Starting phenix.real_space_refine on Thu Feb 5 10:43:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kb9_62221/02_2026/9kb9_62221.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kb9_62221/02_2026/9kb9_62221.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kb9_62221/02_2026/9kb9_62221.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kb9_62221/02_2026/9kb9_62221.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kb9_62221/02_2026/9kb9_62221.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kb9_62221/02_2026/9kb9_62221.map" } resolution = 3.59 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.017 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 108 5.16 5 C 10506 2.51 5 N 2744 2.21 5 O 2994 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16352 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 748, 5834 Classifications: {'peptide': 748} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 710} Chain breaks: 1 Chain: "C" Number of atoms: 1488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1488 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 11, 'TRANS': 178} Chain: "B" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 826 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain: "D" Number of atoms: 5834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 748, 5834 Classifications: {'peptide': 748} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 710} Chain breaks: 1 Chain: "E" Number of atoms: 1488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1488 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 11, 'TRANS': 178} Chain: "F" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 826 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.85, per 1000 atoms: 0.24 Number of scatterers: 16352 At special positions: 0 Unit cell: (112.05, 118.275, 151.89, 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 108 16.00 O 2994 8.00 N 2744 7.00 C 10506 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=29, symmetry=0 Simple disulfide: pdb=" SG CYS A 29 " - pdb=" SG CYS A 35 " distance=2.03 Simple disulfide: pdb=" SG CYS A 33 " - pdb=" SG CYS A 43 " distance=2.03 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 364 " distance=2.03 Simple disulfide: pdb=" SG CYS A 470 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 471 " - pdb=" SG CYS A 532 " distance=2.03 Simple disulfide: pdb=" SG CYS A 618 " - pdb=" SG CYS A 693 " distance=2.03 Simple disulfide: pdb=" SG CYS B 40 " - pdb=" SG CYS B 46 " distance=2.03 Simple disulfide: pdb=" SG CYS B 43 " - pdb=" SG CYS B 52 " distance=2.03 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 74 " distance=2.03 Simple disulfide: pdb=" SG CYS B 78 " - pdb=" SG CYS B 93 " distance=2.03 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 104 " distance=2.03 Simple disulfide: pdb=" SG CYS B 101 " - pdb=" SG CYS B 110 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 124 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 29 " - pdb=" SG CYS D 35 " distance=2.03 Simple disulfide: pdb=" SG CYS D 33 " - pdb=" SG CYS D 43 " distance=2.03 Simple disulfide: pdb=" SG CYS D 339 " - pdb=" SG CYS D 364 " distance=2.03 Simple disulfide: pdb=" SG CYS D 470 " - pdb=" SG CYS D 522 " distance=2.03 Simple disulfide: pdb=" SG CYS D 471 " - pdb=" SG CYS D 532 " distance=2.03 Simple disulfide: pdb=" SG CYS D 618 " - pdb=" SG CYS D 693 " distance=2.03 Simple disulfide: pdb=" SG CYS D 757 " - pdb=" SG CYS D 761 " distance=2.04 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 46 " distance=2.03 Simple disulfide: pdb=" SG CYS F 43 " - pdb=" SG CYS F 52 " distance=2.03 Simple disulfide: pdb=" SG CYS F 55 " - pdb=" SG CYS F 74 " distance=2.03 Simple disulfide: pdb=" SG CYS F 78 " - pdb=" SG CYS F 93 " distance=2.03 Simple disulfide: pdb=" SG CYS F 96 " - pdb=" SG CYS F 104 " distance=2.03 Simple disulfide: pdb=" SG CYS F 101 " - pdb=" SG CYS F 110 " distance=2.03 Simple disulfide: pdb=" SG CYS F 113 " - pdb=" SG CYS F 124 " distance=2.03 Simple disulfide: pdb=" SG CYS F 128 " - pdb=" SG CYS F 141 " 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 Links applied NAG-ASN " NAG A1001 " - " ASN A 68 " " NAG A1002 " - " ASN A 199 " " NAG D1001 " - " ASN D 68 " " NAG D1002 " - " ASN D 199 " Time building additional restraints: 1.58 Conformation dependent library (CDL) restraints added in 717.8 milliseconds 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3920 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 25 sheets defined 36.2% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 169 through 174 Processing helix chain 'A' and resid 241 through 247 removed outlier: 3.510A pdb=" N LEU A 247 " --> pdb=" O ILE A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 381 through 386 removed outlier: 3.696A pdb=" N THR A 384 " --> pdb=" O LYS A 381 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N PHE A 385 " --> pdb=" O GLU A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 456 Processing helix chain 'A' and resid 466 through 471 Processing helix chain 'A' and resid 538 through 565 Processing helix chain 'A' and resid 571 through 601 Processing helix chain 'A' and resid 604 through 615 removed outlier: 3.937A pdb=" N PHE A 608 " --> pdb=" O ARG A 604 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ILE A 610 " --> pdb=" O ALA A 606 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N TRP A 611 " --> pdb=" O GLU A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 653 removed outlier: 3.988A pdb=" N LYS A 619 " --> pdb=" O GLY A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 683 Proline residue: A 680 - end of helix removed outlier: 3.908A pdb=" N HIS A 683 " --> pdb=" O PHE A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 690 removed outlier: 3.756A pdb=" N ALA A 689 " --> pdb=" O GLU A 686 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N SER A 690 " --> pdb=" O TYR A 687 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 686 through 690' Processing helix chain 'A' and resid 700 through 732 removed outlier: 3.836A pdb=" N LEU A 704 " --> pdb=" O GLU A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 738 Processing helix chain 'A' and resid 740 through 773 removed outlier: 3.930A pdb=" N SER A 744 " --> pdb=" O ASN A 740 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N MET A 745 " --> pdb=" O SER A 741 " (cutoff:3.500A) Proline residue: A 762 - end of helix Proline residue: A 770 - end of helix Processing helix chain 'A' and resid 778 through 790 removed outlier: 4.276A pdb=" N MET A 782 " --> pdb=" O SER A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 796 removed outlier: 3.825A pdb=" N LEU A 796 " --> pdb=" O LEU A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 804 Processing helix chain 'A' and resid 805 through 822 Processing helix chain 'C' and resid 102 through 106 removed outlier: 3.861A pdb=" N LEU C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 114 removed outlier: 4.083A pdb=" N GLU C 113 " --> pdb=" O ASN C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 132 removed outlier: 3.549A pdb=" N ASP C 132 " --> pdb=" O PRO C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 149 Processing helix chain 'C' and resid 162 through 170 removed outlier: 4.312A pdb=" N ASP C 166 " --> pdb=" O PRO C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 196 Processing helix chain 'C' and resid 213 through 216 Processing helix chain 'C' and resid 217 through 246 removed outlier: 3.788A pdb=" N ILE C 221 " --> pdb=" O PHE C 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 175 removed outlier: 3.829A pdb=" N ASN D 175 " --> pdb=" O HIS D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 247 Processing helix chain 'D' and resid 337 through 342 Processing helix chain 'D' and resid 381 through 386 removed outlier: 3.747A pdb=" N THR D 384 " --> pdb=" O LYS D 381 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N PHE D 385 " --> pdb=" O GLU