Starting phenix.real_space_refine on Tue Aug 26 10:26:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9czm_46421/08_2025/9czm_46421_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9czm_46421/08_2025/9czm_46421.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9czm_46421/08_2025/9czm_46421_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9czm_46421/08_2025/9czm_46421_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9czm_46421/08_2025/9czm_46421.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9czm_46421/08_2025/9czm_46421.map" } resolution = 2.57 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= 0.003 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: 8 Type Number sf(0) Gaussians Ca 8 9.91 5 K 4 8.98 5 P 28 5.49 5 Mg 4 5.21 5 S 240 5.16 5 C 23512 2.51 5 N 5719 2.21 5 O 6537 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 177 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36052 Number of models: 1 Model: "" Number of chains: 12 Chain: "E" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1579 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 8, 'TRANS': 191} Chain: "F" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1579 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 8, 'TRANS': 191} Chain: "H" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1579 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 8, 'TRANS': 191} Chain: "A" Number of atoms: 7087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 890, 7087 Classifications: {'peptide': 890} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 862} Chain breaks: 5 Chain: "B" Number of atoms: 7087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 890, 7087 Classifications: {'peptide': 890} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 862} Chain breaks: 5 Chain: "C" Number of atoms: 7087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 890, 7087 Classifications: {'peptide': 890} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 862} Chain breaks: 5 Chain: "D" Number of atoms: 7087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 890, 7087 Classifications: {'peptide': 890} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 862} Chain breaks: 5 Chain: "G" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1640 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 8, 'TRANS': 198} Chain breaks: 1 Chain: "A" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 298 Unusual residues: {' K': 4, ' CA': 2, ' MG': 1, 'CLR': 2, 'POV': 7} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 3, 'POV:plan-3': 1} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 369 Unusual residues: {' CA': 2, ' MG': 1, 'CLR': 2, 'POV': 9} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 175 Unresolved non-hydrogen dihedrals: 149 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 3, 'POV:plan-3': 1} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 331 Unusual residues: {' CA': 2, ' MG': 1, 'CLR': 2, 'POV': 8} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 3, 'POV:plan-3': 1} Unresolved non-hydrogen planarities: 15 Chain: "D" Number of atoms: 329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 329 Unusual residues: {' CA': 2, ' MG': 1, 'CLR': 2, 'POV': 8} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 146 Unresolved non-hydrogen angles: 163 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 3, 'POV:plan-3': 1} Unresolved non-hydrogen planarities: 15 Time building chain proxies: 7.48, per 1000 atoms: 0.21 Number of scatterers: 36052 At special positions: 0 Unit cell: (147.675, 169.125, 162.525, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Ca 8 19.99 K 4 19.00 S 240 16.00 P 28 15.00 Mg 4 11.99 O 6537 8.00 N 5719 7.00 C 23512 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 178 " distance=2.02 Simple disulfide: pdb=" SG CYS E 98 " - pdb=" SG CYS E 149 " distance=2.03 Simple disulfide: pdb=" SG CYS E 102 " - pdb=" SG CYS E 106 " distance=2.04 Simple disulfide: pdb=" SG CYS E 114 " - pdb=" SG CYS E 143 " distance=2.03 Simple disulfide: pdb=" SG CYS F 84 " - pdb=" SG CYS F 178 " distance=2.02 Simple disulfide: pdb=" SG CYS F 98 " - pdb=" SG CYS F 149 " distance=2.03 Simple disulfide: pdb=" SG CYS F 102 " - pdb=" SG CYS F 106 " distance=2.04 Simple disulfide: pdb=" SG CYS F 114 " - pdb=" SG CYS F 143 " distance=2.03 Simple disulfide: pdb=" SG CYS H 84 " - pdb=" SG CYS H 178 " distance=2.03 Simple disulfide: pdb=" SG CYS H 98 " - pdb=" SG CYS H 149 " distance=2.03 Simple disulfide: pdb=" SG CYS H 102 " - pdb=" SG CYS H 106 " distance=2.04 Simple disulfide: pdb=" SG CYS H 114 " - pdb=" SG CYS H 143 " distance=2.03 Simple disulfide: pdb=" SG CYS G 84 " - pdb=" SG CYS G 178 " distance=2.02 Simple disulfide: pdb=" SG CYS G 98 " - pdb=" SG CYS G 149 " distance=2.03 Simple disulfide: pdb=" SG CYS G 102 " - pdb=" SG CYS G 106 " distance=2.04 Simple disulfide: pdb=" SG CYS G 114 " - pdb=" SG CYS G 143 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.40 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 1.4 microseconds 8618 Ramachandran restraints generated. 4309 Oldfield, 0 Emsley, 4309 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8276 Finding SS restraints... Secondary structure from input PDB file: 185 helices and 28 sheets defined 54.1% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'E' and resid 40 through 78 removed outlier: 4.495A pdb=" N SER E 71 " --> pdb=" O PHE E 67 " (cutoff:3.500A) Proline residue: E 72 - end of helix Processing helix chain 'E' and resid 133 through 140 removed outlier: 3.560A pdb=" N LEU E 137 " --> pdb=" O ASP E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 170 removed outlier: 4.204A pdb=" N TYR E 166 " --> pdb=" O ASN E 162 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TRP E 167 " --> pdb=" O TRP E 163 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP E 169 " --> pdb=" O GLN E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 235 removed outlier: 3.819A pdb=" N LEU E 200 " --> pdb=" O ASP E 196 " (cutoff:3.500A) Proline residue: E 207 - end of helix removed outlier: 3.706A pdb=" N VAL E 229 " --> pdb=" O LYS E 225 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LYS E 230 " --> pdb=" O SER E 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 78 removed outlier: 4.495A pdb=" N SER F 71 " --> pdb=" O PHE F 67 " (cutoff:3.500A) Proline residue: F 72 - end of helix Processing helix chain 'F' and resid 133 through 140 removed outlier: 3.560A pdb=" N LEU F 137 " --> pdb=" O ASP F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 170 removed outlier: 4.204A pdb=" N TYR F 166 " --> pdb=" O ASN F 162 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TRP F 167 " --> pdb=" O TRP F 163 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP F 169 " --> pdb=" O GLN F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 235 removed outlier: 3.819A pdb=" N LEU F 200 " --> pdb=" O ASP F 196 " (cutoff:3.500A) Proline residue: F 207 - end of helix removed outlier: 3.706A pdb=" N VAL F 229 " --> pdb=" O LYS F 225 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LYS F 230 " --> pdb=" O SER F 226 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 78 removed outlier: 4.494A pdb=" N SER H 71 " --> pdb=" O PHE H 67 " (cutoff:3.500A) Proline residue: H 72 - end of helix Processing helix chain 'H' and resid 133 through 140 removed outlier: 3.560A pdb=" N LEU H 137 " --> pdb=" O ASP H 133 " (cutoff:3.500A) Processing helix chain 'H' and resid 152 through 170 removed outlier: 4.204A pdb=" N TYR H 166 " --> pdb=" O ASN H 162 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TRP H 167 " --> pdb=" O TRP H 163 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP H 169 " --> pdb=" O GLN H 165 " (cutoff:3.500A) Processing helix chain 'H' and resid 196 through 235 removed outlier: 3.820A pdb=" N LEU H 200 " --> pdb=" O ASP H 196 " (cutoff:3.500A) Proline residue: H 207 - end of helix removed outlier: 3.706A pdb=" N VAL H 229 " --> pdb=" O LYS H 225 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LYS H 230 " --> pdb=" O SER H 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 54 removed outlier: 3.762A pdb=" N PHE A 25 " --> pdb=" O MET A 21 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N TYR A 48 " --> pdb=" O ARG A 44 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR A 51 " --> pdb=" O LYS A 47 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL A 52 " --> pdb=" O TYR A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 106 Processing helix chain 'A' and resid 109 through 134 Processing helix chain 'A' and resid 147 through 171 removed outlier: 3.628A pdb=" N GLN A 151 " --> pdb=" O ASP A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 179 Processing helix chain 'A' and resid 180 through 188 Processing helix chain 'A' and resid 190 through 200 removed outlier: 3.710A pdb=" N PHE A 194 " --> pdb=" O VAL A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 215 removed outlier: 4.349A pdb=" N PHE A 208 " --> pdb=" O GLY A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 224 Processing helix chain 'A' and resid 229 through 259 Processing helix chain 'A' and resid 273 through 286 Processing helix chain 'A' and resid 297 through 325 removed outlier: 3.654A pdb=" N LEU A 312 " --> pdb=" O ILE A 308 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ALA A 313 " --> pdb=" O LEU A 309 " (cutoff:3.500A) Proline residue: A 320 - end of helix Processing helix chain 'A' and resid 352 through 364 Processing helix chain 'A' and resid 384 through 393 Processing helix chain 'A' and resid 407 through 414 Processing helix chain 'A' and resid 415 through 419 Processing helix chain 'A' and resid 432 through 451 Processing helix chain 'A' and resid 462 through 470 removed outlier: 3.539A pdb=" N LYS A 466 " --> pdb=" O GLN A 462 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N HIS A 468 " --> pdb=" O HIS A 464 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 470 " --> pdb=" O LYS A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 480 removed outlier: 3.644A pdb=" N GLY A 480 " --> pdb=" O TRP A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 500 removed outlier: 3.782A pdb=" N LEU A 499 " --> pdb=" O ALA A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 512 removed outlier: 3.717A pdb=" N PHE A 511 " --> pdb=" O LEU A 507 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER A 512 " --> pdb=" O ALA A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 533 removed outlier: 4.088A pdb=" N TYR A 527 " --> pdb=" O THR A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 560 Processing helix chain 'A' and resid 601 through 606 removed outlier: 3.546A pdb=" N VAL A 605 " --> pdb=" O ASP A 601 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS A 606 " --> pdb=" O ALA A 602 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 601 through 606' Processing helix chain 'A' and resid 607 through 609 No H-bonds generated for 'chain 'A' and resid 607 through 609' Processing helix chain 'A' and resid 699 through 704 Processing helix chain 'A' and resid 706 through 713 Processing helix chain 'A' and resid 734 through 739 Processing helix chain 'A' and resid 740 through 743 removed outlier: 3.596A pdb=" N ALA A 743 " --> pdb=" O PRO A 740 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 740 through 743' Processing helix chain 'A' and resid 759 through 771 removed outlier: 5.031A pdb=" N GLU A 768 " --> pdb=" O LYS A 764 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N THR A 769 " --> pdb=" O ARG A 765 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU A 770 " --> pdb=" O GLU A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 792 Processing helix chain 'A' and resid 793 through 795 No H-bonds generated for 'chain 'A' and resid 793 through 795' Processing helix chain 'A' and resid 817 through 830 Processing helix chain 'A' and resid 884 through 891 removed outlier: 3.870A pdb=" N GLN A 889 " --> pdb=" O THR A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 905 Processing helix chain 'A' and resid 906 through 911 Processing helix chain 'A' and resid 916 through 920 Processing helix chain 'A' and resid 921 through 930 removed outlier: 4.461A pdb=" N SER A 925 " --> pdb=" O ASP A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 943 Processing helix chain 'A' and resid 946 through 957 Processing helix chain 'A' and resid 965 through 971 removed outlier: 3.773A pdb=" N ASN A 971 " --> pdb=" O GLN A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 994 Processing helix chain 'B' and resid 21 through 54 removed outlier: 3.762A pdb=" N PHE B 25 " --> pdb=" O MET B 21 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TYR B 48 " --> pdb=" O ARG B 44 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU B 49 " --> pdb=" O THR B 45 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR B 51 " --> pdb=" O LYS B 47 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL B 52 " --> pdb=" O TYR B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 106 Processing helix chain 'B' and resid 109 through 134 Processing helix chain 'B' and resid 147 through 171 removed outlier: 3.627A pdb=" N GLN B 151 " --> pdb=" O ASP B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 179 Processing helix chain 'B' and resid 180 through 188 Processing helix chain 'B' and resid 190 through 200 removed outlier: 3.709A pdb=" N PHE B 194 " --> pdb=" O VAL B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 215 removed outlier: 4.349A pdb=" N PHE B 208 " --> pdb=" O GLY B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 224 Processing helix chain 'B' and resid 229 through 259 Processing helix chain 'B' and resid 273 through 286 Processing helix chain 'B' and resid 