-restraints excluded: chain F residue 735 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 386 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 422 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 262 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 195 optimal weight: 0.9990 chunk 170 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 400 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 97 ASN ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 693 HIS ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 340 GLN F 693 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.148726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.088854 restraints weight = 56419.170| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 3.65 r_work: 0.3366 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 34926 Z= 0.120 Angle : 0.584 10.412 47304 Z= 0.304 Chirality : 0.047 0.272 5310 Planarity : 0.003 0.032 6198 Dihedral : 5.258 21.673 4758 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer: Outliers : 1.51 % Allowed : 10.26 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.72 (0.12), residues: 4476 helix: -1.67 (0.36), residues: 156 sheet: -2.80 (0.14), residues: 1272 loop : -2.49 (0.10), residues: 3048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 50 TYR 0.008 0.001 TYR D 574 PHE 0.025 0.001 PHE A 635 TRP 0.033 0.002 TRP D 773 HIS 0.002 0.000 HIS A 385 Details of bonding type rmsd covalent geometry : bond 0.00270 (34920) covalent geometry : angle 0.58419 (47292) SS BOND : bond 0.00117 ( 6) SS BOND : angle 0.79474 ( 12) hydrogen bonds : bond 0.02716 ( 297) hydrogen bonds : angle 6.11318 ( 786) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8135.23 seconds wall clock time: 140 minutes 8.63 seconds (8408.63 seconds total)