D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 456 Processing helix chain 'D' and resid 466 through 471 Processing helix chain 'D' and resid 541 through 565 Processing helix chain 'D' and resid 571 through 601 Processing helix chain 'D' and resid 604 through 615 removed outlier: 3.941A pdb=" N PHE D 608 " --> pdb=" O ARG D 604 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ILE D 610 " --> pdb=" O ALA D 606 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N TRP D 611 " --> pdb=" O GLU D 607 " (cutoff:3.500A) Processing helix chain 'D' and resid 615 through 652 removed outlier: 3.996A pdb=" N LYS D 619 " --> pdb=" O GLY D 615 " (cutoff:3.500A) Processing helix chain 'D' and resid 658 through 679 Processing helix chain 'D' and resid 680 through 684 Processing helix chain 'D' and resid 686 through 690 removed outlier: 3.914A pdb=" N ALA D 689 " --> pdb=" O GLU D 686 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER D 690 " --> pdb=" O TYR D 687 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 686 through 690' Processing helix chain 'D' and resid 700 through 732 removed outlier: 3.792A pdb=" N LEU D 704 " --> pdb=" O GLU D 700 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 738 Processing helix chain 'D' and resid 741 through 773 removed outlier: 3.885A pdb=" N MET D 745 " --> pdb=" O SER D 741 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N CYS D 757 " --> pdb=" O ILE D 753 " (cutoff:3.500A) Proline residue: D 762 - end of helix Proline residue: D 770 - end of helix Processing helix chain 'D' and resid 778 through 790 removed outlier: 4.041A pdb=" N MET D 782 " --> pdb=" O SER D 778 " (cutoff:3.500A) Processing helix chain 'D' and resid 791 through 796 removed outlier: 3.796A pdb=" N LEU D 796 " --> pdb=" O LEU D 792 " (cutoff:3.500A) Processing helix chain 'D' and resid 796 through 804 Processing helix chain 'D' and resid 805 through 822 Processing helix chain 'E' and resid 102 through 106 removed outlier: 3.830A pdb=" N LEU E 106 " --> pdb=" O PRO E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 115 removed outlier: 4.013A pdb=" N GLU E 113 " --> pdb=" O ASN E 110 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU E 115 " --> pdb=" O GLU E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 132 Processing helix chain 'E' and resid 138 through 149 Processing helix chain 'E' and resid 162 through 170 removed outlier: 4.346A pdb=" N ASP E 166 " --> pdb=" O PRO E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 196 Processing helix chain 'E' and resid 214 through 246 removed outlier: 3.939A pdb=" N ASP E 218 " --> pdb=" O THR E 214 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N MET E 219 " --> pdb=" O GLU E 215 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLY E 220 " --> pdb=" O TYR E 216 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 42 removed outlier: 6.795A pdb=" N LEU A 110 " --> pdb=" O ARG A 135 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU A 253 " --> pdb=" O THR A 276 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N HIS A 278 " --> pdb=" O LEU A 253 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA3, first strand: chain 'A' and resid 191 through 192 removed outlier: 3.842A pdb=" N ILE A 192 " --> pdb=" O SER A 215 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 262 through 263 Processing sheet with id=AA5, first strand: chain 'A' and resid 300 through 304 removed outlier: 6.750A pdb=" N LEU A 301 " --> pdb=" O THR A 325 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N THR A 327 " --> pdb=" O LEU A 301 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE A 303 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER A 371 " --> pdb=" O LEU A 348 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 379 through 380 Processing sheet with id=AA7, first strand: chain 'A' and resid 417 through 419 removed outlier: 3.574A pdb=" N LYS A 440 " --> pdb=" O LEU A 418 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 58 through 68 removed outlier: 3.544A pdb=" N TYR C 77 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ALA C 153 " --> pdb=" O TRP C 120 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LYS C 125 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ALA C 201 " --> pdb=" O ILE C 98 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 46 through 47 Processing sheet with id=AB1, first strand: chain 'B' and resid 69 through 75 removed outlier: 3.718A pdb=" N CYS B 93 " --> pdb=" O PHE B 61 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU B 63 " --> pdb=" O CYS B 93 " (cutoff:3.500A) removed outlier: 9.297A pdb=" N ARG B 95 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 14.867A pdb=" N ARG B 65 " --> pdb=" O ARG B 95 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 101 through 104 removed outlier: 6.993A pdb=" N LYS B 112 " --> pdb=" O ASP B 102 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N CYS B 104 " --> pdb=" O CYS B 110 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N CYS B 110 " --> pdb=" O CYS B 104 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 118 through 120 Processing sheet with id=AB4, first strand: chain 'D' and resid 40 through 42 removed outlier: 6.801A pdb=" N LEU D 110 " --> pdb=" O ARG D 135 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU D 253 " --> pdb=" O THR D 276 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N HIS D 278 " --> pdb=" O LEU D 253 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AB6, first strand: chain 'D' and resid 191 through 192 removed outlier: 3.842A pdb=" N ILE D 192 " --> pdb=" O SER D 215 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 262 through 263 Processing sheet with id=AB8, first strand: chain 'D' and resid 302 through 304 removed outlier: 6.905A pdb=" N ILE D 303 " --> pdb=" O THR D 327 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER D 371 " --> pdb=" O LEU D 348 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 379 through 380 Processing sheet with id=AC1, first strand: chain 'D' and resid 417 through 419 Processing sheet with id=AC2, first strand: chain 'E' and resid 58 through 68 removed outlier: 5.669A pdb=" N TRP E 120 " --> pdb=" O ALA E 151 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ALA E 153 " --> pdb=" O TRP E 120 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LYS E 125 " --> pdb=" O MET E 101 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 46 through 47 Processing sheet with id=AC4, first strand: chain 'F' and resid 69 through 75 removed outlier: 3.730A pdb=" N CYS F 93 " --> pdb=" O PHE F 61 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU F 63 " --> pdb=" O CYS F 93 " (cutoff:3.500A) removed outlier: 9.264A pdb=" N ARG F 95 " --> pdb=" O LEU F 63 " (cutoff:3.500A) removed outlier: 14.822A pdb=" N ARG F 65 " --> pdb=" O ARG F 95 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA F 94 " --> pdb=" O TYR F 83 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 101 through 104 Processing sheet with id=AC6, first strand: chain 'F' and resid 118 through 120 Processing sheet with id=AC7, first strand: chain 'F' and resid 133 through 135 668 hydrogen bonds defined for protein. 1872 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: 3.12 Time building geometry restraints manager: 2.