297 through 325 removed outlier: 3.654A pdb=" N LEU B 312 " --> pdb=" O ILE B 308 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ALA B 313 " --> pdb=" O LEU B 309 " (cutoff:3.500A) Proline residue: B 320 - end of helix Processing helix chain 'B' and resid 352 through 364 Processing helix chain 'B' and resid 384 through 393 Processing helix chain 'B' and resid 407 through 414 Processing helix chain 'B' and resid 415 through 419 Processing helix chain 'B' and resid 432 through 451 Processing helix chain 'B' and resid 462 through 470 removed outlier: 3.539A pdb=" N LYS B 466 " --> pdb=" O GLN B 462 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N HIS B 468 " --> pdb=" O HIS B 464 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU B 470 " --> pdb=" O LYS B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 480 removed outlier: 3.644A pdb=" N GLY B 480 " --> pdb=" O TRP B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 500 removed outlier: 3.782A pdb=" N LEU B 499 " --> pdb=" O ALA B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 512 removed outlier: 3.718A pdb=" N PHE B 511 " --> pdb=" O LEU B 507 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER B 512 " --> pdb=" O ALA B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 533 removed outlier: 4.088A pdb=" N TYR B 527 " --> pdb=" O THR B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 560 Processing helix chain 'B' and resid 601 through 606 removed outlier: 3.547A pdb=" N VAL B 605 " --> pdb=" O ASP B 601 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS B 606 " --> pdb=" O ALA B 602 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 601 through 606' Processing helix chain 'B' and resid 607 through 609 No H-bonds generated for 'chain 'B' and resid 607 through 609' Processing helix chain 'B' and resid 699 through 704 Processing helix chain 'B' and resid 706 through 713 Processing helix chain 'B' and resid 734 through 739 Processing helix chain 'B' and resid 740 through 743 removed outlier: 3.596A pdb=" N ALA B 743 " --> pdb=" O PRO B 740 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 740 through 743' Processing helix chain 'B' and resid 759 through 771 removed outlier: 5.031A pdb=" N GLU B 768 " --> pdb=" O LYS B 764 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N THR B 769 " --> pdb=" O ARG B 765 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU B 770 " --> pdb=" O GLU B 766 " (cutoff:3.500A) Processing helix chain 'B' and resid 785 through 792 Processing helix chain 'B' and resid 793 through 795 No H-bonds generated for 'chain 'B' and resid 793 through 795' Processing helix chain 'B' and resid 817 through 830 Processing helix chain 'B' and resid 884 through 891 removed outlier: 3.871A pdb=" N GLN B 889 " --> pdb=" O THR B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 902 through 905 Processing helix chain 'B' and resid 906 through 911 Processing helix chain 'B' and resid 916 through 920 Processing helix chain 'B' and resid 921 through 930 removed outlier: 4.461A pdb=" N SER B 925 " --> pdb=" O ASP B 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 932 through 943 Processing helix chain 'B' and resid 946 through 957 Processing helix chain 'B' and resid 965 through 971 removed outlier: 3.773A pdb=" N ASN B 971 " --> pdb=" O GLN B 967 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 994 Processing helix chain 'C' and resid 21 through 54 removed outlier: 3.762A pdb=" N PHE C 25 " --> pdb=" O MET C 21 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N TYR C 48 " --> pdb=" O ARG C 44 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU C 49 " --> pdb=" O THR C 45 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR C 51 " --> pdb=" O LYS C 47 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL C 52 " --> pdb=" O TYR C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 106 Processing helix chain 'C' and resid 109 through 134 Processing helix chain 'C' and resid 147 through 171 removed outlier: 3.628A pdb=" N GLN C 151 " --> pdb=" O ASP C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 179 Processing helix chain 'C' and resid 180 through 188 Processing helix chain 'C' and resid 190 through 200 removed outlier: 3.709A pdb=" N PHE C 194 " --> pdb=" O VAL C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 215 removed outlier: 4.350A pdb=" N PHE C 208 " --> pdb=" O GLY C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 224 Processing helix chain 'C' and resid 229 through 259 Processing helix chain 'C' and resid 273 through 286 Processing helix chain 'C' and resid 297 through 325 removed outlier: 3.654A pdb=" N LEU C 312 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ALA C 313 " --> pdb=" O LEU C 309 " (cutoff:3.500A) Proline residue: C 320 - end of helix Processing helix chain 'C' and resid 352 through 364 Processing helix chain 'C' and resid 384 through 393 Processing helix chain 'C' and resid 407 through 414 Processing helix chain 'C' and resid 415 through 419 Processing helix chain 'C' and resid 432 through 451 Processing helix chain 'C' and resid 462 through 470 removed outlier: 3.539A pdb=" N LYS C 466 " --> pdb=" O GLN C 462 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N HIS C 468 " --> pdb=" O HIS C 464 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU C 470 " --> pdb=" O LYS C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 480 removed outlier: 3.645A pdb=" N GLY C 480 " --> pdb=" O TRP C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 500 removed outlier: 3.782A pdb=" N LEU C 499 " --> pdb=" O ALA C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 512 removed outlier: 3.717A pdb=" N PHE C 511 " --> pdb=" O LEU C 507 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER C 512 " --> pdb=" O ALA C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 533 removed outlier: 4.087A pdb=" N TYR C 527 " --> pdb=" O THR C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 560 Processing helix chain 'C' and resid 601 through 606 removed outlier: 3.546A pdb=" N VAL C 605 " --> pdb=" O ASP C 601 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS C 606 " --> pdb=" O ALA C 602 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 601 through 606' Processing helix chain 'C' and resid 607 through 609 No H-bonds generated for 'chain 'C' and resid 607 through 609' Processing helix chain 'C' and resid 699 through 704 Processing helix chain 'C' and resid 706 through 713 Processing helix chain 'C' and resid 734 through 739 Processing helix chain 'C' and resid 740 through 743 removed outlier: 3.596A pdb=" N ALA C 743 " --> pdb=" O PRO C 740 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 740 through 743' Processing helix chain 'C' and resid 759 through 771 removed outlier: 5.031A pdb=" N GLU C 768 " --> pdb=" O LYS C 764 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N THR C 769 " --> pdb=" O ARG C 765 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU C 770 " --> pdb=" O GLU C 766 " (cutoff:3.500A) Processing helix chain 'C' and resid 785 through 792 Processing helix chain 'C' and resid 793 through 795 No H-bonds generated for 'chain 'C' and resid 793 through 795' Processing helix chain 'C' and resid 817 through 830 Processing helix chain 'C' and resid 884 through 891 removed outlier: 3.870A pdb=" N GLN C 889 " --> pdb=" O THR C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 902 through 905 Processing helix chain 'C' and resid 906 through 911 Processing helix chain 'C' and resid 916 through 920 Processing helix chain 'C' and resid 921 through 930 removed outlier: 4.462A pdb=" N SER C 925 " --> pdb=" O ASP C 921 " (cutoff:3.500A) Processing helix chain 'C' and resid 932 through 943 Processing helix chain 'C' and resid 946 through 957 Processing helix chain 'C' and resid 965 through 971 removed outlier: 3.772A pdb=" N ASN C 971 " --> pdb=" O GLN C 967 " (cutoff:3.500A) Processing helix chain 'C' and resid 987 through 994 Processing helix chain 'D' and resid 21 through 54 removed outlier: 3.762A pdb=" N PHE D 25 " --> pdb=" O MET D 21 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TYR D 48 " --> pdb=" O ARG D 44 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU D 49 " --> pdb=" O THR D 45 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR D 51 " --> pdb=" O LYS D 47 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL D 52 " --> pdb=" O TYR D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 106 Processing helix chain 'D' and resid 109 through 134 Processing helix chain 'D' and resid 147 through 171 removed outlier: 3.627A pdb=" N GLN D 151 " --> pdb=" O ASP D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 179 Processing helix chain 'D' and resid 180 through 188 Processing helix chain 'D' and resid 190 through 200 removed outlier: 3.710A pdb=" N PHE D 194 " --> pdb=" O VAL D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 215 removed outlier: 4.349A pdb=" N PHE D 208 " --> pdb=" O GLY D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 224 Processing helix chain 'D' and resid 229 through 259 Processing helix chain 'D' and resid 273 through 286 Processing helix chain 'D' and resid 297 through 325 removed outlier: 3.654A pdb=" N LEU D 312 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ALA D 313 " --> pdb=" O LEU D 309 " (cutoff:3.500A) Proline residue: D 320 - end of helix Processing helix chain 'D' and resid 352 through 364 Processing helix chain 'D' and resid 384 through 393 Processing helix chain 'D' and resid 407 through 414 Processing helix chain 'D' and resid 415 through 419 Processing helix chain 'D' and resid 432 through 451 Processing helix chain 'D' and resid 462 through 470 removed outlier: 3.540A pdb=" N LYS D 466 " --> pdb=" O GLN D 462 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N HIS D 468 " --> pdb=" O HIS D 464 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU D 470 " --> pdb=" O LYS D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 480 removed outlier: 3.644A pdb=" N GLY D 480 " --> pdb=" O TRP D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 500 removed outlier: 3.782A pdb=" N LEU D 499 " --> pdb=" O ALA D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 512 removed outlier: 3.718A pdb=" N PHE D 511 " --> pdb=" O LEU D 507 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER D 512 " --> pdb=" O ALA D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 533 removed outlier: 4.089A pdb=" N TYR D 527 " --> pdb=" O THR D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 560 Processing helix chain 'D' and resid 601 through 606 removed outlier: 3.546A pdb=" N VAL D 605 " --> pdb=" O ASP D 601 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS D 606 " --> pdb=" O ALA D 602 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 601 through 606' Processing helix chain 'D' and resid 607 through 609 No H-bonds generated for 'chain 'D' and resid 607 through 609' Processing helix chain 'D' and resid 699 through 704 Processing helix chain 'D' and resid 706 through 713 Processing helix chain 'D' and resid 734 through 739 Processing helix chain 'D' and resid 740 through 743 removed outlier: 3.596A pdb=" N ALA D 743 " --> pdb=" O PRO D 740 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 740 through 743' Processing helix chain 'D' and resid 759 through 771 removed outlier: 5.030A pdb=" N GLU D 768 " --> pdb=" O LYS D 764 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N THR D 769 " --> pdb=" O ARG D 765 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU D 770 " --> pdb=" O GLU D 766 " (cutoff:3.500A) Processing helix chain 'D' and resid 785 through 792 Processing helix chain 'D' and resid 793 through 795 No H-bonds generated for 'chain 'D' and resid 793 through 795' Processing helix chain 'D' and resid 817 through 830 Processing helix chain 'D' and resid 884 through 891 removed outlier: 3.870A pdb=" N GLN D 889 " --> pdb=" O THR D 886 " (cutoff:3.500A) Processing helix chain 'D' and resid 902 through 905 Processing helix chain 'D' and resid 906 through 911 Processing helix chain 'D' and resid 916 through 920 Processing helix chain 'D' and resid 921 through 930 removed outlier: 4.462A pdb=" N SER D 925 " --> pdb=" O ASP D 921 " (cutoff:3.500A) Processing helix chain 'D' and resid 932 through 943 Processing helix chain 'D' and resid 946 through 957 Processing helix chain 'D' and resid 965 through 971 removed outlier: 3.773A pdb=" N ASN D 971 " --> pdb=" O GLN D 967 " (cutoff:3.500A) Processing helix chain 'D' and resid 987 through 994 Processing helix chain 'G' and resid 2 through 6 Processing helix chain 'G' and resid 40 through 78 removed outlier: 4.495A pdb=" N SER G 71 " --> pdb=" O PHE G 67 " (cutoff:3.500A) Proline residue: G 72 - end of helix Processing helix chain 'G' and resid 133 through 140 removed outlier: 3.560A pdb=" N LEU G 137 " --> pdb=" O ASP G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 152 through 170 removed outlier: 4.204A pdb=" N TYR G 166 " --> pdb=" O ASN G 162 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TRP G 167 " --> pdb=" O TRP G 163 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASP G 169 " --> pdb=" O GLN G 165 " (cutoff:3.500A) Processing helix chain 'G' and resid 196 through 235 removed outlier: 3.819A pdb=" N LEU G 200 " --> pdb=" O ASP G 196 " (cutoff:3.500A) Proline residue: G 207 - end of helix removed outlier: 3.706A pdb=" N VAL G 229 " --> pdb=" O LYS G 225 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LYS G 230 " --> pdb=" O SER G 226 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 80 through 99 removed outlier: 5.944A pdb=" N VAL E 86 " --> pdb=" O ASN E 120 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N ASN E 120 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N CYS E 114 " --> pdb=" O ILE E 92 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N GLU E 94 " --> pdb=" O TYR E 112 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N TYR E 112 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N PHE E 96 " --> pdb=" O SER E 110 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N SER E 110 " --> pdb=" O PHE E 96 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N VAL E 117 " --> pdb=" O LEU E 130 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA E 128 " --> pdb=" O VAL E 119 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ASP E 188 " --> pdb=" O ASN E 181 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ASN E 181 " --> pdb=" O ASP E 188 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 80 through 99 removed outlier: 5.944A pdb=" N VAL F 86 " --> pdb=" O ASN F 120 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N ASN F 120 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N CYS F 114 " --> pdb=" O ILE F 92 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N GLU F 94 " --> pdb=" O TYR F 112 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N TYR F 112 " --> pdb=" O GLU F 94 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N PHE F 96 " --> pdb=" O SER F 110 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N SER F 110 " --> pdb=" O PHE F 96 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N VAL F 117 " --> pdb=" O LEU F 130 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA F 128 " --> pdb=" O VAL F 119 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ASP F 188 " --> pdb=" O ASN F 181 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ASN F 181 " --> pdb=" O ASP F 188 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 80 through 99 removed outlier: 5.944A pdb=" N VAL H 86 " --> pdb=" O ASN H 120 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ASN H 120 " --> pdb=" O VAL H 86 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N CYS H 114 " --> pdb=" O ILE H 92 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N GLU H 94 " --> pdb=" O TYR H 112 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N TYR H 112 " --> pdb=" O GLU H 94 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N PHE H 96 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N SER H 110 " --> pdb=" O PHE H 96 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N VAL H 117 " --> pdb=" O LEU H 130 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA H 128 " --> pdb=" O VAL H 119 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ASP H 188 " --> pdb=" O ASN H 181 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ASN H 181 " --> pdb=" O ASP H 188 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 139 through 141 Processing sheet with id=AA5, first strand: chain 'A' and resid 398 through 402 removed outlier: 4.586A pdb=" N GLY A 349 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N HIS A 344 " --> pdb=" O ALA A 421 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N LEU A 423 " --> pdb=" O HIS A 344 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL A 346 " --> pdb=" O LEU A 423 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N LEU A 425 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N CYS A 348 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE A 456 " --> pdb=" O ASP A 482 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ILE A 484 " --> pdb=" O ILE A 456 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N THR A 458 " --> pdb=" O ILE A 484 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 535 through 540 Processing sheet with id=AA7, first strand: chain 'A' and resid 686 through 687 removed outlier: 4.165A pdb=" N TYR A 686 " --> pdb=" O GLY A 962 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 776 through 780 removed outlier: 6.613A pdb=" N ILE A 754 " --> pdb=" O SER A 777 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N LEU A 779 " --> pdb=" O ILE A 754 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N PHE A 756 " --> pdb=" O LEU A 779 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N HIS A 718 " --> pdb=" O CYS A 797 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N SER A 804 " --> pdb=" O GLU A 881 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N PHE A 915 " --> pdb=" O ILE A 878 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N THR A 880 " --> pdb=" O PHE A 915 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 976 through 981 removed outlier: 3.636A pdb=" N GLY A1013 " --> pdb=" O PHE A1050 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU A1052 " --> pdb=" O CYS A1011 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N CYS A1011 " --> pdb=" O LEU A1052 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 139 through 141 Processing sheet with id=AB2, first strand: chain 'B' and resid 398 through 402 removed outlier: 4.587A pdb=" N GLY B 349 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N HIS B 344 " --> pdb=" O ALA B 421 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N LEU B 423 " --> pdb=" O HIS B 344 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL B 346 " --> pdb=" O LEU B 423 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N LEU B 425 " --> pdb=" O VAL B 346 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N CYS B 348 " --> pdb=" O LEU B 425 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE B 456 " --> pdb=" O ASP B 482 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N ILE B 484 " --> pdb=" O ILE B 456 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N THR B 458 " --> pdb=" O ILE B 484 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 535 through 540 Processing sheet with id=AB4, first strand: chain 'B' and resid 686 through 687 removed outlier: 4.165A pdb=" N TYR B 686 " --> pdb=" O GLY B 962 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 776 through 780 removed outlier: 6.613A pdb=" N ILE B 754 " --> pdb=" O SER B 777 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N LEU B 779 " --> pdb=" O ILE B 754 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N PHE B 756 " --> pdb=" O LEU B 779 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N HIS B 718 " --> pdb=" O CYS B 797 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N SER B 804 " --> pdb=" O GLU B 881 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N PHE B 915 " --> pdb=" O ILE B 878 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N THR B 880 " --> pdb=" O PHE B 915 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 976 through 981 removed outlier: 3.636A pdb=" N GLY B1013 " --> pdb=" O PHE B1050 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU B1052 " --> pdb=" O CYS B1011 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N CYS B1011 " --> pdb=" O LEU B1052 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 139 through 141 Processing sheet with id=AB8, first strand: chain 'C' and resid 398 through 402 removed outlier: 4.586A pdb=" N GLY C 349 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N HIS C 344 " --> pdb=" O ALA C 421 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N LEU C 423 " --> pdb=" O HIS C 344 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL C 346 " --> pdb=" O LEU C 423 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N LEU C 425 " --> pdb=" O VAL C 346 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N CYS C 348 " --> pdb=" O LEU C 425 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 535 through 540 Processing sheet with id=AC1, first strand: chain 'C' and resid 686 through 687 removed outlier: 4.165A pdb=" N TYR C 686 " --> pdb=" O GLY C 962 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 776 through 780 removed outlier: 6.613A pdb=" N ILE C 754 " --> pdb=" O SER C 777 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N LEU C 779 " --> pdb=" O ILE C 754 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N PHE C 756 " --> pdb=" O LEU C 779 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N HIS C 718 " --> pdb=" O CYS C 797 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N SER C 804 " --> pdb=" O GLU C 881 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N PHE C 915 " --> pdb=" O ILE C 878 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N THR C 880 " --> pdb=" O PHE C 915 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 976 through 981 removed outlier: 3.637A pdb=" N GLY C1013 " --> pdb=" O PHE C1050 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU C1052 " --> pdb=" O CYS C1011 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N CYS C1011 " --> pdb=" O LEU C1052 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 139 through 141 Processing sheet with id=AC5, first strand: chain 'D' and resid 398 through 402 removed outlier: 4.586A pdb=" N GLY D 349 " --> pdb=" O LEU D 378 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N HIS D 344 " --> pdb=" O ALA D 421 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N LEU D 423 " --> pdb=" O HIS D 344 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL D 346 " --> pdb=" O LEU D 423 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N LEU D 425 " --> pdb=" O VAL D 346 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N CYS D 348 " --> pdb=" O LEU D 425 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 535 through 540 Processing sheet with id=AC7, first strand: chain 'D' and resid 686 through 687 removed outlier: 4.165A pdb=" N TYR D 686 " --> pdb=" O GLY D 962 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 776 through 780 removed outlier: 6.613A pdb=" N ILE D 754 " --> pdb=" O SER D 777 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N LEU D 779 " --> pdb=" O ILE D 754 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N PHE D 756 " --> pdb=" O LEU D 779 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N HIS D 718 " --> pdb=" O CYS D 797 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N SER D 804 " --> pdb=" O GLU D 881 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N PHE D 915 " --> pdb=" O ILE D 878 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N THR D 880 " --> pdb=" O PHE D 915 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 976 through 981 removed outlier: 3.636A pdb=" N GLY D1013 " --> pdb=" O PHE D1050 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU D1052 " --> pdb=" O CYS D1011 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N CYS D1011 " --> pdb=" O LEU D1052 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 80 through 99 removed outlier: 5.944A pdb=" N VAL G 86 " --> pdb=" O ASN G 120 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N ASN G 120 " --> pdb=" O VAL G 86 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N CYS G 114 " --> pdb=" O ILE G 92 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N GLU G 94 " --> pdb=" O TYR G 112 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N TYR G 112 " --> pdb=" O GLU G 94 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N PHE G 96 " --> pdb=" O SER G 110 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N SER G 110 " --> pdb=" O PHE G 96 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N VAL G 117 " --> pdb=" O LEU G 130 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA G 128 " --> pdb=" O VAL G 119 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ASP G 188 " --> pdb=" O ASN G 181 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ASN G 181 " --> pdb=" O ASP G 188 " (cutoff:3.500A) 1742 hydrogen bonds defined for protein. 4962 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.16 Time building geometry restraints manager: 3.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 5822 1.30 - 1.43: 9638 1.43 - 1.56: 20935 1.56 - 1.69: 95 1.69 - 1.82: 336 Bond restraints: 36826 Sorted by residual: bond pdb=" C31 POV A1115 " pdb=" O31 POV A1115 " ideal model delta sigma weight residual 1.327 1.455 -0.128 2.00e-02 2.50e+03 4.09e+01 bond pdb=" C31 POV D1112 " pdb=" O31 POV D1112 " ideal model delta sigma weight residual 1.327 1.455 -0.128 2.00e-02 2.50e+03 4.07e+01 bond pdb=" C31 POV A1106 " pdb=" O31 POV A1106 " ideal model delta sigma weight residual 1.327 1.455 -0.128 2.00e-02 2.50e+03 4.07e+01 bond pdb=" C31 POV B1105 " pdb=" O31 POV B1105 " ideal model delta sigma weight residual 1.327 1.454 -0.127 2.00e-02 2.50e+03 4.06e+01 bond pdb=" C31 POV C1109 " pdb=" O31 POV C1109 " ideal model delta sigma weight residual 1.327 1.454 -0.127 2.00e-02 2.50e+03 4.06e+01 ... (remaining 36821 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.26: 49408 5.26 - 10.52: 409 10.52 - 15.78: 22 15.78 - 21.04: 0 21.04 - 26.30: 33 Bond angle restraints: 49872 Sorted by residual: angle pdb=" C19 CLR A1108 " pdb=" C10 CLR A1108 " pdb=" C9 CLR A1108 " ideal model delta sigma weight residual 111.86 85.56 26.30 3.00e+00 1.11e-01 7.69e+01 angle pdb=" C12 POV B1106 " pdb=" N POV B1106 " pdb=" C15 POV B1106 " ideal model delta sigma weight residual 112.10 86.43 25.67 3.00e+00 1.11e-01 7.32e+01 angle pdb=" C12 POV D1111 " pdb=" N POV D1111 " pdb=" C15 POV D1111 " ideal model delta sigma weight residual 112.10 86.48 25.62 3.00e+00 1.11e-01 7.29e+01 angle pdb=" C12 POV A1106 " pdb=" N POV A1106 " pdb=" C15 POV A1106 " ideal model delta sigma weight residual 112.10 86.49 25.61 3.00e+00 1.11e-01 7.29e+01 angle pdb=" C12 POV A1114 " pdb=" N POV A1114 " pdb=" C15 POV A1114 " ideal model delta sigma weight residual 112.10 86.49 25.61 3.00e+00 1.11e-01 7.28e+01 ... (remaining 49867 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.21: 21438 34.21 - 68.42: 820 68.42 - 102.63: 70 102.63 - 136.84: 1 136.84 - 171.05: 7 Dihedral angle restraints: 22336 sinusoidal: 9578 harmonic: 12758 Sorted by