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 5266 1.35 - 1.47: 4046 1.47 - 1.60: 7266 1.60 - 1.73: 0 1.73 - 1.86: 140 Bond restraints: 16718 Sorted by residual: bond pdb=" N MET D 540 " pdb=" CA MET D 540 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.23e-02 6.61e+03 9.51e+00 bond pdb=" N ASN A 797 " pdb=" CA ASN A 797 " ideal model delta sigma weight residual 1.462 1.489 -0.027 9.50e-03 1.11e+04 8.20e+00 bond pdb=" N ILE A 593 " pdb=" CA ILE A 593 " ideal model delta sigma weight residual 1.461 1.491 -0.030 1.17e-02 7.31e+03 6.56e+00 bond pdb=" N ILE C 221 " pdb=" CA ILE C 221 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.34e-02 5.57e+03 5.60e+00 bond pdb=" N PHE D 718 " pdb=" CA PHE D 718 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.20e-02 6.94e+03 5.31e+00 ... (remaining 16713 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 22272 2.20 - 4.40: 323 4.40 - 6.61: 59 6.61 - 8.81: 9 8.81 - 11.01: 3 Bond angle restraints: 22666 Sorted by residual: angle pdb=" N ILE D 541 " pdb=" CA ILE D 541 " pdb=" C ILE D 541 " ideal model delta sigma weight residual 111.67 102.26 9.41 9.50e-01 1.11e+00 9.80e+01 angle pdb=" CA MET D 721 " pdb=" CB MET D 721 " pdb=" CG MET D 721 " ideal model delta sigma weight residual 114.10 121.60 -7.50 2.00e+00 2.50e-01 1.40e+01 angle pdb=" CA PHE D 718 " pdb=" CB PHE D 718 " pdb=" CG PHE D 718 " ideal model delta sigma weight residual 113.80 117.53 -3.73 1.00e+00 1.00e+00 1.39e+01 angle pdb=" C LYS C 134 " pdb=" CA LYS C 134 " pdb=" CB LYS C 134 " ideal model delta sigma weight residual 110.65 114.52 -3.87 1.04e+00 9.25e-01 1.38e+01 angle pdb=" CB MET D 721 " pdb=" CG MET D 721 " pdb=" SD MET D 721 " ideal model delta sigma weight residual 112.70 123.71 -11.01 3.00e+00 1.11e-01 1.35e+01 ... (remaining 22661 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 8685 17.64 - 35.28: 1137 35.28 - 52.92: 290 52.92 - 70.55: 37 70.55 - 88.19: 18 Dihedral angle restraints: 10167 sinusoidal: 4127 harmonic: 6040 Sorted by residual: dihedral pdb=" CB CYS A 618 " pdb=" SG CYS A 618 " pdb=" SG CYS A 693 " pdb=" CB CYS A 693 " ideal model delta sinusoidal sigma weight residual -86.00 -137.60 51.60 1 1.00e+01 1.00e-02 3.64e+01 dihedral pdb=" CB CYS D 618 " pdb=" SG CYS D 618 " pdb=" SG CYS D 693 " pdb=" CB CYS D 693 " ideal model delta sinusoidal sigma weight residual -86.00 -136.86 50.86 1 1.00e+01 1.00e-02 3.54e+01 dihedral pdb=" CB CYS F 128 " pdb=" SG CYS F 128 " pdb=" SG CYS F 141 " pdb=" CB CYS F 141 " ideal model delta sinusoidal sigma weight residual -86.00 -125.16 39.16 1 1.00e+01 1.00e-02 2.16e+01 ... (remaining 10164 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2336 0.073 - 0.147: 263 0.147 - 0.220: 8 0.220 - 0.293: 1 0.293 - 0.366: 2 Chirality restraints: 2610 Sorted by residual: chirality pdb=" C1 NAG D1001 " pdb=" ND2 ASN D 68 " pdb=" C2 NAG D1001 " pdb=" O5 NAG D1001 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.35e+00 chirality pdb=" CA ILE D 541 " pdb=" N ILE D 541 " pdb=" C ILE D 541 " pdb=" CB ILE D 541 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CG LEU A 550 " pdb=" CB LEU A 550 " pdb=" CD1 LEU A 550 " pdb=" CD2 LEU A 550 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 2607 not shown) Planarity restraints: 2900 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 216 " -0.022 2.00e-02 2.50e+03 1.94e-02 7.51e+00 pdb=" CG TYR C 216 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR C 216 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR C 216 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR C 216 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR C 216 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR C 216 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR C 216 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 751 " 0.017 2.00e-02 2.50e+03 1.72e-02 7.39e+00 pdb=" CG TRP D 751 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP D 751 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP D 751 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 751 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 751 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 751 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 751 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 751 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP D 751 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 711 " 0.010 2.00e-02 2.50e+03 2.00e-02 4.02e+00 pdb=" C VAL D 711 " -0.035 2.00e-02 2.50e+03 pdb=" O VAL D 711 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU D 712 " 0.012 2.00e-02 2.50e+03 ... (remaining 2897 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.94: 7803 2.94 - 3.43: 17585 3.43 - 3.92: 27540 3.92 - 4.41: 31041 4.41 - 4.90: 49840 Nonbonded interactions: 133809 Sorted by model distance: nonbonded pdb=" N GLU E 97 " pdb=" OE1 GLU E 97 " model vdw 2.445 3.120 nonbonded pdb=" N GLU C 97 " pdb=" OE1 GLU C 97 " model vdw 2.467 3.120 nonbonded pdb=" N GLU E 117 " pdb=" OE1 GLU E 117 " model vdw 2.512 3.120 nonbonded pdb=" O GLY D 677 " pdb=" OH TYR D 687 " model vdw 2.512 3.040 nonbonded pdb=" N ASP C 174 " pdb=" OD1 ASP C 174 " model vdw 2.514 3.120 ... (remaining 133804 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.660 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 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 : 0.005 0.048 16751 Z= 0.230 Angle : 0.676 11.010 22736 Z= 0.364 Chirality : 0.046 0.366 2610 Planarity : 0.004 0.035 2896 Dihedral : 16.721 88.193 6160 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.75 % Favored : 94.15 % Rotamer: Outliers : 2.63 % Allowed : 24.37 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.20), residues: 2068 helix: 1.53 (0.21), residues: 616 sheet: -0.98 (0.28), residues: 384 loop : -0.37 (0.21), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 123 TYR 0.046 0.002 TYR C 216 PHE 0.018 0.001 PHE A 549 TRP 0.047 0.002 TRP D 751 HIS 0.006 0.001 HIS A 748 Details of bonding type rmsd covalent geometry : bond 0.00480 (16718) covalent geometry : angle 0.66970 (22666) SS BOND : bond 0.00330 ( 29) SS BOND : angle 1.00919 ( 58) hydrogen bonds : bond 0.16453 ( 668) hydrogen bonds : angle 6.76916 ( 1872) link_NAG-ASN : bond 0.00832 ( 4) link_NAG-ASN : angle 3.57195 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 90 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 344 MET cc_start: 0.7927 (ppp) cc_final: 0.7665 (ppp) REVERT: A 374 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.8168 (mtp-110) REVERT: C 199 LYS cc_start: 0.8893 (tppt) cc_final: 0.8563 (tppt) REVERT: C 219 MET cc_start: 0.6130 (ptm) cc_final: 0.5669 (ptt) REVERT: B 44 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8637 (mp) REVERT: D 252 GLU cc_start: 0.7245 (mp0) cc_final: 0.6651 (mp0) REVERT: D 374 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8188 (mtp-110) REVERT: E 144 LYS cc_start: 0.9615 (tptt) cc_final: 0.9288 (tptp) REVERT: E 199 LYS cc_start: 0.8748 (tppt) cc_final: 0.8428 (tppt) REVERT: E 217 PHE cc_start: 0.8811 (OUTLIER) cc_final: 0.8483 (m-80) REVERT: E 219 MET cc_start: 0.5820 (ppp) cc_final: 0.5531 (ppp) REVERT: F 44 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8644 (mp) outliers start: 48 outliers final: 31 residues processed: 131 average time/residue: 0.1248 time to fit residues: 25.4954 Evaluate side-chains 116 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 80 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 374 ARG Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 690 SER Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 184 LYS Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 91 ASN Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 374 ARG Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 747 LYS Chi-restraints excluded: chain D residue 751 TRP Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 217 PHE Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 91 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 30.0000 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 30.0000 chunk 200 optimal weight: 5.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 0.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 ASN ** E 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.088954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.059425 restraints weight = 59141.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.061436 restraints weight = 29748.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.062768 restraints weight = 19506.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.063665 restraints weight = 14869.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.064216 restraints weight = 12487.803| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.0733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 16751 Z= 0.244 Angle : 0.633 9.903 22736 Z= 0.321 Chirality : 0.044 0.326 2610 Planarity : 0.004 0.037 2896 Dihedral : 6.604 58.965 2357 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.53 % Favored : 93.38 % Rotamer: Outliers : 4.98 % Allowed : 23.71 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.20), residues: 2068 helix: 1.73 (0.21), residues: 620 sheet: -0.92 (0.28), residues: 368 loop : -0.45 (0.21), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 542 TYR 0.029 0.002 TYR C 216 PHE 0.033 0.002 PHE A 586 TRP 0.016 0.002 TRP A 751 HIS 0.003 0.001 HIS A 140 Details of bonding type rmsd covalent geometry : bond 0.00543 (16718) covalent geometry : angle 0.62633 (22666) SS BOND : bond 0.00447 ( 29) SS BOND : angle 1.06075 ( 58) hydrogen bonds : bond 0.04485 ( 668) hydrogen bonds : angle 5.23933 ( 1872) link_NAG-ASN : bond 0.00777 ( 4) link_NAG-ASN : angle 3.40524 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 93 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 252 GLU cc_start: 0.6871 (mp0) cc_final: 0.6574 (mp0) REVERT: A 438 GLN cc_start: 0.8859 (OUTLIER) cc_final: 0.8289 (tm-30) REVERT: C 87 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.7910 (ttp80) REVERT: C 219 MET cc_start: 0.6593 (ptm) cc_final: 0.6275 (ptm) REVERT: B 44 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8794 (mp) REVERT: D 252 GLU cc_start: 0.7035 (mp0) cc_final: 0.6440 (mp0) REVERT: D 344 MET cc_start: 0.8105 (ptp) cc_final: 0.7896 (ptt) REVERT: E 217 PHE cc_start: 0.9048 (OUTLIER) cc_final: 0.8581 (m-80) REVERT: E 219 MET cc_start: 0.6021 (ppp) cc_final: 0.5529 (ppp) REVERT: F 44 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8795 (mp) outliers start: 91 outliers final: 49 residues processed: 174 average time/residue: 0.1195 time to fit residues: 32.1924 Evaluate side-chains 135 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 81 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 91 ASN Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain D residue 157 HIS Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 255 PHE Chi-restraints excluded: chain D residue 271 ASN Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 388 LEU Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 471 CYS Chi-restraints excluded: chain D residue 522 CYS Chi-restraints excluded: chain D residue 549 PHE Chi-restraints excluded: chain D residue 630 GLU Chi-restraints excluded: chain D residue 671 LEU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 217 PHE Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 91 ASN Chi-restraints excluded: chain F residue 138 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 129 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 198 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 39 optimal weight: 0.7980 chunk 195 optimal weight: 30.0000 chunk 74 optimal weight: 4.9990 chunk 199 optimal weight: 0.5980 chunk 42 optimal weight: 7.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 756 ASN ** C 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 299 HIS ** E 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.090405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.060755 restraints weight = 59594.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.062829 restraints weight = 29375.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.064243 restraints weight = 19057.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.065183 restraints weight = 14383.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.065690 restraints weight = 12005.935| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.0946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16751 Z= 0.136 Angle : 0.575 9.580 22736 Z= 0.289 Chirality : 0.043 0.316 2610 Planarity : 0.003 0.038 2896 Dihedral : 5.706 59.629 2323 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.69 % Favored : 95.21 % Rotamer: Outliers : 4.49 % Allowed : 23.77 % Favored : 71.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.20), residues: 2068 helix: 1.74 (0.21), residues: 622 sheet: -0.84 (0.28), residues: 372 loop : -0.31 (0.21), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 123 TYR 0.018 0.001 TYR C 216 PHE 0.038 0.001 PHE A 586 TRP 0.014 0.001 TRP A 751 HIS 0.006 0.001 HIS A 748 Details of bonding type rmsd covalent geometry : bond 0.00307 (16718) covalent geometry : angle 0.56932 (22666) SS BOND : bond 0.00290 ( 29) SS BOND : angle 0.95022 ( 58) hydrogen bonds : bond 0.04030 ( 668) hydrogen bonds : angle 4.92298 ( 1872) link_NAG-ASN : bond 0.00806 ( 4) link_NAG-ASN : angle 3.30482 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 97 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 THR cc_start: 0.8776 (OUTLIER) cc_final: 0.8569 (t) REVERT: A 369 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7033 (mp0) REVERT: A 438 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.8324 (tm-30) REVERT: C 114 ASP cc_start: 0.7693 (p0) cc_final: 0.7275 (p0) REVERT: C 219 MET cc_start: 0.6658 (ptm) cc_final: 0.6385 (ptm) REVERT: B 44 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8644 (mp) REVERT: D 252 GLU cc_start: 0.6907 (mp0) cc_final: 0.6453 (mp0) REVERT: D 255 PHE cc_start: 0.8064 (OUTLIER) cc_final: 0.7857 (p90) REVERT: D 322 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7482 (mp0) REVERT: D 801 TYR cc_start: 0.7711 (t80) cc_final: 0.7113 (t80) REVERT: E 199 LYS cc_start: 0.8545 (tppt) cc_final: 0.8047 (tppt) REVERT: E 217 PHE cc_start: 0.8936 (OUTLIER) cc_final: 0.8478 (m-80) REVERT: E 219 MET cc_start: 0.5995 (ppp) cc_final: 0.5567 (ppp) REVERT: F 44 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8667 (mp) outliers start: 82 outliers final: 44 residues processed: 174 average time/residue: 0.0999 time to fit residues: 27.8558 Evaluate side-chains 140 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 88 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 748 HIS Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 790 PHE Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 184 LYS Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 91 ASN Chi-restraints excluded: chain D residue 35 CYS Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain D residue 255 PHE Chi-restraints excluded: chain D residue 271 ASN Chi-restraints excluded: chain D residue 322 GLU Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 327 THR Chi-restraints excluded: chain D residue 357 ASP Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 471 CYS Chi-restraints excluded: chain D residue 522 CYS Chi-restraints excluded: chain D residue 671 LEU Chi-restraints excluded: chain D residue 790 PHE Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 217 PHE Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 91 ASN Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 138 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 114 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 chunk 160 optimal weight: 5.9990 chunk 202 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 189 optimal weight: 0.0050 chunk 69 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 chunk 105 optimal weight: 0.0670 overall best weight: 0.7534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 GLN ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 ASN D 299 HIS ** E 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.091313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.061835 restraints weight = 59022.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.063991 restraints weight = 28793.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.065410 restraints weight = 18465.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.066340 restraints weight = 13936.