residual: dihedral pdb=" CA PHE F 176 " pdb=" C PHE F 176 " pdb=" N THR F 177 " pdb=" CA THR F 177 " ideal model delta harmonic sigma weight residual 180.00 150.82 29.18 0 5.00e+00 4.00e-02 3.41e+01 dihedral pdb=" CA PHE H 176 " pdb=" C PHE H 176 " pdb=" N THR H 177 " pdb=" CA THR H 177 " ideal model delta harmonic sigma weight residual 180.00 150.83 29.17 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA PHE E 176 " pdb=" C PHE E 176 " pdb=" N THR E 177 " pdb=" CA THR E 177 " ideal model delta harmonic sigma weight residual 180.00 150.86 29.14 0 5.00e+00 4.00e-02 3.40e+01 ... (remaining 22333 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.419: 5635 0.419 - 0.838: 0 0.838 - 1.257: 0 1.257 - 1.676: 0 1.676 - 2.095: 1 Chirality restraints: 5636 Sorted by residual: chirality pdb=" C10 CLR A1108 " pdb=" C1 CLR A1108 " pdb=" C5 CLR A1108 " pdb=" C9 CLR A1108 " both_signs ideal model delta sigma weight residual False -2.85 -0.75 -2.09 2.00e-01 2.50e+01 1.10e+02 chirality pdb=" CA SER H 132 " pdb=" N SER H 132 " pdb=" C SER H 132 " pdb=" CB SER H 132 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.15e+00 chirality pdb=" CA SER E 132 " pdb=" N SER E 132 " pdb=" C SER E 132 " pdb=" CB SER E 132 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.13e+00 ... (remaining 5633 not shown) Planarity restraints: 6137 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 167 " -0.119 2.00e-02 2.50e+03 6.09e-02 9.27e+01 pdb=" CG TRP H 167 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP H 167 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP H 167 " 0.060 2.00e-02 2.50e+03 pdb=" NE1 TRP H 167 " 0.032 2.00e-02 2.50e+03 pdb=" CE2 TRP H 167 " 0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP H 167 " 0.090 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 167 " -0.061 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 167 " 0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP H 167 " -0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 167 " -0.119 2.00e-02 2.50e+03 6.09e-02 9.26e+01 pdb=" CG TRP F 167 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP F 167 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP F 167 " 0.060 2.00e-02 2.50e+03 pdb=" NE1 TRP F 167 " 0.033 2.00e-02 2.50e+03 pdb=" CE2 TRP F 167 " 0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP F 167 " 0.090 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 167 " -0.061 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 167 " 0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP F 167 " -0.070 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 167 " 0.120 2.00e-02 2.50e+03 6.08e-02 9.25e+01 pdb=" CG TRP G 167 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP G 167 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP G 167 " -0.060 2.00e-02 2.50e+03 pdb=" NE1 TRP G 167 " -0.032 2.00e-02 2.50e+03 pdb=" CE2 TRP G 167 " -0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP G 167 " -0.090 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 167 " 0.061 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 167 " -0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP G 167 " 0.071 2.00e-02 2.50e+03 ... (remaining 6134 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.39: 74 2.39 - 3.08: 22700 3.08 - 3.77: 63734 3.77 - 4.45: 99757 4.45 - 5.14: 165924 Nonbonded interactions: 352189 Sorted by model distance: nonbonded pdb=" OE2 GLU B 374 " pdb="MG MG B1102 " model vdw 1.707 2.170 nonbonded pdb=" OE2 GLU D 374 " pdb="MG MG D1103 " model vdw 1.724 2.170 nonbonded pdb=" OE2 GLU C 374 " pdb="MG MG C1101 " model vdw 1.735 2.170 nonbonded pdb=" OE2 GLU D 399 " pdb="MG MG D1103 " model vdw 1.778 2.170 nonbonded pdb=" OE2 GLU B 399 " pdb="MG MG B1102 " model vdw 1.799 2.170 ... (remaining 352184 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 16 through 1056 or (resid 1106 and (name C1 or name C2 or \ name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 \ or name C28 or name C3 or name O11 or name O12 or name O13 or name O14 or name \ O21 or name O22 or name P )))) selection = (chain 'B' and (resid 16 through 1056 or (resid 1106 and (name C1 or name C2 or \ name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 \ or name C28 or name C3 or name O11 or name O12 or name O13 or name O14 or name \ O21 or name O22 or name P )))) selection = (chain 'C' and (resid 16 through 1056 or (resid 1106 and (name C1 or name C2 or \ name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 \ or name C28 or name C3 or name O11 or name O12 or name O13 or name O14 or name \ O21 or name O22 or name P )))) selection = (chain 'D' and (resid 16 through 1056 or (resid 1106 and (name C1 or name C2 or \ name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 \ or name C28 or name C3 or name O11 or name O12 or name O13 or name O14 or name \ O21 or name O22 or name P )))) } ncs_group { reference = chain 'E' selection = chain 'F' selection = (chain 'G' and resid 36 through 235) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.580 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 28.870 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 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 : 0.013 0.291 36843 Z= 0.754 Angle : 1.912 26.303 49904 Z= 1.161 Chirality : 0.102 2.095 5636 Planarity : 0.012 0.127 6137 Dihedral : 16.844 171.050 14012 Min Nonbonded Distance : 1.707 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.56 % Allowed : 3.83 % Favored : 95.61 % Rotamer: Outliers : 2.75 % Allowed : 6.56 % Favored : 90.69 % Cbeta Deviations : 0.41 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.40 (0.11), residues: 4309 helix: -1.02 (0.09), residues: 2096 sheet: 0.16 (0.23), residues: 480 loop : -0.91 (0.14), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C1018 TYR 0.113 0.014 TYR H 166 PHE 0.096 0.011 PHE A 511 TRP 0.120 0.021 TRP G 167 HIS 0.012 0.002 HIS B 749 Details of bonding type rmsd covalent geometry : bond 0.01274 (36826) covalent geometry : angle 1.91196 (49872) SS BOND : bond 0.00472 ( 16) SS BOND : angle 1.74607 ( 32) hydrogen bonds : bond 0.18855 ( 1742) hydrogen bonds : angle 7.33298 ( 4962) Misc. bond : bond 0.29124 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8618 Ramachandran restraints generated. 4309 Oldfield, 0 Emsley, 4309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8618 Ramachandran restraints generated. 4309 Oldfield, 0 Emsley, 4309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 3854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 588 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 92 ILE cc_start: 0.8261 (pt) cc_final: 0.7927 (pt) REVERT: E 96 PHE cc_start: 0.8919 (m-80) cc_final: 0.8478 (m-80) REVERT: E 230 LYS cc_start: 0.8132 (mttt) cc_final: 0.7857 (mmtp) REVERT: F 76 ASP cc_start: 0.7412 (t70) cc_final: 0.6864 (m-30) REVERT: F 142 LYS cc_start: 0.8815 (mtpt) cc_final: 0.8054 (mtpp) REVERT: F 188 ASP cc_start: 0.6752 (m-30) cc_final: 0.6337 (m-30) REVERT: H 105 ASP cc_start: 0.8423 (t0) cc_final: 0.8159 (OUTLIER) REVERT: H 145 TYR cc_start: 0.9153 (t80) cc_final: 0.8872 (t80) REVERT: H 188 ASP cc_start: 0.5981 (m-30) cc_final: 0.5502 (m-30) REVERT: A 806 ASN cc_start: 0.7438 (p0) cc_final: 0.7217 (p0) REVERT: A 952 LEU cc_start: 0.8605 (mt) cc_final: 0.8084 (tm) REVERT: A 960 ARG cc_start: 0.7486 (OUTLIER) cc_final: 0.7250 (mtm110) REVERT: A 982 LEU cc_start: 0.8567 (tp) cc_final: 0.8189 (tp) REVERT: B 332 TYR cc_start: 0.7040 (m-80) cc_final: 0.6165 (m-80) REVERT: B 386 GLU cc_start: 0.6363 (OUTLIER) cc_final: 0.6099 (mt-10) REVERT: B 436 GLU cc_start: 0.5514 (tp30) cc_final: 0.4909 (tt0) REVERT: B 465 ASN cc_start: 0.5690 (m-40) cc_final: 0.5196 (m-40) REVERT: B 751 LEU cc_start: 0.8238 (tt) cc_final: 0.7803 (mt) REVERT: B 811 ASP cc_start: 0.7195 (OUTLIER) cc_final: 0.6137 (p0) REVERT: B 1053 MET cc_start: 0.6278 (mmm) cc_final: 0.5926 (mmm) REVERT: B 1055 PHE cc_start: 0.6450 (t80) cc_final: 0.6065 (t80) REVERT: C 21 MET cc_start: 0.9280 (mmm) cc_final: 0.9039 (mmm) REVERT: D 332 TYR cc_start: 0.6980 (m-80) cc_final: 0.6384 (m-80) REVERT: D 436 GLU cc_start: 0.5040 (tp30) cc_final: 0.4576 (tt0) REVERT: D 559 VAL cc_start: 0.7256 (t) cc_final: 0.6734 (t) REVERT: D 700 ILE cc_start: 0.8558 (tt) cc_final: 0.7941 (tt) REVERT: D 987 PHE cc_start: 0.6957 (m-80) cc_final: 0.6702 (m-80) REVERT: G 76 ASP cc_start: 0.8037 (t70) cc_final: 0.7171 (m-30) REVERT: G 230 LYS cc_start: 0.7961 (mttt) cc_final: 0.7671 (mtpm) outliers start: 106 outliers final: 18 residues processed: 673 average time/residue: 0.5485 time to fit residues: 450.6784 Evaluate side-chains 356 residues out of total 3854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 336 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 786 ARG Chi-restraints excluded: chain A residue 960 ARG Chi-restraints excluded: chain A residue 974 ARG Chi-restraints excluded: chain A residue 1001 CYS Chi-restraints excluded: chain A residue 1026 SER Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 811 ASP Chi-restraints excluded: chain B residue 1001 CYS Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 974 ARG Chi-restraints excluded: chain C residue 992 ASP Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 811 ASP Chi-restraints excluded: chain G residue 2 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 432 optimal weight: 10.0000 chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 0.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 5.9990 chunk 401 optimal weight: 1.9990 chunk 424 optimal weight: 8.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 83 ASN F 156 ASN F 195 HIS A 142 GLN A 157 ASN A 254 HIS A 471 ASN A 585 ASN A 718 HIS A 771 HIS A 807 GLN B 157 ASN B 254 HIS B 440 ASN B 451 HIS B 464 HIS B 471 ASN B 718 HIS B 749 HIS B 771 HIS B 772 ASN B 807 GLN C 157 ASN C 254 HIS C 365 HIS C 471 ASN C 718 HIS C 771 HIS C 807 GLN C 893 GLN D 157 ASN D 254 HIS D 449 ASN D 451 HIS D 464 HIS D 471 ASN D 585 ASN D 718 HIS D 749 HIS D 772 ASN D 807 GLN G 116 GLN G 156 ASN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.114856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.087033 restraints weight = 84249.190| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.59 r_work: 0.3391 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 36843 Z= 0.155 Angle : 0.714 29.700 49904 Z= 0.348 Chirality : 0.052 1.827 5636 Planarity : 0.004 0.083 6137 Dihedral : 13.977 172.543 6053 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.04 % Allowed : 12.56 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.12), residues: 4309 helix: 0.56 (0.11), residues: 2201 sheet: 0.79 (0.25), residues: 466 loop : -0.81 (0.14), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 342 TYR 0.024 0.002 TYR B 527 PHE 0.024 0.002 PHE B 148 TRP 0.039 0.002 TRP B 475 HIS 0.012 0.001 HIS B 464 Details of bonding type rmsd covalent geometry : bond 0.00336 (36826) covalent geometry : angle 0.71364 (49872) SS BOND : bond 0.00459 ( 16) SS BOND : angle 1.28445 ( 32) hydrogen bonds : bond 0.04997 ( 1742) hydrogen bonds : angle 4.86751 ( 4962) Misc. bond : bond 0.00200 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8618 Ramachandran restraints generated. 4309 Oldfield, 0 Emsley, 4309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8618 Ramachandran restraints generated. 4309 Oldfield, 0 Emsley, 4309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 3854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 371 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 96 PHE cc_start: 0.8659 (m-80) cc_final: 0.8175 (m-80) REVERT: E 230 LYS cc_start: 0.7843 (mttt) cc_final: 0.7469 (mmtp) REVERT: F 96 PHE cc_start: 0.8750 (m-80) cc_final: 0.8350 (m-80) REVERT: F 162 ASN cc_start: 0.8807 (p0) cc_final: 0.8299 (p0) REVERT: F 166 TYR cc_start: 0.7979 (t80) cc_final: 0.7637 (t80) REVERT: H 49 ARG cc_start: 0.7928 (mtm110) cc_final: 0.7479 (mtm-85) REVERT: H 96 PHE cc_start: 0.8790 (m-80) cc_final: 0.7982 (m-80) REVERT: H 105 ASP cc_start: 0.8243 (t0) cc_final: 0.7994 (t0) REVERT: H 185 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.8226 (mtp85) REVERT: H 188 ASP cc_start: 0.6308 (m-30) cc_final: 0.6106 (m-30) REVERT: A 93 TRP cc_start: 0.7854 (OUTLIER) cc_final: 0.7233 (p-90) REVERT: A 94 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.8366 (mpp) REVERT: A 952 LEU cc_start: 0.8773 (mt) cc_final: 0.8410 (tm) REVERT: A 960 ARG cc_start: 0.8126 (mtm110) cc_final: 0.7865 (mtm180) REVERT: B 104 MET cc_start: 0.7613 (mmp) cc_final: 0.7406 (mmp) REVERT: B 219 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7931 (tt0) REVERT: B 454 ILE cc_start: 0.7337 (OUTLIER) cc_final: 0.6957 (pp) REVERT: B 506 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.8653 (ttm) REVERT: B 553 VAL cc_start: 0.8776 (t) cc_final: 0.8543 (p) REVERT: B 747 HIS cc_start: 0.6577 (m170) cc_final: 0.6360 (m-70) REVERT: C 53 CYS cc_start: 0.7874 (t) cc_final: 0.7621 (p) REVERT: C 104 MET cc_start: 0.9073 (mmm) cc_final: 0.8741 (tpp) REVERT: C 561 LEU cc_start: 0.7049 (mp) cc_final: 0.6831 (mt) REVERT: C 562 LYS cc_start: 0.7885 (mmmt) cc_final: 0.7345 (mtmt) REVERT: D 314 MET cc_start: 0.8919 (tmm) cc_final: 0.8553 (ttp) REVERT: D 352 THR cc_start: 0.8851 (m) cc_final: 0.8356 (p) REVERT: D 436 GLU cc_start: 0.6072 (tp30) cc_final: 0.5557 (tp30) REVERT: D 447 ILE cc_start: 0.8327 (mp) cc_final: 0.8045 (mp) REVERT: D 454 ILE cc_start: 0.7427 (OUTLIER) cc_final: 0.7175 (pp) REVERT: D 739 MET cc_start: 0.8718 (ttm) cc_final: 0.8502 (ttp) REVERT: G 127 ARG cc_start: 0.8133 (ppp80) cc_final: 0.7911 (ttt180) REVERT: G 138 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8554 (tm) REVERT: G 150 LYS cc_start: 0.9090 (mmmm) cc_final: 0.8869 (ttpp) outliers start: 117 outliers final: 39 residues processed: 457 average time/residue: 0.5106 time to fit residues: 288.3402 Evaluate side-chains 341 residues out of total 3854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 295 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 176 PHE Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain F residue 234 MET Chi-restraints excluded: chain H residue 102 CYS Chi-restraints excluded: chain H residue 185 ARG Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 93 TRP Chi-restraints excluded: chain A residue 94 MET Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 506 MET Chi-restraints excluded: chain B residue 516 PHE Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 737 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 874 VAL Chi-restraints excluded: chain B residue 1001 CYS Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 557 CYS Chi-restraints excluded: chain C residue 933 ILE Chi-restraints excluded: chain C residue 974 ARG Chi-restraints excluded: chain C residue 977 VAL Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 454 ILE Chi-restraints excluded: chain D residue 694 TRP Chi-restraints excluded: chain D residue 763 LEU Chi-restraints excluded: chain D residue 811 ASP Chi-restraints excluded: chain D residue 874 VAL Chi-restraints excluded: chain D residue 1001 CYS Chi-restraints excluded: chain D residue 1024 THR Chi-restraints excluded: chain G residue 2 PHE Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 102 CYS Chi-restraints excluded: chain G residue 138 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 247 optimal weight: 0.0570 chunk 343 optimal weight: 0.9990 chunk 384 optimal weight: 7.9990 chunk 217 optimal weight: 20.0000 chunk 167 optimal weight: 6.9990 chunk 426 optimal weight: 30.0000 chunk 200 optimal weight: 10.0000 chunk 173 optimal weight: 6.9990 chunk 337 optimal weight: 0.9990 chunk 419 optimal weight: 10.0000 chunk 46 optimal weight: 30.0000 overall best weight: 3.