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.066954 restraints weight = 11588.089| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 16751 Z= 0.106 Angle : 0.568 9.553 22736 Z= 0.279 Chirality : 0.043 0.318 2610 Planarity : 0.003 0.038 2896 Dihedral : 5.302 59.457 2319 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.50 % Favored : 95.41 % Rotamer: Outliers : 4.16 % Allowed : 23.99 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.20), residues: 2068 helix: 1.75 (0.21), residues: 622 sheet: -0.65 (0.29), residues: 366 loop : -0.20 (0.21), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 123 TYR 0.015 0.001 TYR C 216 PHE 0.039 0.001 PHE E 225 TRP 0.013 0.001 TRP A 751 HIS 0.006 0.001 HIS A 748 Details of bonding type rmsd covalent geometry : bond 0.00236 (16718) covalent geometry : angle 0.56235 (22666) SS BOND : bond 0.00226 ( 29) SS BOND : angle 0.87778 ( 58) hydrogen bonds : bond 0.03695 ( 668) hydrogen bonds : angle 4.74663 ( 1872) link_NAG-ASN : bond 0.00834 ( 4) link_NAG-ASN : angle 3.28979 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 97 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 GLU cc_start: 0.6574 (OUTLIER) cc_final: 0.6158 (mp0) REVERT: A 329 THR cc_start: 0.8696 (OUTLIER) cc_final: 0.8479 (t) REVERT: A 369 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7033 (mp0) REVERT: A 418 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8071 (tt) REVERT: A 438 GLN cc_start: 0.8850 (OUTLIER) cc_final: 0.8080 (tm-30) REVERT: A 782 MET cc_start: 0.7238 (mpp) cc_final: 0.6963 (mpp) REVERT: C 114 ASP cc_start: 0.7802 (p0) cc_final: 0.7083 (p0) REVERT: C 219 MET cc_start: 0.6742 (ptm) cc_final: 0.6497 (ptm) REVERT: B 44 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8676 (mp) REVERT: D 93 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8926 (mp) REVERT: D 252 GLU cc_start: 0.6713 (OUTLIER) cc_final: 0.6248 (mp0) REVERT: D 756 ASN cc_start: 0.8561 (m110) cc_final: 0.8344 (m-40) REVERT: D 801 TYR cc_start: 0.7700 (t80) cc_final: 0.7161 (t80) REVERT: E 199 LYS cc_start: 0.8482 (tppt) cc_final: 0.8005 (tppt) REVERT: E 217 PHE cc_start: 0.8913 (OUTLIER) cc_final: 0.8462 (m-80) REVERT: E 219 MET cc_start: 0.6140 (ppp) cc_final: 0.5767 (ppp) outliers start: 76 outliers final: 42 residues processed: 166 average time/residue: 0.1164 time to fit residues: 30.9713 Evaluate side-chains 137 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 86 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 790 PHE Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 184 LYS Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 91 ASN Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 252 GLU Chi-restraints excluded: chain D residue 271 ASN Chi-restraints excluded: chain D residue 299 HIS Chi-restraints excluded: chain D residue 327 THR Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 357 ASP Chi-restraints excluded: chain D residue 388 LEU Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 471 CYS Chi-restraints excluded: chain D residue 671 LEU Chi-restraints excluded: chain D residue 790 PHE Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 217 PHE Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain F residue 91 ASN Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 138 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 128 optimal weight: 0.9990 chunk 106 optimal weight: 10.0000 chunk 60 optimal weight: 30.0000 chunk 176 optimal weight: 3.9990 chunk 148 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 112 optimal weight: 0.8980 chunk 185 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.090883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.061291 restraints weight = 59013.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.063400 restraints weight = 29151.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.064808 restraints weight = 18940.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.065732 restraints weight = 14282.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.066356 restraints weight = 11921.354| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16751 Z= 0.131 Angle : 0.573 9.749 22736 Z= 0.281 Chirality : 0.042 0.287 2610 Planarity : 0.003 0.037 2896 Dihedral : 5.026 57.710 2311 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.79 % Favored : 95.12 % Rotamer: Outliers : 4.55 % Allowed : 23.33 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.20), residues: 2068 helix: 1.81 (0.21), residues: 622 sheet: -0.66 (0.29), residues: 370 loop : -0.20 (0.21), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 123 TYR 0.013 0.001 TYR C 216 PHE 0.039 0.001 PHE A 586 TRP 0.012 0.001 TRP D 751 HIS 0.009 0.001 HIS A 748 Details of bonding type rmsd covalent geometry : bond 0.00296 (16718) covalent geometry : angle 0.56759 (22666) SS BOND : bond 0.00260 ( 29) SS BOND : angle 0.89744 ( 58) hydrogen bonds : bond 0.03710 ( 668) hydrogen bonds : angle 4.69465 ( 1872) link_NAG-ASN : bond 0.00815 ( 4) link_NAG-ASN : angle 3.22204 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 86 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 GLU cc_start: 0.6700 (OUTLIER) cc_final: 0.6387 (mp0) REVERT: A 255 PHE cc_start: 0.8210 (OUTLIER) cc_final: 0.7944 (p90) REVERT: A 329 THR cc_start: 0.8723 (OUTLIER) cc_final: 0.8495 (t) REVERT: A 369 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7041 (mp0) REVERT: A 418 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8058 (tt) REVERT: A 438 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.7825 (tm-30) REVERT: A 752 LEU cc_start: 0.6978 (mt) cc_final: 0.6734 (mt) REVERT: C 114 ASP cc_start: 0.7708 (p0) cc_final: 0.7039 (p0) REVERT: C 219 MET cc_start: 0.6688 (ptm) cc_final: 0.6487 (ptm) REVERT: B 44 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8673 (mp) REVERT: D 322 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7728 (mp0) REVERT: D 329 THR cc_start: 0.8735 (OUTLIER) cc_final: 0.8521 (t) REVERT: D 756 ASN cc_start: 0.8551 (m110) cc_final: 0.8322 (m110) REVERT: D 801 TYR cc_start: 0.7706 (t80) cc_final: 0.7234 (t80) REVERT: E 217 PHE cc_start: 0.8928 (OUTLIER) cc_final: 0.8521 (m-80) REVERT: E 219 MET cc_start: 0.6208 (ppp) cc_final: 0.5859 (ppp) outliers start: 83 outliers final: 50 residues processed: 161 average time/residue: 0.0976 time to fit residues: 25.7013 Evaluate side-chains 141 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 81 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 790 PHE Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 184 LYS Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 91 ASN Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain D residue 35 CYS Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 271 ASN Chi-restraints excluded: chain D residue 322 GLU Chi-restraints excluded: chain D residue 327 THR Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 357 ASP Chi-restraints excluded: chain D residue 388 LEU Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 470 CYS Chi-restraints excluded: chain D residue 471 CYS Chi-restraints excluded: chain D residue 522 CYS Chi-restraints excluded: chain D residue 547 PHE Chi-restraints excluded: chain D residue 671 LEU Chi-restraints excluded: chain D residue 748 HIS Chi-restraints excluded: chain D residue 790 PHE Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 217 PHE Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain F residue 91 ASN Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 138 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 171 optimal weight: 7.9990 chunk 112 optimal weight: 0.0030 chunk 38 optimal weight: 8.9990 chunk 66 optimal weight: 30.0000 chunk 43 optimal weight: 9.9990 chunk 70 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 42 optimal weight: 9.9990 chunk 198 optimal weight: 5.9990 chunk 104 optimal weight: 20.0000 chunk 115 optimal weight: 5.9990 overall best weight: 5.