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 91 GLN E 116 GLN E 131 HIS E 195 HIS F 116 GLN F 125 ASN F 156 ASN ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 771 HIS B 142 GLN B 344 HIS B 449 ASN B 585 ASN B 887 ASN B 893 GLN B 971 ASN C 771 HIS D 143 ASN D 459 GLN ** D 464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 771 HIS D 808 ASN D 887 ASN D 893 GLN D 971 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.100394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.069777 restraints weight = 80523.794| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.53 r_work: 0.3025 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.4708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.135 36843 Z= 0.180 Angle : 0.707 29.549 49904 Z= 0.349 Chirality : 0.052 1.839 5636 Planarity : 0.004 0.058 6137 Dihedral : 12.677 175.909 6023 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.14 % Allowed : 13.39 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.13), residues: 4309 helix: 0.93 (0.11), residues: 2177 sheet: 0.13 (0.24), residues: 500 loop : -0.74 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 342 TYR 0.023 0.002 TYR F 166 PHE 0.053 0.002 PHE B 516 TRP 0.047 0.002 TRP B 475 HIS 0.007 0.001 HIS B 771 Details of bonding type rmsd covalent geometry : bond 0.00416 (36826) covalent geometry : angle 0.70668 (49872) SS BOND : bond 0.00323 ( 16) SS BOND : angle 1.23764 ( 32) hydrogen bonds : bond 0.05369 ( 1742) hydrogen bonds : angle 4.65145 ( 4962) Misc. bond : bond 0.00305 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8618 Ramachandran restraints generated. 4309 Oldfield, 0 Emsley, 4309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8618 Ramachandran restraints generated. 4309 Oldfield, 0 Emsley, 4309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 3854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 329 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 96 PHE cc_start: 0.8637 (m-80) cc_final: 0.8128 (m-80) REVERT: E 142 LYS cc_start: 0.8301 (mtpt) cc_final: 0.8006 (tppt) REVERT: E 193 ARG cc_start: 0.7139 (mmm160) cc_final: 0.6766 (mmt-90) REVERT: E 230 LYS cc_start: 0.7875 (mttt) cc_final: 0.7479 (mmtp) REVERT: F 96 PHE cc_start: 0.8707 (m-80) cc_final: 0.8123 (m-80) REVERT: F 142 LYS cc_start: 0.8591 (mtpt) cc_final: 0.8357 (mmtt) REVERT: F 162 ASN cc_start: 0.8920 (p0) cc_final: 0.8458 (p0) REVERT: F 192 HIS cc_start: 0.8505 (m-70) cc_final: 0.8066 (m90) REVERT: H 49 ARG cc_start: 0.8102 (mtm110) cc_final: 0.7699 (mtp180) REVERT: H 105 ASP cc_start: 0.8235 (t0) cc_final: 0.7955 (t0) REVERT: H 188 ASP cc_start: 0.6827 (m-30) cc_final: 0.6516 (m-30) REVERT: A 94 MET cc_start: 0.8842 (tpp) cc_final: 0.8542 (mmp) REVERT: A 154 MET cc_start: 0.9116 (OUTLIER) cc_final: 0.8777 (mmm) REVERT: A 514 ARG cc_start: 0.9129 (OUTLIER) cc_final: 0.7806 (mtp85) REVERT: A 952 LEU cc_start: 0.8904 (mt) cc_final: 0.8540 (tm) REVERT: A 960 ARG cc_start: 0.8385 (mtm110) cc_final: 0.8067 (mtm180) REVERT: B 50 TRP cc_start: 0.7158 (t-100) cc_final: 0.6914 (t-100) REVERT: B 94 MET cc_start: 0.6710 (tmm) cc_final: 0.6000 (mpp) REVERT: B 104 MET cc_start: 0.8790 (mmp) cc_final: 0.8521 (mmm) REVERT: B 386 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8600 (mt-10) REVERT: B 436 GLU cc_start: 0.6894 (mm-30) cc_final: 0.5953 (tp30) REVERT: B 536 MET cc_start: 0.9304 (ttm) cc_final: 0.9063 (ttm) REVERT: B 816 GLN cc_start: 0.7808 (OUTLIER) cc_final: 0.7602 (mp10) REVERT: C 53 CYS cc_start: 0.7848 (t) cc_final: 0.7643 (p) REVERT: C 154 MET cc_start: 0.9241 (mmm) cc_final: 0.8971 (tpt) REVERT: C 370 ASP cc_start: 0.7223 (t70) cc_final: 0.6882 (t70) REVERT: D 314 MET cc_start: 0.9151 (OUTLIER) cc_final: 0.8706 (ttp) REVERT: D 329 ARG cc_start: 0.7235 (tpp-160) cc_final: 0.7030 (mtt180) REVERT: D 352 THR cc_start: 0.9299 (m) cc_final: 0.8862 (p) REVERT: D 354 GLU cc_start: 0.8098 (pm20) cc_final: 0.7872 (pm20) REVERT: D 436 GLU cc_start: 0.6831 (tp30) cc_final: 0.6186 (tp30) REVERT: D 553 VAL cc_start: 0.9390 (t) cc_final: 0.9098 (m) REVERT: D 565 MET cc_start: 0.7449 (tpt) cc_final: 0.6801 (tpt) REVERT: D 568 ILE cc_start: 0.7128 (OUTLIER) cc_final: 0.6923 (tt) REVERT: D 704 ILE cc_start: 0.9157 (OUTLIER) cc_final: 0.8953 (mp) REVERT: D 782 THR cc_start: 0.9024 (m) cc_final: 0.8731 (t) REVERT: G 138 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8421 (tm) REVERT: G 150 LYS cc_start: 0.9074 (mmmm) cc_final: 0.8673 (ttpp) REVERT: G 155 LYS cc_start: 0.9396 (mptm) cc_final: 0.9087 (tmtt) REVERT: G 176 PHE cc_start: 0.7067 (OUTLIER) cc_final: 0.6812 (m-80) outliers start: 121 outliers final: 36 residues processed: 424 average time/residue: 0.5205 time to fit residues: 270.3230 Evaluate side-chains 318 residues out of total 3854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 273 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 102 CYS Chi-restraints excluded: chain E residue 176 PHE Chi-restraints excluded: chain F residue 102 CYS Chi-restraints excluded: chain F residue 176 PHE Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 102 CYS Chi-restraints excluded: chain H residue 176 PHE Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 93 TRP Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 816 GLN Chi-restraints excluded: chain B residue 874 VAL Chi-restraints excluded: chain B residue 989 ASP Chi-restraints excluded: chain B residue 1022 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 566 ILE Chi-restraints excluded: chain C residue 803 LEU Chi-restraints excluded: chain C residue 883 VAL Chi-restraints excluded: chain C residue 933 ILE Chi-restraints excluded: chain C residue 1022 LEU Chi-restraints excluded: chain D residue 314 MET Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 386 GLU Chi-restraints excluded: chain D residue 566 ILE Chi-restraints excluded: chain D residue 568 ILE Chi-restraints excluded: chain D residue 704 ILE Chi-restraints excluded: chain D residue 763 LEU Chi-restraints excluded: chain D residue 874 VAL Chi-restraints excluded: chain D residue 1022 LEU Chi-restraints excluded: chain D residue 1024 THR Chi-restraints excluded: chain G residue 2 PHE Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 176 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 101 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 chunk 319 optimal weight: 7.9990 chunk 53 optimal weight: 30.0000 chunk 16 optimal weight: 6.9990 chunk 211 optimal weight: 9.9990 chunk 299 optimal weight: 7.9990 chunk 400 optimal weight: 6.9990 chunk 122 optimal weight: 0.0070 chunk 271 optimal weight: 8.9990 chunk 170 optimal weight: 0.9980 overall best weight: 4.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 116 GLN ** E 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 156 ASN ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 771 HIS A 893 GLN B 142 GLN B 143 ASN B 772 ASN B 930 ASN C 771 HIS D 464 HIS D 930 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.096056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.065478 restraints weight = 79289.153| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.46 r_work: 0.2922 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.5512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 36843 Z= 0.190 Angle : 0.665 28.879 49904 Z= 0.326 Chirality : 0.052 1.861 5636 Planarity : 0.004 0.064 6137 Dihedral : 12.310 173.277 6013 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.69 % Favored : 97.28 % Rotamer: Outliers : 3.43 % Allowed : 13.83 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.13), residues: 4309 helix: 1.09 (0.11), residues: 2158 sheet: 0.10 (0.23), residues: 534 loop : -0.67 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 443 TYR 0.017 0.002 TYR G 166 PHE 0.038 0.002 PHE B 550 TRP 0.034 0.002 TRP B 475 HIS 0.007 0.001 HIS B 771 Details of bonding type rmsd covalent geometry : bond 0.00445 (36826) covalent geometry : angle 0.66494 (49872) SS BOND : bond 0.00264 ( 16) SS BOND : angle 1.24790 ( 32) hydrogen bonds : bond 0.05079 ( 1742) hydrogen bonds : angle 4.53979 ( 4962) Misc. bond : bond 0.00805 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8618 Ramachandran restraints generated. 4309 Oldfield, 0 Emsley, 4309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8618 Ramachandran restraints generated. 4309 Oldfield, 0 Emsley, 4309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 3854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 278 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 96 PHE cc_start: 0.8628 (m-80) cc_final: 0.8085 (m-80) REVERT: E 142 LYS cc_start: 0.8314 (mtpt) cc_final: 0.7939 (tppp) REVERT: E 193 ARG cc_start: 0.7124 (mmm160) cc_final: 0.6820 (mmt90) REVERT: F 96 PHE cc_start: 0.8734 (m-80) cc_final: 0.8130 (m-80) REVERT: F 162 ASN cc_start: 0.8879 (p0) cc_final: 0.8478 (p0) REVERT: F 166 TYR cc_start: 0.7996 (t80) cc_final: 0.7723 (t80) REVERT: F 192 HIS cc_start: 0.8674 (m-70) cc_final: 0.8264 (m90) REVERT: H 49 ARG cc_start: 0.8058 (mtm110) cc_final: 0.7630 (mtp180) REVERT: H 96 PHE cc_start: 0.8456 (m-80) cc_final: 0.7956 (m-80) REVERT: H 105 ASP cc_start: 0.8335 (t0) cc_final: 0.8066 (t0) REVERT: A 154 MET cc_start: 0.9147 (OUTLIER) cc_final: 0.8820 (mmm) REVERT: A 514 ARG cc_start: 0.9144 (OUTLIER) cc_final: 0.7867 (mtp85) REVERT: A 556 LEU cc_start: 0.9148 (mt) cc_final: 0.8837 (pp) REVERT: A 609 PHE cc_start: 0.7127 (OUTLIER) cc_final: 0.6906 (t80) REVERT: A 889 GLN cc_start: 0.8889 (OUTLIER) cc_final: 0.8609 (pp30) REVERT: A 952 LEU cc_start: 0.8923 (mt) cc_final: 0.8579 (tm) REVERT: B 50 TRP cc_start: 0.7533 (t-100) cc_final: 0.7191 (t-100) REVERT: B 104 MET cc_start: 0.8992 (mmp) cc_final: 0.8775 (mmm) REVERT: B 267 GLN cc_start: 0.9133 (OUTLIER) cc_final: 0.8649 (mp10) REVERT: B 314 MET cc_start: 0.9229 (ttp) cc_final: 0.8963 (ttp) REVERT: B 369 ASP cc_start: 0.7754 (p0) cc_final: 0.7451 (p0) REVERT: B 386 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8621 (mt-10) REVERT: B 436 GLU cc_start: 0.7280 (mm-30) cc_final: 0.6663 (tp30) REVERT: B 989 ASP cc_start: 0.8346 (OUTLIER) cc_final: 0.7986 (p0) REVERT: C 154 MET cc_start: 0.9163 (mmm) cc_final: 0.8938 (tpt) REVERT: D 314 MET cc_start: 0.9160 (tmm) cc_final: 0.8743 (ttp) REVERT: D 436 GLU cc_start: 0.7294 (tp30) cc_final: 0.6829 (tp30) REVERT: D 550 PHE cc_start: 0.8499 (t80) cc_final: 0.7909 (t80) REVERT: D 963 TYR cc_start: 0.7905 (m-80) cc_final: 0.7263 (m-80) REVERT: D 1053 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.8385 (mtm) REVERT: G 138 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8469 (tm) REVERT: G 150 LYS cc_start: 0.9130 (mmmm) cc_final: 0.8548 (ttpp) REVERT: G 155 LYS cc_start: 0.9400 (mptm) cc_final: 0.9066 (tmmt) outliers start: 132 outliers final: 48 residues processed: 380 average time/residue: 0.5176 time to fit residues: 242.7241 Evaluate side-chains 308 residues out of total 3854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 251 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 102 CYS Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain F residue 102 CYS Chi-restraints excluded: chain F residue 176 PHE Chi-restraints excluded: chain H residue 102 CYS Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 609 PHE Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 889 GLN Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 267 GLN Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 694 TRP Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 874 VAL Chi-restraints excluded: chain B residue 933 ILE Chi-restraints excluded: chain B residue 989 ASP Chi-restraints excluded: chain B residue 1022 LEU Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain B residue 1043 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 557 CYS Chi-restraints excluded: chain C residue 565 MET Chi-restraints excluded: chain C residue 704 ILE Chi-restraints excluded: chain C residue 731 LEU Chi-restraints excluded: chain C residue 803 LEU Chi-restraints excluded: chain C residue 883 VAL Chi-restraints excluded: chain C residue 905 LEU Chi-restraints excluded: chain C residue 933 ILE Chi-restraints excluded: chain C residue 1015 TYR Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 557 CYS Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 763 LEU Chi-restraints excluded: chain D residue 874 VAL Chi-restraints excluded: chain D residue 1022 LEU Chi-restraints excluded: chain D residue 1024 THR Chi-restraints excluded: chain D residue 1053 MET Chi-restraints excluded: chain G residue 2 PHE Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 102 CYS Chi-restraints excluded: chain G residue 138 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 3 optimal weight: 3.9990 chunk 50 optimal weight: 40.0000 chunk 2 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 264 optimal weight: 0.5980 chunk 176 optimal weight: 0.0000 chunk 278 optimal weight: 3.9990 chunk 420 optimal weight: 10.0000 chunk 199 optimal weight: 9.9990 chunk 34 optimal weight: 40.0000 chunk 124 optimal weight: 6.9990 overall best weight: 2.