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 GLN D 299 HIS ** E 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 161 ASN ** E 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.087024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.057460 restraints weight = 59915.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.059403 restraints weight = 29924.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.060694 restraints weight = 19622.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.061536 restraints weight = 14950.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.062096 restraints weight = 12566.506| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.053 16751 Z= 0.387 Angle : 0.787 11.078 22736 Z= 0.390 Chirality : 0.049 0.320 2610 Planarity : 0.004 0.044 2896 Dihedral : 6.068 59.639 2311 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.37 % Favored : 91.54 % Rotamer: Outliers : 5.59 % Allowed : 22.84 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.20), residues: 2068 helix: 1.70 (0.21), residues: 612 sheet: -0.89 (0.29), residues: 352 loop : -0.53 (0.20), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 135 TYR 0.018 0.002 TYR C 216 PHE 0.036 0.002 PHE A 586 TRP 0.018 0.002 TRP D 159 HIS 0.008 0.002 HIS A 748 Details of bonding type rmsd covalent geometry : bond 0.00859 (16718) covalent geometry : angle 0.78147 (22666) SS BOND : bond 0.00611 ( 29) SS BOND : angle 1.33139 ( 58) hydrogen bonds : bond 0.04612 ( 668) hydrogen bonds : angle 5.11930 ( 1872) link_NAG-ASN : bond 0.00846 ( 4) link_NAG-ASN : angle 3.34154 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 84 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 GLU cc_start: 0.7080 (mp0) cc_final: 0.6505 (mp0) REVERT: A 329 THR cc_start: 0.9018 (OUTLIER) cc_final: 0.8774 (t) REVERT: A 369 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7203 (mp0) REVERT: A 752 LEU cc_start: 0.6626 (mt) cc_final: 0.6216 (mt) REVERT: C 219 MET cc_start: 0.7000 (ptm) cc_final: 0.6726 (ptm) REVERT: D 329 THR cc_start: 0.9046 (OUTLIER) cc_final: 0.8796 (t) REVERT: D 369 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7497 (mp0) REVERT: D 756 ASN cc_start: 0.8618 (m110) cc_final: 0.8342 (m110) REVERT: D 801 TYR cc_start: 0.7901 (t80) cc_final: 0.7596 (t80) REVERT: E 136 CYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8495 (p) REVERT: F 44 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8769 (mp) outliers start: 102 outliers final: 64 residues processed: 176 average time/residue: 0.1192 time to fit residues: 32.6632 Evaluate side-chains 148 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 78 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain A residue 760 PHE Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 790 PHE Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 184 LYS Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain B residue 91 ASN Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain D residue 35 CYS Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 255 PHE Chi-restraints excluded: chain D residue 271 ASN Chi-restraints excluded: chain D residue 299 HIS Chi-restraints excluded: chain D residue 327 THR Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 369 GLU Chi-restraints excluded: chain D residue 388 LEU Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 470 CYS Chi-restraints excluded: chain D residue 471 CYS Chi-restraints excluded: chain D residue 522 CYS Chi-restraints excluded: chain D residue 583 SER Chi-restraints excluded: chain D residue 596 PHE Chi-restraints excluded: chain D residue 671 LEU Chi-restraints excluded: chain D residue 748 HIS Chi-restraints excluded: chain D residue 790 PHE Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 136 CYS Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 91 ASN Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 138 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 199 optimal weight: 0.9990 chunk 192 optimal weight: 9.9990 chunk 194 optimal weight: 20.0000 chunk 180 optimal weight: 10.0000 chunk 62 optimal weight: 0.8980 chunk 144 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 153 optimal weight: 6.9990 chunk 112 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.089278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.059779 restraints weight = 58750.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.061857 restraints weight = 28641.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.063243 restraints weight = 18428.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.064113 restraints weight = 13867.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.064724 restraints weight = 11599.824| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16751 Z= 0.169 Angle : 0.639 11.659 22736 Z= 0.314 Chirality : 0.044 0.296 2610 Planarity : 0.003 0.039 2896 Dihedral : 5.319 59.826 2307 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.27 % Favored : 94.63 % Rotamer: Outliers : 4.05 % Allowed : 24.53 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.20), residues: 2068 helix: 1.67 (0.21), residues: 620 sheet: -0.86 (0.28), residues: 368 loop : -0.46 (0.21), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 123 TYR 0.013 0.001 TYR C 216 PHE 0.042 0.001 PHE A 586 TRP 0.010 0.001 TRP D 159 HIS 0.005 0.001 HIS A 748 Details of bonding type rmsd covalent geometry : bond 0.00382 (16718) covalent geometry : angle 0.63423 (22666) SS BOND : bond 0.00351 ( 29) SS BOND : angle 1.03166 ( 58) hydrogen bonds : bond 0.03930 ( 668) hydrogen bonds : angle 4.86846 ( 1872) link_NAG-ASN : bond 0.00770 ( 4) link_NAG-ASN : angle 3.14226 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 91 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 PHE cc_start: 0.8139 (OUTLIER) cc_final: 0.7854 (p90) REVERT: A 329 THR cc_start: 0.8888 (OUTLIER) cc_final: 0.8665 (t) REVERT: A 369 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7037 (mp0) REVERT: A 612 TRP cc_start: 0.9011 (OUTLIER) cc_final: 0.8776 (t-100) REVERT: A 752 LEU cc_start: 0.6478 (mt) cc_final: 0.6134 (mt) REVERT: C 87 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.8064 (ttp80) REVERT: C 114 ASP cc_start: 0.7950 (p0) cc_final: 0.7098 (p0) REVERT: D 322 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7592 (mp0) REVERT: D 329 THR cc_start: 0.8896 (OUTLIER) cc_final: 0.8674 (t) REVERT: D 344 MET cc_start: 0.7978 (ptp) cc_final: 0.7698 (ptp) REVERT: D 369 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7360 (mp0) REVERT: D 420 VAL cc_start: 0.9057 (OUTLIER) cc_final: 0.8853 (t) REVERT: D 716 LEU cc_start: 0.9404 (OUTLIER) cc_final: 0.9111 (pp) REVERT: D 756 ASN cc_start: 0.8587 (m110) cc_final: 0.8344 (m110) REVERT: D 801 TYR cc_start: 0.7759 (t80) cc_final: 0.7366 (t80) REVERT: E 87 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.8336 (ttp80) REVERT: F 44 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8773 (mp) outliers start: 74 outliers final: 53 residues processed: 155 average time/residue: 0.1062 time to fit residues: 26.5642 Evaluate side-chains 147 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 82 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 612 TRP Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 790 PHE Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 184 LYS Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain B residue 91 ASN Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain D residue 35 CYS Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 255 PHE Chi-restraints excluded: chain D residue 271 ASN Chi-restraints excluded: chain D residue 322 GLU Chi-restraints excluded: chain D residue 327 THR Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 369 GLU Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain D residue 470 CYS Chi-restraints excluded: chain D residue 471 CYS Chi-restraints excluded: chain D residue 522 CYS Chi-restraints excluded: chain D residue 583 SER Chi-restraints excluded: chain D residue 596 PHE Chi-restraints excluded: chain D residue 671 LEU Chi-restraints excluded: chain D residue 716 LEU Chi-restraints excluded: chain D residue 790 PHE Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 217 PHE Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 91 ASN Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 138 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 154 optimal weight: 9.9990 chunk 8 optimal weight: 0.6980 chunk 131 optimal weight: 0.9990 chunk 71 optimal weight: 8.9990 chunk 34 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 16 optimal weight: 0.4980 chunk 72 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.090180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.060530 restraints weight = 58650.