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 136 GLN ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 771 HIS B 142 GLN C 771 HIS G 91 GLN G 164 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.095173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.064530 restraints weight = 79034.286| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.47 r_work: 0.2903 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.5877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 36843 Z= 0.150 Angle : 0.625 29.045 49904 Z= 0.301 Chirality : 0.050 1.862 5636 Planarity : 0.004 0.054 6137 Dihedral : 11.949 173.324 6012 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.18 % Favored : 96.77 % Rotamer: Outliers : 3.14 % Allowed : 14.71 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.13), residues: 4309 helix: 1.23 (0.11), residues: 2158 sheet: -0.00 (0.23), residues: 538 loop : -0.58 (0.15), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 151 TYR 0.017 0.001 TYR E 166 PHE 0.021 0.001 PHE B 550 TRP 0.042 0.001 TRP D 477 HIS 0.004 0.001 HIS C 365 Details of bonding type rmsd covalent geometry : bond 0.00345 (36826) covalent geometry : angle 0.62468 (49872) SS BOND : bond 0.00282 ( 16) SS BOND : angle 1.00761 ( 32) hydrogen bonds : bond 0.04730 ( 1742) hydrogen bonds : angle 4.41783 ( 4962) Misc. bond : bond 0.00241 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8618 Ramachandran restraints generated. 4309 Oldfield, 0 Emsley, 4309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8618 Ramachandran restraints generated. 4309 Oldfield, 0 Emsley, 4309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 3854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 256 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 96 PHE cc_start: 0.8595 (m-80) cc_final: 0.8029 (m-80) REVERT: E 142 LYS cc_start: 0.8154 (mtpt) cc_final: 0.7751 (tppp) REVERT: E 193 ARG cc_start: 0.7106 (mmm160) cc_final: 0.6837 (mmt90) REVERT: E 230 LYS cc_start: 0.7791 (mttt) cc_final: 0.7376 (mmtp) REVERT: F 96 PHE cc_start: 0.8700 (m-80) cc_final: 0.8053 (m-80) REVERT: F 155 LYS cc_start: 0.9460 (mttm) cc_final: 0.9184 (mttp) REVERT: F 162 ASN cc_start: 0.8862 (p0) cc_final: 0.8417 (p0) REVERT: F 192 HIS cc_start: 0.8761 (m-70) cc_final: 0.8447 (OUTLIER) REVERT: H 49 ARG cc_start: 0.8047 (mtm110) cc_final: 0.7622 (mtp180) REVERT: H 96 PHE cc_start: 0.8524 (m-80) cc_final: 0.8036 (m-80) REVERT: H 105 ASP cc_start: 0.8327 (t0) cc_final: 0.8086 (t0) REVERT: A 94 MET cc_start: 0.8892 (tpp) cc_final: 0.8497 (mpp) REVERT: A 154 MET cc_start: 0.9085 (OUTLIER) cc_final: 0.8726 (mmm) REVERT: A 514 ARG cc_start: 0.9160 (OUTLIER) cc_final: 0.7934 (mtp85) REVERT: A 556 LEU cc_start: 0.9193 (mt) cc_final: 0.8932 (pp) REVERT: A 565 MET cc_start: 0.7734 (OUTLIER) cc_final: 0.7532 (tpt) REVERT: A 609 PHE cc_start: 0.7185 (OUTLIER) cc_final: 0.6903 (t80) REVERT: A 952 LEU cc_start: 0.8951 (mt) cc_final: 0.8589 (tm) REVERT: B 104 MET cc_start: 0.8925 (mmp) cc_final: 0.8716 (mmm) REVERT: B 436 GLU cc_start: 0.7384 (mm-30) cc_final: 0.6890 (tp30) REVERT: B 556 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.9026 (tm) REVERT: B 568 ILE cc_start: 0.8083 (OUTLIER) cc_final: 0.7778 (tt) REVERT: B 816 GLN cc_start: 0.7877 (OUTLIER) cc_final: 0.7604 (pt0) REVERT: B 948 GLU cc_start: 0.8603 (tm-30) cc_final: 0.8343 (mp0) REVERT: C 154 MET cc_start: 0.9188 (OUTLIER) cc_final: 0.8962 (tpt) REVERT: C 514 ARG cc_start: 0.9034 (OUTLIER) cc_final: 0.7867 (mtt-85) REVERT: D 148 PHE cc_start: 0.7804 (m-80) cc_final: 0.7278 (m-10) REVERT: D 314 MET cc_start: 0.9151 (OUTLIER) cc_final: 0.8627 (ttp) REVERT: D 436 GLU cc_start: 0.7304 (tp30) cc_final: 0.6921 (tp30) REVERT: D 443 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.7093 (mpp80) REVERT: D 564 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8744 (tt) REVERT: D 816 GLN cc_start: 0.7662 (OUTLIER) cc_final: 0.7318 (pt0) REVERT: D 948 GLU cc_start: 0.8547 (tp30) cc_final: 0.8225 (tt0) REVERT: G 138 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8471 (tm) REVERT: G 150 LYS cc_start: 0.9097 (mmmm) cc_final: 0.8503 (ttpp) REVERT: G 155 LYS cc_start: 0.9395 (mptm) cc_final: 0.9047 (tmmt) outliers start: 121 outliers final: 51 residues processed: 347 average time/residue: 0.5266 time to fit residues: 223.9262 Evaluate side-chains 301 residues out of total 3854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 237 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 102 CYS Chi-restraints excluded: chain F residue 102 CYS Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 166 TYR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 102 CYS Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 609 PHE Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 330 LYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 816 GLN Chi-restraints excluded: chain B residue 874 VAL Chi-restraints excluded: chain B residue 933 ILE Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain B residue 952 LEU Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1022 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 285 MET Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 514 ARG Chi-restraints excluded: chain C residue 565 MET Chi-restraints excluded: chain C residue 566 ILE Chi-restraints excluded: chain C residue 568 ILE Chi-restraints excluded: chain C residue 803 LEU Chi-restraints excluded: chain C residue 883 VAL Chi-restraints excluded: chain C residue 933 ILE Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 1015 TYR Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 314 MET Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 443 ARG Chi-restraints excluded: chain D residue 557 CYS Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 816 GLN Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 949 LEU Chi-restraints excluded: chain D residue 1015 TYR Chi-restraints excluded: chain D residue 1022 LEU Chi-restraints excluded: chain D residue 1024 THR Chi-restraints excluded: chain G residue 2 PHE Chi-restraints excluded: chain G residue 102 CYS Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 176 PHE Chi-restraints excluded: chain G residue 183 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 364 optimal weight: 2.9990 chunk 366 optimal weight: 5.9990 chunk 260 optimal weight: 0.6980 chunk 277 optimal weight: 1.9990 chunk 212 optimal weight: 1.9990 chunk 251 optimal weight: 5.9990 chunk 353 optimal weight: 5.9990 chunk 315 optimal weight: 6.9990 chunk 379 optimal weight: 0.9980 chunk 50 optimal weight: 9.9990 chunk 339 optimal weight: 10.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 164 GLN H 136 GLN ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 771 HIS A1027 GLN B 142 GLN ** B 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 GLN C 771 HIS C 808 ASN G 136 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.095602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.065241 restraints weight = 79086.857| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.45 r_work: 0.2925 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.6090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 36843 Z= 0.120 Angle : 0.596 28.467 49904 Z= 0.286 Chirality : 0.049 1.880 5636 Planarity : 0.003 0.049 6137 Dihedral : 11.559 171.826 6012 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.92 % Favored : 97.03 % Rotamer: Outliers : 2.78 % Allowed : 15.33 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.13), residues: 4309 helix: 1.39 (0.11), residues: 2162 sheet: 0.01 (0.23), residues: 538 loop : -0.47 (0.15), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 976 TYR 0.029 0.001 TYR F 166 PHE 0.017 0.001 PHE B 550 TRP 0.042 0.001 TRP D 477 HIS 0.003 0.000 HIS B 771 Details of bonding type rmsd covalent geometry : bond 0.00265 (36826) covalent geometry : angle 0.59589 (49872) SS BOND : bond 0.00272 ( 16) SS BOND : angle 1.09317 ( 32) hydrogen bonds : bond 0.04284 ( 1742) hydrogen bonds : angle 4.29829 ( 4962) Misc. bond : bond 0.00170 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8618 Ramachandran restraints generated. 4309 Oldfield, 0 Emsley, 4309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8618 Ramachandran restraints generated. 4309 Oldfield, 0 Emsley, 4309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 248 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 96 PHE cc_start: 0.8592 (m-80) cc_final: 0.8012 (m-80) REVERT: E 131 HIS cc_start: 0.7410 (m-70) cc_final: 0.7153 (m-70) REVERT: E 142 LYS cc_start: 0.8079 (mtpt) cc_final: 0.7739 (tppp) REVERT: E 230 LYS cc_start: 0.7822 (mttt) cc_final: 0.7379 (mmtp) REVERT: F 96 PHE cc_start: 0.8701 (m-80) cc_final: 0.8127 (m-80) REVERT: F 150 LYS cc_start: 0.8789 (ptmm) cc_final: 0.8532 (ptmm) REVERT: F 162 ASN cc_start: 0.8899 (p0) cc_final: 0.8463 (p0) REVERT: F 192 HIS cc_start: 0.8787 (m-70) cc_final: 0.8494 (OUTLIER) REVERT: H 49 ARG cc_start: 0.8043 (mtm110) cc_final: 0.7618 (mtp180) REVERT: H 96 PHE cc_start: 0.8535 (m-80) cc_final: 0.8022 (m-80) REVERT: H 105 ASP cc_start: 0.8411 (t0) cc_final: 0.8136 (t0) REVERT: H 168 LYS cc_start: 0.8891 (pptt) cc_final: 0.8647 (ptpp) REVERT: A 154 MET cc_start: 0.9084 (OUTLIER) cc_final: 0.8748 (mmm) REVERT: A 352 THR cc_start: 0.9076 (OUTLIER) cc_final: 0.8851 (p) REVERT: A 514 ARG cc_start: 0.9146 (OUTLIER) cc_final: 0.7910 (mtp85) REVERT: A 556 LEU cc_start: 0.9177 (mt) cc_final: 0.8953 (pp) REVERT: A 761 GLU cc_start: 0.8357 (mp0) cc_final: 0.8018 (mm-30) REVERT: A 952 LEU cc_start: 0.8971 (mt) cc_final: 0.8613 (tm) REVERT: B 104 MET cc_start: 0.8884 (mmp) cc_final: 0.8679 (mmm) REVERT: B 436 GLU cc_start: 0.7488 (mm-30) cc_final: 0.7007 (tp30) REVERT: B 556 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9059 (tm) REVERT: B 568 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7909 (tt) REVERT: B 948 GLU cc_start: 0.8623 (tm-30) cc_final: 0.8390 (mp0) REVERT: C 154 MET cc_start: 0.9178 (OUTLIER) cc_final: 0.8957 (tpt) REVERT: D 148 PHE cc_start: 0.7755 (m-80) cc_final: 0.7252 (m-10) REVERT: D 314 MET cc_start: 0.9187 (tmm) cc_final: 0.8592 (ttp) REVERT: D 352 THR cc_start: 0.9328 (OUTLIER) cc_final: 0.9064 (p) REVERT: D 436 GLU cc_start: 0.7351 (tp30) cc_final: 0.6930 (tp30) REVERT: D 443 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.7005 (mpp80) REVERT: D 816 GLN cc_start: 0.7707 (OUTLIER) cc_final: 0.7340 (pt0) REVERT: D 948 GLU cc_start: 0.8551 (tp30) cc_final: 0.8247 (tt0) REVERT: G 138 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8470 (tm) REVERT: G 167 TRP cc_start: 0.8611 (OUTLIER) cc_final: 0.8258 (m-90) outliers start: 107 outliers final: 53 residues processed: 333 average time/residue: 0.5431 time to fit residues: 222.5991 Evaluate side-chains 296 residues out of total 3854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 233 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 102 CYS Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain F residue 102 CYS Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 166 TYR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 84 CYS Chi-restraints excluded: chain H residue 102 CYS Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 506 MET Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 609 PHE Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 1015 TYR Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain B residue 330 LYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 874 VAL Chi-restraints excluded: chain B residue 933 ILE Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1022 LEU Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain B residue 1043 LEU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 566 ILE Chi-restraints excluded: chain C residue 609 PHE Chi-restraints excluded: chain C residue 731 LEU Chi-restraints excluded: chain C residue 803 LEU Chi-restraints excluded: chain C residue 883 VAL Chi-restraints excluded: chain C residue 933 ILE Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 1015 TYR Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 443 ARG Chi-restraints excluded: chain D residue 557 CYS Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 816 GLN Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 949 LEU Chi-restraints excluded: chain D residue 1015 TYR Chi-restraints excluded: chain D residue 1022 LEU Chi-restraints excluded: chain D residue 1024 THR Chi-restraints excluded: chain G residue 2 PHE Chi-restraints excluded: chain G residue 102 CYS Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 167 TRP Chi-restraints excluded: chain G residue 176 PHE Chi-restraints excluded: chain G residue 183 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 320 optimal weight: 10.0000 chunk 192 optimal weight: 10.0000 chunk 91 optimal weight: 0.3980 chunk 32 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 418 optimal weight: 9.9990 chunk 404 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 24 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 136 GLN ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 771 HIS B 142 GLN B 157 ASN ** B 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 771 HIS G 136 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.094107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.064021 restraints weight = 79186.848| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 2.42 r_work: 0.2893 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.6292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 36843 Z= 0.144 Angle : 0.615 29.180 49904 Z= 0.297 Chirality : 0.049 1.861 5636 Planarity : 0.004 0.049 6137 Dihedral : 11.456 173.527 6012 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.04 % Favored : 96.87 % Rotamer: Outliers : 2.62 % Allowed : 15.52 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.13), residues: 4309 helix: 1.34 (0.11), residues: 2167 sheet: -0.00 (0.23), residues: 538 loop : -0.43 (0.15), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 185 TYR 0.030 0.001 TYR F 166 PHE 0.019 0.001 PHE B 550 TRP 0.048 0.001 TRP D 477 HIS 0.006 0.001 HIS H 131 Details of bonding type rmsd covalent geometry : bond 0.00332 (36826) covalent geometry : angle 0.61438 (49872) SS BOND : bond 0.00414 ( 16) SS BOND : angle 1.02337 ( 32) hydrogen bonds : bond 0.04605 ( 1742) hydrogen bonds : angle 4.32829 ( 4962) Misc. bond : bond 0.00209 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8618 Ramachandran restraints generated. 4309 Oldfield, 0 Emsley, 4309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8618 Ramachandran restraints generated. 4309 Oldfield, 0 Emsley, 4309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 242 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 96 PHE cc_start: 0.8576 (m-80) cc_final: 0.8012 (m-80) REVERT: E 131 HIS cc_start: 0.7285 (m-70) cc_final: 0.6961 (m-70) REVERT: E 142 LYS cc_start: 0.8045 (mtpt) cc_final: 0.7702 (tppp) REVERT: E 230 LYS cc_start: 0.7806 (mttt) cc_final: 0.7367 (mmtp) REVERT: F 96 PHE cc_start: 0.8665 (m-80) cc_final: 0.8009 (m-80) REVERT: F 162 ASN cc_start: 0.8899 (p0) cc_final: 0.8460 (p0) REVERT: F 192 HIS cc_start: 0.8834 (m-70) cc_final: 0.8527 (m90) REVERT: H 49 ARG cc_start: 0.8013 (mtm110) cc_final: 0.7631 (mtp180) REVERT: H 96 PHE cc_start: 0.8548 (m-80) cc_final: 0.8029 (m-80) REVERT: A 154 MET cc_start: 0.9092 (OUTLIER) cc_final: 0.8750 (mmm) REVERT: A 352 THR cc_start: 0.9106 (OUTLIER) cc_final: 0.8881 (p) REVERT: A 514 ARG cc_start: 0.9173 (OUTLIER) cc_final: 0.7902 (mtp85) REVERT: A 556 LEU cc_start: 0.9226 (mt) cc_final: 0.9009 (pp) REVERT: A 609 PHE cc_start: 0.7212 (OUTLIER) cc_final: 0.7010 (m-80) REVERT: B 330 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.7804 (pptt) REVERT: B 556 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9130 (tm) REVERT: B 568 ILE cc_start: 0.8404 (OUTLIER) cc_final: 0.8088 (tt) REVERT: B 694 TRP cc_start: 0.7765 (OUTLIER) cc_final: 0.7402 (t60) REVERT: B 772 ASN cc_start: 0.7544 (t0) cc_final: 0.7277 (t0) REVERT: B 948 GLU cc_start: 0.8694 (tm-30) cc_final: 0.8485 (mp0) REVERT: C 154 MET cc_start: 0.9185 (OUTLIER) cc_final: 0.8953 (tpt) REVERT: C 1022 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8301 (pp) REVERT: D 94 MET cc_start: 0.7199 (mpp) cc_final: 0.6726 (mmp) REVERT: D 148 PHE cc_start: 0.7749 (m-80) cc_final: 0.7241 (m-10) REVERT: D 314 MET cc_start: 0.9166 (OUTLIER) cc_final: 0.8664 (ttp) REVERT: D 352 THR cc_start: 0.9303 (OUTLIER) cc_final: 0.9047 (p) REVERT: D 436 GLU cc_start: 0.7514 (tp30) cc_final: 0.7064 (tp30) REVERT: D 443 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.7051 (mpp80) REVERT: D 568 ILE cc_start: 0.7837 (OUTLIER) cc_final: 0.7591 (tt) REVERT: D 816 GLN cc_start: 0.7719 (OUTLIER) cc_final: 0.7367 (pt0) REVERT: D 948 GLU cc_start: 0.8545 (tp30) cc_final: 0.8293 (tt0) REVERT: G 120 ASN cc_start: 0.7791 (t0) cc_final: 0.7256 (p0) REVERT: G 138 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8478 (tm) REVERT: G 167 TRP cc_start: 0.8606 (OUTLIER) cc_final: 0.8219 (m-90) outliers start: 101 outliers final: 56 residues processed: 323 average time/residue: 0.5984 time to fit residues: 237.1701 Evaluate side-chains 305 residues out of total 3854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 232 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 102 CYS Chi-restraints excluded: chain F residue 102 CYS Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 166 TYR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 84 CYS Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 609 PHE Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 1015 TYR Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain B residue 330 LYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 530 GLU Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 694 TRP Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 933 ILE Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain B residue 949 LEU Chi-restraints excluded: chain B residue 952 LEU Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1022 LEU Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain B residue 1043 LEU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 565 MET Chi-restraints excluded: chain C residue 566 ILE Chi-restraints excluded: chain C residue 568 ILE Chi-restraints excluded: chain C residue 609 PHE Chi-restraints excluded: chain C residue 731 LEU Chi-restraints excluded: chain C residue 803 LEU Chi-restraints excluded: chain C residue 883 VAL Chi-restraints excluded: chain C residue 933 ILE Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 1015 TYR Chi-restraints excluded: chain C residue 1022 LEU Chi-restraints excluded: chain D residue 314 MET Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 443 ARG Chi-restraints excluded: chain D residue 557 CYS Chi-restraints excluded: chain D residue 568 ILE Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 803 LEU Chi-restraints excluded: chain D residue 816 GLN Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 949 LEU Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 1015 TYR Chi-restraints excluded: chain D residue 1022 LEU Chi-restraints excluded: chain D residue 1024 THR Chi-restraints excluded: chain G residue 2 PHE Chi-restraints excluded: chain G residue 84 CYS Chi-restraints excluded: chain G residue 102 CYS Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 167 TRP Chi-restraints excluded: chain G residue 176 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 143 optimal weight: 6.9990 chunk 114 optimal weight: 9.9990 chunk 382 optimal weight: 20.0000 chunk 61 optimal weight: 1.9990 chunk 4 optimal weight: 40.0000 chunk 259 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 228 optimal weight: 7.9990 chunk 48 optimal weight: 9.9990 chunk 231 optimal weight: 9.9990 chunk 362 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 771 HIS B 142 GLN B 816 GLN ** C 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 771 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.090727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.060595 restraints weight = 79439.116| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.39 r_work: 0.2816 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.6693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 36843 Z= 0.248 Angle : 0.707 30.757 49904 Z= 0.348 Chirality : 0.052 1.811 5636 Planarity : 0.004 0.049 6137 Dihedral : 12.103 177.378 6012 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.34 % Favored : 96.57 % Rotamer: Outliers : 2.85 % Allowed : 15.54 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.13), residues: 4309 helix: 0.99 (0.11), residues: 2168 sheet: -0.00 (0.23), residues: 556 loop : -0.52 (0.15), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 151 TYR 0.028 0.002 TYR G 166 PHE 0.038 0.002 PHE B 550 TRP 0.057 0.002 TRP D 477 HIS 0.007 0.001 HIS B 771 Details of bonding type rmsd covalent geometry : bond 0.00586 (36826) covalent geometry : angle 0.70624 (49872) SS BOND : bond 0.01016 ( 16) SS BOND : angle 1.33854 ( 32) hydrogen bonds : bond 0.05710 ( 1742) hydrogen bonds : angle 4.64609 ( 4962) Misc. bond : bond 0.00353 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8618 Ramachandran restraints generated. 4309 Oldfield, 0 Emsley, 4309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8618 Ramachandran restraints generated. 4309 Oldfield, 0 Emsley, 4309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 233 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 96 PHE cc_start: 0.8644 (m-80) cc_final: 0.8106 (m-80) REVERT: E 131 HIS cc_start: 0.7097 (m-70) cc_final: 0.6635 (m-70) REVERT: E 142 LYS cc_start: 0.8145 (mtpt) cc_final: 0.7889 (tppp) REVERT: E 230 LYS cc_start: 0.7786 (mttt) cc_final: 0.7373 (mmtp) REVERT: E 232 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8178 (pp20) REVERT: F 96 PHE cc_start: 0.8636 (m-80) cc_final: 0.7843 (m-80) REVERT: F 162 ASN cc_start: 0.8908 (p0) cc_final: 0.8469 (p0) REVERT: F 192 HIS cc_start: 0.8980 (m-70) cc_final: 0.8686 (m90) REVERT: H 96 PHE cc_start: 0.8568 (m-80) cc_final: 0.8043 (m-80) REVERT: A 154 MET cc_start: 0.9179 (OUTLIER) cc_final: 0.8851 (mmm) REVERT: A 352 THR cc_start: 0.9117 (OUTLIER) cc_final: 0.8855 (p) REVERT: A 514 ARG cc_start: 0.9186 (OUTLIER) cc_final: 0.7813 (mtp85) REVERT: A 609 PHE cc_start: 0.7215 (OUTLIER) cc_final: 0.6892 (t80) REVERT: A 761 GLU cc_start: 0.8489 (mp0) cc_final: 0.8251 (mm-30) REVERT: B 314 MET cc_start: 0.9244 (ttp) cc_final: 0.9035 (ttp) REVERT: B 330 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.7947 (pptt) REVERT: B 556 LEU cc_start: 0.9457 (OUTLIER) cc_final: 0.9217 (tm) REVERT: B 772 ASN cc_start: 0.8253 (OUTLIER) cc_final: 0.8046 (t0) REVERT: C 154 MET cc_start: 0.9219 (mmm) cc_final: 0.9004 (tpt) REVERT: C 514 ARG cc_start: 0.9060 (OUTLIER) cc_final: 0.7921 (mtt-85) REVERT: D 94 MET cc_start: 0.7797 (mpp) cc_final: 0.7459 (mmp) REVERT: D 148 PHE cc_start: 0.7806 (m-80) cc_final: 0.7291 (m-10) REVERT: D 314 MET cc_start: 0.9141 (OUTLIER) cc_final: 0.8833 (ttp) REVERT: D 329 ARG cc_start: 0.7232 (mtt180) cc_final: 0.7031 (mtt180) REVERT: D 352 THR cc_start: 0.9300 (OUTLIER) cc_final: 0.9066 (p) REVERT: D 460 MET cc_start: 0.8924 (mmt) cc_final: 0.8689 (mmt) REVERT: D 564 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8695 (tt) REVERT: D 568 ILE cc_start: 0.8316 (OUTLIER) cc_final: 0.8064 (tt) REVERT: D 694 TRP cc_start: 0.8192 (OUTLIER) cc_final: 0.7727 (t60) REVERT: D 816 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.7643 (pt0) REVERT: G 127 ARG cc_start: 0.8260 (ppp80) cc_final: 0.8031 (ttt180) REVERT: G 138 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8563 (tm) REVERT: G 167 TRP cc_start: 0.8667 (OUTLIER) cc_final: 0.8326 (m-90) outliers start: 110 outliers final: 51 residues processed: 317 average time/residue: 0.5705 time to fit residues: 221.7693 Evaluate side-chains 287 residues out of total 3854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 219 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 102 CYS Chi-restraints excluded: chain E residue 232 GLU Chi-restraints excluded: chain F residue 102 CYS Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain H residue 84 CYS Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 176 PHE Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 609 PHE Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 330 LYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 530 GLU Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 772 ASN Chi-restraints excluded: chain B residue 933 ILE Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain B residue 960 ARG Chi-restraints excluded: chain B residue 965 THR Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1022 LEU Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain B residue 1043 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 514 ARG Chi-restraints excluded: chain C residue 565 MET Chi-restraints excluded: chain C residue 566 ILE Chi-restraints excluded: chain C residue 609 PHE Chi-restraints excluded: chain C residue 731 LEU Chi-restraints excluded: chain C residue 803 LEU Chi-restraints excluded: chain C residue 883 VAL Chi-restraints excluded: chain C residue 933 ILE Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 1015 TYR Chi-restraints excluded: chain D residue 314 MET Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 568 ILE Chi-restraints excluded: chain D residue 694 TRP Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 816 GLN Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 1022 LEU Chi-restraints excluded: chain D residue 1024 THR Chi-restraints excluded: chain G residue 2 PHE Chi-restraints excluded: chain G residue 84 CYS Chi-restraints excluded: chain G residue 102 CYS Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 167 TRP Chi-restraints excluded: chain G residue 176 PHE Chi-restraints excluded: chain G residue 183 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 235 optimal weight: 6.9990 chunk 54 optimal weight: 20.0000 chunk 65 optimal weight: 3.9990 chunk 153 optimal weight: 20.0000 chunk 97 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 203 optimal weight: 7.9990 chunk 379 optimal weight: 0.0470 chunk 256 optimal weight: 3.9990 chunk 326 optimal weight: 20.0000 overall best weight: 4.