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.062640 restraints weight = 28562.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.064037 restraints weight = 18369.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.064951 restraints weight = 13833.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.065529 restraints weight = 11549.079| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16751 Z= 0.138 Angle : 0.624 12.314 22736 Z= 0.304 Chirality : 0.044 0.296 2610 Planarity : 0.003 0.038 2896 Dihedral : 5.126 59.732 2307 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.66 % Favored : 94.25 % Rotamer: Outliers : 4.22 % Allowed : 24.42 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.20), residues: 2068 helix: 1.66 (0.21), residues: 622 sheet: -0.76 (0.28), residues: 368 loop : -0.37 (0.21), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 123 TYR 0.015 0.001 TYR E 216 PHE 0.040 0.001 PHE A 586 TRP 0.009 0.001 TRP D 751 HIS 0.004 0.001 HIS A 748 Details of bonding type rmsd covalent geometry : bond 0.00314 (16718) covalent geometry : angle 0.61939 (22666) SS BOND : bond 0.00285 ( 29) SS BOND : angle 0.94203 ( 58) hydrogen bonds : bond 0.03781 ( 668) hydrogen bonds : angle 4.79837 ( 1872) link_NAG-ASN : bond 0.00786 ( 4) link_NAG-ASN : angle 3.15437 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 89 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 PHE cc_start: 0.8082 (OUTLIER) cc_final: 0.7788 (p90) REVERT: A 329 THR cc_start: 0.8824 (OUTLIER) cc_final: 0.8622 (t) REVERT: A 369 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7052 (mp0) REVERT: A 438 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.8260 (tm-30) REVERT: A 612 TRP cc_start: 0.9017 (OUTLIER) cc_final: 0.8788 (t-100) REVERT: A 752 LEU cc_start: 0.6439 (mt) cc_final: 0.6108 (mt) REVERT: C 114 ASP cc_start: 0.7888 (p0) cc_final: 0.7042 (p0) REVERT: C 219 MET cc_start: 0.6797 (ptm) cc_final: 0.6544 (ptm) REVERT: B 139 MET cc_start: 0.6168 (tpt) cc_final: 0.5839 (tpt) REVERT: D 329 THR cc_start: 0.8837 (OUTLIER) cc_final: 0.8627 (t) REVERT: D 344 MET cc_start: 0.7948 (ptp) cc_final: 0.7652 (ptp) REVERT: D 369 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7372 (mp0) REVERT: D 420 VAL cc_start: 0.9102 (OUTLIER) cc_final: 0.8885 (t) REVERT: D 612 TRP cc_start: 0.9010 (OUTLIER) cc_final: 0.8732 (t-100) REVERT: D 716 LEU cc_start: 0.9430 (OUTLIER) cc_final: 0.9150 (pp) REVERT: D 756 ASN cc_start: 0.8557 (m110) cc_final: 0.8282 (m110) REVERT: D 801 TYR cc_start: 0.7758 (t80) cc_final: 0.7399 (t80) outliers start: 77 outliers final: 56 residues processed: 155 average time/residue: 0.1150 time to fit residues: 28.2009 Evaluate side-chains 151 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 85 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 612 TRP Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 790 PHE Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 184 LYS Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain B residue 91 ASN Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain D residue 35 CYS Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 255 PHE Chi-restraints excluded: chain D residue 271 ASN Chi-restraints excluded: chain D residue 299 HIS Chi-restraints excluded: chain D residue 327 THR Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 357 ASP Chi-restraints excluded: chain D residue 369 GLU Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain D residue 470 CYS Chi-restraints excluded: chain D residue 471 CYS Chi-restraints excluded: chain D residue 522 CYS Chi-restraints excluded: chain D residue 583 SER Chi-restraints excluded: chain D residue 596 PHE Chi-restraints excluded: chain D residue 612 TRP Chi-restraints excluded: chain D residue 671 LEU Chi-restraints excluded: chain D residue 716 LEU Chi-restraints excluded: chain D residue 790 PHE Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 217 PHE Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain F residue 91 ASN Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 138 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 67 optimal weight: 0.9990 chunk 202 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 91 optimal weight: 20.0000 chunk 107 optimal weight: 4.9990 chunk 127 optimal weight: 0.7980 chunk 119 optimal weight: 5.9990 chunk 168 optimal weight: 20.0000 chunk 53 optimal weight: 0.9980 chunk 162 optimal weight: 9.9990 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 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 299 HIS ** E 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.089061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.059559 restraints weight = 58619.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.061590 restraints weight = 28808.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.062935 restraints weight = 18644.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.063862 restraints weight = 14074.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.064441 restraints weight = 11730.858| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 16751 Z= 0.203 Angle : 0.661 13.123 22736 Z= 0.322 Chirality : 0.045 0.309 2610 Planarity : 0.004 0.038 2896 Dihedral : 5.281 56.673 2307 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.77 % Favored : 93.13 % Rotamer: Outliers : 4.05 % Allowed : 24.64 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.20), residues: 2068 helix: 1.63 (0.22), residues: 622 sheet: -0.80 (0.28), residues: 368 loop : -0.44 (0.21), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 123 TYR 0.016 0.001 TYR E 216 PHE 0.039 0.001 PHE A 586 TRP 0.013 0.001 TRP A 159 HIS 0.005 0.001 HIS A 748 Details of bonding type rmsd covalent geometry : bond 0.00458 (16718) covalent geometry : angle 0.65587 (22666) SS BOND : bond 0.00362 ( 29) SS BOND : angle 1.00427 ( 58) hydrogen bonds : bond 0.03949 ( 668) hydrogen bonds : angle 4.88401 ( 1872) link_NAG-ASN : bond 0.00796 ( 4) link_NAG-ASN : angle 3.23996 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 86 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 329 THR cc_start: 0.8935 (OUTLIER) cc_final: 0.8686 (t) REVERT: A 369 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7050 (mp0) REVERT: A 418 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8090 (tt) REVERT: A 438 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.7758 (tm-30) REVERT: A 612 TRP cc_start: 0.9023 (OUTLIER) cc_final: 0.8768 (t-100) REVERT: A 752 LEU cc_start: 0.6489 (mt) cc_final: 0.6063 (mt) REVERT: C 87 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.8084 (ttp80) REVERT: C 114 ASP cc_start: 0.7914 (p0) cc_final: 0.7082 (p0) REVERT: C 219 MET cc_start: 0.6964 (ptm) cc_final: 0.6679 (ptm) REVERT: B 139 MET cc_start: 0.6197 (tpt) cc_final: 0.5834 (tpt) REVERT: D 329 THR cc_start: 0.8860 (OUTLIER) cc_final: 0.8645 (t) REVERT: D 344 MET cc_start: 0.8012 (ptp) cc_final: 0.7722 (ptp) REVERT: D 369 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7407 (mp0) REVERT: D 420 VAL cc_start: 0.9117 (OUTLIER) cc_final: 0.8907 (t) REVERT: D 612 TRP cc_start: 0.9002 (OUTLIER) cc_final: 0.8720 (t-100) REVERT: D 716 LEU cc_start: 0.9452 (OUTLIER) cc_final: 0.9179 (pp) REVERT: D 756 ASN cc_start: 0.8632 (m110) cc_final: 0.8334 (m110) REVERT: D 801 TYR cc_start: 0.7733 (t80) cc_final: 0.7175 (t80) REVERT: E 87 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.8316 (ttp80) outliers start: 74 outliers final: 57 residues processed: 151 average time/residue: 0.1113 time to fit residues: 26.9705 Evaluate side-chains 155 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 86 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 612 TRP Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 790 PHE Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 184 LYS Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain B residue 91 ASN Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain D residue 35 CYS Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 255 PHE Chi-restraints excluded: chain D residue 271 ASN Chi-restraints excluded: chain D residue 327 THR Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 357 ASP Chi-restraints excluded: chain D residue 369 GLU Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain D residue 470 CYS Chi-restraints excluded: chain D residue 471 CYS Chi-restraints excluded: chain D residue 522 CYS Chi-restraints excluded: chain D residue 583 SER Chi-restraints excluded: chain D residue 596 PHE Chi-restraints excluded: chain D residue 612 TRP Chi-restraints excluded: chain D residue 671 LEU Chi-restraints excluded: chain D residue 716 LEU Chi-restraints excluded: chain D residue 790 PHE Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain F residue 91 ASN Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 138 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 84 optimal weight: 2.9990 chunk 182 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 59 optimal weight: 9.9990 chunk 125 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 120 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 chunk 77 optimal weight: 9.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.089140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.059656 restraints weight = 58583.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.061690 restraints weight = 28723.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.063040 restraints weight = 18601.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.063932 restraints weight = 14016.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.064529 restraints weight = 11699.088| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16751 Z= 0.195 Angle : 0.654 13.874 22736 Z= 0.319 Chirality : 0.045 0.307 2610 Planarity : 0.004 0.038 2896 Dihedral : 5.262 56.280 2307 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.58 % Favored : 93.33 % Rotamer: Outliers : 3.89 % Allowed : 24.92 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.20), residues: 2068 helix: 1.60 (0.22), residues: 622 sheet: -0.81 (0.28), residues: 368 loop : -0.43 (0.21), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 123 TYR 0.018 0.001 TYR E 216 PHE 0.042 0.001 PHE A 586 TRP 0.012 0.001 TRP A 159 HIS 0.004 0.001 HIS A 748 Details of bonding type rmsd covalent geometry : bond 0.00439 (16718) covalent geometry : angle 0.64853 (22666) SS BOND : bond 0.00348 ( 29) SS BOND : angle 0.97794 ( 58) hydrogen bonds : bond 0.03913 ( 668) hydrogen bonds : angle 4.86437 ( 1872) link_NAG-ASN : bond 0.00770 ( 4) link_NAG-ASN : angle 3.22507 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 84 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 THR cc_start: 0.8891 (OUTLIER) cc_final: 0.8665 (t) REVERT: A 369 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7039 (mp0) REVERT: A 418 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8012 (tt) REVERT: A 438 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.7757 (tm-30) REVERT: A 612 TRP cc_start: 0.9116 (OUTLIER) cc_final: 0.8842 (t-100) REVERT: A 752 LEU cc_start: 0.6499 (mt) cc_final: 0.6065 (mt) REVERT: C 114 ASP cc_start: 0.7924 (p0) cc_final: 0.7138 (p0) REVERT: B 139 MET cc_start: 0.6194 (tpt) cc_final: 0.5801 (tpt) REVERT: D 329 THR cc_start: 0.8878 (OUTLIER) cc_final: 0.8659 (t) REVERT: D 369 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7384 (mp0) REVERT: D 420 VAL cc_start: 0.9123 (OUTLIER) cc_final: 0.8905 (t) REVERT: D 612 TRP cc_start: 0.8982 (OUTLIER) cc_final: 0.8689 (t-100) REVERT: D 716 LEU cc_start: 0.9454 (OUTLIER) cc_final: 0.9183 (pp) REVERT: D 756 ASN cc_start: 0.8644 (m110) cc_final: 0.8349 (m110) REVERT: D 801 TYR cc_start: 0.7767 (t80) cc_final: 0.7182 (t80) REVERT: E 87 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.8299 (ttp80) outliers start: 71 outliers final: 56 residues processed: 146 average time/residue: 0.1066 time to fit residues: 24.8031 Evaluate side-chains 150 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 83 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 612 TRP Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 790 PHE Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 184 LYS Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain B residue 91 ASN Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain D residue 35 CYS Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 255 PHE Chi-restraints excluded: chain D residue 271 ASN Chi-restraints excluded: chain D residue 327 THR Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 357 ASP Chi-restraints excluded: chain D residue 369 GLU Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain D residue 470 CYS Chi-restraints excluded: chain D residue 471 CYS Chi-restraints excluded: chain D residue 522 CYS Chi-restraints excluded: chain D residue 583 SER Chi-restraints excluded: chain D residue 596 PHE Chi-restraints excluded: chain D residue 612 TRP Chi-restraints excluded: chain D residue 671 LEU Chi-restraints excluded: chain D residue 716 LEU Chi-restraints excluded: chain D residue 790 PHE Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain F residue 91 ASN Chi-restraints excluded: chain F residue 135 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 81 optimal weight: 4.9990 chunk 16 optimal weight: 0.1980 chunk 57 optimal weight: 8.9990 chunk 180 optimal weight: 9.9990 chunk 106 optimal weight: 6.9990 chunk 128 optimal weight: 0.8980 chunk 47 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 196 optimal weight: 7.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 GLN ** E 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.089836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.060255 restraints weight = 58371.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.062347 restraints weight = 28461.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.063753 restraints weight = 18343.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.064678 restraints weight = 13797.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.065227 restraints weight = 11470.919| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16751 Z= 0.155 Angle : 0.637 13.591 22736 Z= 0.309 Chirality : 0.044 0.305 2610 Planarity : 0.003 0.038 2896 Dihedral : 5.133 56.298 2307 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.90 % Favored : 94.00 % Rotamer: Outliers : 3.83 % Allowed : 25.03 % Favored : 71.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.20), residues: 2068 helix: 1.62 (0.22), residues: 622 sheet: -0.55 (0.29), residues: 346 loop : -0.42 (0.21), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 123 TYR 0.018 0.001 TYR E 216 PHE 0.041 0.001 PHE A 586 TRP 0.010 0.001 TRP A 159 HIS 0.003 0.001 HIS A 748 Details of bonding type rmsd covalent geometry : bond 0.00352 (16718) covalent geometry : angle 0.63240 (22666) SS BOND : bond 0.00291 ( 29) SS BOND : angle 0.92370 ( 58) hydrogen bonds : bond 0.03784 ( 668) hydrogen bonds : angle 4.80405 ( 1872) link_NAG-ASN : bond 0.00775 ( 4) link_NAG-ASN : angle 3.19105 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2939.44 seconds wall clock time: 51 minutes 38.68 seconds (3098.68 seconds total)