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 771 HIS ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 772 ASN B 816 GLN ** C 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 771 HIS G 136 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.091355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.061349 restraints weight = 79978.183| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 2.41 r_work: 0.2834 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.6848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 36843 Z= 0.190 Angle : 0.656 29.514 49904 Z= 0.319 Chirality : 0.051 1.843 5636 Planarity : 0.004 0.048 6137 Dihedral : 11.840 174.351 6012 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.20 % Favored : 96.70 % Rotamer: Outliers : 2.15 % Allowed : 16.32 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.13), residues: 4309 helix: 1.11 (0.11), residues: 2169 sheet: -0.00 (0.23), residues: 556 loop : -0.53 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 735 TYR 0.016 0.002 TYR E 166 PHE 0.026 0.002 PHE B 550 TRP 0.053 0.001 TRP D 477 HIS 0.005 0.001 HIS B 771 Details of bonding type rmsd covalent geometry : bond 0.00449 (36826) covalent geometry : angle 0.65536 (49872) SS BOND : bond 0.00267 ( 16) SS BOND : angle 1.22065 ( 32) hydrogen bonds : bond 0.05009 ( 1742) hydrogen bonds : angle 4.48487 ( 4962) Misc. bond : bond 0.00148 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8618 Ramachandran restraints generated. 4309 Oldfield, 0 Emsley, 4309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8618 Ramachandran restraints generated. 4309 Oldfield, 0 Emsley, 4309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 227 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 96 PHE cc_start: 0.8609 (m-80) cc_final: 0.8078 (m-80) REVERT: E 131 HIS cc_start: 0.6973 (m-70) cc_final: 0.6404 (m-70) REVERT: E 142 LYS cc_start: 0.8050 (mtpt) cc_final: 0.7785 (tppp) REVERT: F 96 PHE cc_start: 0.8607 (m-80) cc_final: 0.7833 (m-80) REVERT: F 127 ARG cc_start: 0.6983 (mtm180) cc_final: 0.6465 (ttt-90) REVERT: F 162 ASN cc_start: 0.8872 (p0) cc_final: 0.8456 (p0) REVERT: F 192 HIS cc_start: 0.8984 (m-70) cc_final: 0.8699 (m90) REVERT: H 96 PHE cc_start: 0.8536 (m-80) cc_final: 0.8019 (m-80) REVERT: H 168 LYS cc_start: 0.8834 (pptt) cc_final: 0.8581 (ptpp) REVERT: A 154 MET cc_start: 0.9120 (OUTLIER) cc_final: 0.8765 (mmm) REVERT: A 352 THR cc_start: 0.9076 (OUTLIER) cc_final: 0.8811 (p) REVERT: A 514 ARG cc_start: 0.9088 (OUTLIER) cc_final: 0.7838 (mtp85) REVERT: A 609 PHE cc_start: 0.7264 (OUTLIER) cc_final: 0.6961 (t80) REVERT: A 761 GLU cc_start: 0.8380 (mp0) cc_final: 0.8167 (mm-30) REVERT: B 314 MET cc_start: 0.9180 (ttp) cc_final: 0.8861 (ttp) REVERT: B 330 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.7947 (pptt) REVERT: C 154 MET cc_start: 0.9166 (mmm) cc_final: 0.8935 (tpt) REVERT: C 514 ARG cc_start: 0.8965 (OUTLIER) cc_final: 0.7869 (mtt-85) REVERT: D 94 MET cc_start: 0.7926 (mpp) cc_final: 0.7557 (mmp) REVERT: D 148 PHE cc_start: 0.7787 (m-80) cc_final: 0.7284 (m-10) REVERT: D 314 MET cc_start: 0.9149 (OUTLIER) cc_final: 0.8684 (ttp) REVERT: D 329 ARG cc_start: 0.7182 (mtt180) cc_final: 0.6955 (mtt180) REVERT: D 352 THR cc_start: 0.9300 (OUTLIER) cc_final: 0.9066 (p) REVERT: D 460 MET cc_start: 0.8928 (mmt) cc_final: 0.8664 (mmt) REVERT: D 568 ILE cc_start: 0.8230 (OUTLIER) cc_final: 0.7954 (tt) REVERT: D 694 TRP cc_start: 0.8065 (OUTLIER) cc_final: 0.7753 (t60) REVERT: D 816 GLN cc_start: 0.7925 (OUTLIER) cc_final: 0.7695 (pt0) REVERT: G 138 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8542 (tm) REVERT: G 167 TRP cc_start: 0.8632 (OUTLIER) cc_final: 0.8254 (m-90) outliers start: 83 outliers final: 47 residues processed: 293 average time/residue: 0.5660 time to fit residues: 204.1788 Evaluate side-chains 282 residues out of total 3854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 222 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 83 ASN Chi-restraints excluded: chain E residue 102 CYS Chi-restraints excluded: chain F residue 102 CYS Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain H residue 84 CYS Chi-restraints excluded: chain H residue 105 ASP Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 609 PHE Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 330 LYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 712 MET Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 933 ILE Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain B residue 960 ARG Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1015 TYR Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain B residue 1043 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 514 ARG Chi-restraints excluded: chain C residue 566 ILE Chi-restraints excluded: chain C residue 568 ILE Chi-restraints excluded: chain C residue 731 LEU Chi-restraints excluded: chain C residue 803 LEU Chi-restraints excluded: chain C residue 883 VAL Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 1015 TYR Chi-restraints excluded: chain D residue 314 MET Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 477 TRP Chi-restraints excluded: chain D residue 568 ILE Chi-restraints excluded: chain D residue 694 TRP Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 816 GLN Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 1015 TYR Chi-restraints excluded: chain D residue 1022 LEU Chi-restraints excluded: chain D residue 1024 THR Chi-restraints excluded: chain G residue 2 PHE Chi-restraints excluded: chain G residue 84 CYS Chi-restraints excluded: chain G residue 102 CYS Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 167 TRP Chi-restraints excluded: chain G residue 176 PHE Chi-restraints excluded: chain G residue 183 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 170 optimal weight: 3.9990 chunk 323 optimal weight: 0.0370 chunk 337 optimal weight: 2.9990 chunk 192 optimal weight: 8.9990 chunk 257 optimal weight: 4.9990 chunk 392 optimal weight: 0.0010 chunk 236 optimal weight: 0.1980 chunk 370 optimal weight: 4.9990 chunk 37 optimal weight: 8.9990 chunk 30 optimal weight: 20.0000 chunk 409 optimal weight: 10.0000 overall best weight: 1.4468 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 GLN A 771 HIS B 142 GLN B 816 GLN ** C 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 771 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.092698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.062888 restraints weight = 79643.100| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.40 r_work: 0.2873 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.6930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 36843 Z= 0.124 Angle : 0.638 28.805 49904 Z= 0.306 Chirality : 0.049 1.866 5636 Planarity : 0.004 0.047 6137 Dihedral : 11.505 172.585 6012 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.83 % Favored : 97.10 % Rotamer: Outliers : 1.74 % Allowed : 16.89 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.13), residues: 4309 helix: 1.28 (0.11), residues: 2171 sheet: -0.04 (0.23), residues: 556 loop : -0.49 (0.16), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 151 TYR 0.026 0.001 TYR G 166 PHE 0.016 0.001 PHE B 148 TRP 0.049 0.001 TRP D 477 HIS 0.002 0.000 HIS C 771 Details of bonding type rmsd covalent geometry : bond 0.00275 (36826) covalent geometry : angle 0.63693 (49872) SS BOND : bond 0.00387 ( 16) SS BOND : angle 1.59164 ( 32) hydrogen bonds : bond 0.04438 ( 1742) hydrogen bonds : angle 4.35096 ( 4962) Misc. bond : bond 0.00222 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8618 Ramachandran restraints generated. 4309 Oldfield, 0 Emsley, 4309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8618 Ramachandran restraints generated. 4309 Oldfield, 0 Emsley, 4309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 3854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 229 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 96 PHE cc_start: 0.8597 (m-80) cc_final: 0.8073 (m-80) REVERT: E 142 LYS cc_start: 0.7991 (mtpt) cc_final: 0.7705 (tppp) REVERT: F 96 PHE cc_start: 0.8613 (m-80) cc_final: 0.7781 (m-80) REVERT: F 127 ARG cc_start: 0.6922 (mtm180) cc_final: 0.6439 (ttt-90) REVERT: F 162 ASN cc_start: 0.8865 (p0) cc_final: 0.8441 (p0) REVERT: F 192 HIS cc_start: 0.8993 (m-70) cc_final: 0.8721 (m90) REVERT: H 96 PHE cc_start: 0.8539 (m-80) cc_final: 0.8014 (m-80) REVERT: H 161 MET cc_start: 0.9138 (mmm) cc_final: 0.8714 (mmm) REVERT: H 180 PHE cc_start: 0.8088 (t80) cc_final: 0.7578 (t80) REVERT: A 154 MET cc_start: 0.9076 (OUTLIER) cc_final: 0.8736 (mmm) REVERT: A 352 THR cc_start: 0.9061 (OUTLIER) cc_final: 0.8822 (p) REVERT: A 514 ARG cc_start: 0.9091 (OUTLIER) cc_final: 0.8044 (mtp85) REVERT: A 565 MET cc_start: 0.7539 (OUTLIER) cc_final: 0.6883 (mmm) REVERT: A 609 PHE cc_start: 0.7263 (OUTLIER) cc_final: 0.6913 (t80) REVERT: A 761 GLU cc_start: 0.8354 (mp0) cc_final: 0.8047 (mm-30) REVERT: B 94 MET cc_start: 0.8831 (OUTLIER) cc_final: 0.8463 (mpp) REVERT: B 330 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.7899 (pptt) REVERT: B 460 MET cc_start: 0.8955 (mmp) cc_final: 0.8454 (mmt) REVERT: B 816 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.7872 (pm20) REVERT: B 950 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7555 (mp0) REVERT: C 154 MET cc_start: 0.9152 (mmm) cc_final: 0.8914 (tpt) REVERT: C 514 ARG cc_start: 0.8943 (OUTLIER) cc_final: 0.7330 (mtt-85) REVERT: D 148 PHE cc_start: 0.7748 (m-80) cc_final: 0.7252 (m-10) REVERT: D 329 ARG cc_start: 0.7201 (mtt180) cc_final: 0.6986 (mtt180) REVERT: D 352 THR cc_start: 0.9285 (OUTLIER) cc_final: 0.9064 (p) REVERT: D 460 MET cc_start: 0.8894 (mmt) cc_final: 0.8552 (mmp) REVERT: D 694 TRP cc_start: 0.7966 (OUTLIER) cc_final: 0.7728 (t60) REVERT: D 816 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7650 (pt0) REVERT: G 167 TRP cc_start: 0.8651 (OUTLIER) cc_final: 0.8229 (m-90) outliers start: 67 outliers final: 42 residues processed: 284 average time/residue: 0.5363 time to fit residues: 186.1549 Evaluate side-chains 275 residues out of total 3854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 220 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 83 ASN Chi-restraints excluded: chain E residue 102 CYS Chi-restraints excluded: chain F residue 84 CYS Chi-restraints excluded: chain F residue 102 CYS Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain H residue 84 CYS Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 609 PHE Chi-restraints excluded: chain A residue 771 HIS Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 330 LYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 816 GLN Chi-restraints excluded: chain B residue 933 ILE Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain B residue 960 ARG Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain B residue 1043 LEU Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 514 ARG Chi-restraints excluded: chain C residue 566 ILE Chi-restraints excluded: chain C residue 609 PHE Chi-restraints excluded: chain C residue 731 LEU Chi-restraints excluded: chain C residue 803 LEU Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 1015 TYR Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 694 TRP Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 816 GLN Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 949 LEU Chi-restraints excluded: chain D residue 1015 TYR Chi-restraints excluded: chain D residue 1022 LEU Chi-restraints excluded: chain D residue 1024 THR Chi-restraints excluded: chain G residue 2 PHE Chi-restraints excluded: chain G residue 84 CYS Chi-restraints excluded: chain G residue 102 CYS Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 167 TRP Chi-restraints excluded: chain G residue 176 PHE Chi-restraints excluded: chain G residue 183 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 103 optimal weight: 10.0000 chunk 425 optimal weight: 6.9990 chunk 165 optimal weight: 8.9990 chunk 428 optimal weight: 5.9990 chunk 187 optimal weight: 0.0980 chunk 212 optimal weight: 10.0000 chunk 276 optimal weight: 4.9990 chunk 54 optimal weight: 20.0000 chunk 316 optimal weight: 8.9990 chunk 287 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 overall best weight: 5.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 816 GLN ** C 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 771 HIS G 136 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.090066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.060090 restraints weight = 79578.455| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.39 r_work: 0.2813 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.7009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 36843 Z= 0.238 Angle : 0.709 30.431 49904 Z= 0.345 Chirality : 0.052 1.818 5636 Planarity : 0.004 0.057 6137 Dihedral : 11.834 176.489 6012 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.32 % Favored : 96.59 % Rotamer: Outliers : 2.13 % Allowed : 16.45 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 aren not related in a simple way. whole: 0.46 (0.13), residues: 4309 helix: 1.05 (0.11), residues: 2180 sheet: -0.00 (0.23), residues: 556 loop : -0.52 (0.16), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 735 TYR 0.021 0.002 TYR A 928 PHE 0.029 0.002 PHE B 550 TRP 0.062 0.002 TRP D 477 HIS 0.008 0.001 HIS A 771 Details of bonding type rmsd covalent geometry : bond 0.00564 (36826) covalent geometry : angle 0.70895 (49872) SS BOND : bond 0.00310 ( 16) SS BOND : angle 1.19861 ( 32) hydrogen bonds : bond 0.05462 ( 1742) hydrogen bonds : angle 4.53003 ( 4962) Misc. bond : bond 0.00354 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14466.25 seconds wall clock time: 246 minutes 9.79 seconds (14769.79 seconds total)