Starting phenix.real_space_refine on Wed Mar 4 23:21:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7usy_26743/03_2026/7usy_26743.cif Found real_map, /net/cci-nas-00/data/ceres_data/7usy_26743/03_2026/7usy_26743.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7usy_26743/03_2026/7usy_26743.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7usy_26743/03_2026/7usy_26743.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7usy_26743/03_2026/7usy_26743.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7usy_26743/03_2026/7usy_26743.map" } resolution = 3.54 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= -0.000 sd= 1.000 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: 6 Type Number sf(0) Gaussians Ca 8 9.91 5 P 4 5.49 5 S 95 5.16 5 C 10812 2.51 5 N 2770 2.21 5 O 2893 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16582 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4864 Classifications: {'peptide': 602} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 18, 'TRANS': 583} Chain breaks: 1 Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 5, 'GLN:plan1': 2, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "B" Number of atoms: 4864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4864 Classifications: {'peptide': 602} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 18, 'TRANS': 583} Chain breaks: 1 Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 5, 'GLN:plan1': 2, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "C" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1536 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 176} Chain: "D" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 343 Classifications: {'peptide': 46} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 43} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1536 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 176} Chain: "F" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 343 Classifications: {'peptide': 46} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 43} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 2878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2878 Classifications: {'peptide': 361} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 339} Chain breaks: 1 Chain: "A" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 93 Unusual residues: {' CA': 2, '3PE': 1, 'NAG': 1, 'PEE': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 93 Unusual residues: {' CA': 2, '3PE': 1, 'NAG': 1, 'PEE': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 3.86, per 1000 atoms: 0.23 Number of scatterers: 16582 At special positions: 0 Unit cell: (143.469, 119.138, 156.893, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 8 19.99 S 95 16.00 P 4 15.00 O 2893 8.00 N 2770 7.00 C 10812 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 667 " - pdb=" SG CYS A 816 " distance=2.03 Simple disulfide: pdb=" SG CYS B 667 " - pdb=" SG CYS B 816 " 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: 1.50 Conformation dependent library (CDL) restraints added in 586.4 milliseconds 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3868 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 9 sheets defined 61.7% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 75 through 93 Processing helix chain 'A' and resid 94 through 96 No H-bonds generated for 'chain 'A' and resid 94 through 96' Processing helix chain 'A' and resid 99 through 119 removed outlier: 4.330A pdb=" N SER A 119 " --> pdb=" O GLU A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 147 Processing helix chain 'A' and resid 152 through 164 Processing helix chain 'A' and resid 167 through 191 removed outlier: 3.888A pdb=" N PHE A 171 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE A 191 " --> pdb=" O ILE A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 202 Processing helix chain 'A' and resid 204 through 216 removed outlier: 5.126A pdb=" N THR A 213 " --> pdb=" O ASN A 209 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ARG A 214 " --> pdb=" O ARG A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 223 removed outlier: 3.996A pdb=" N VAL A 223 " --> pdb=" O ALA A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 248 removed outlier: 3.706A pdb=" N TYR A 247 " --> pdb=" O PHE A 244 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR A 248 " --> pdb=" O TYR A 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 244 through 248' Processing helix chain 'A' and resid 261 through 290 removed outlier: 3.608A pdb=" N PHE A 274 " --> pdb=" O THR A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 309 Processing helix chain 'A' and resid 318 through 343 Processing helix chain 'A' and resid 349 through 381 removed outlier: 3.625A pdb=" N CYS A 364 " --> pdb=" O ASN A 360 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 417 removed outlier: 3.536A pdb=" N VAL A 399 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER A 400 " --> pdb=" O PRO A 396 " (cutoff:3.500A) Proline residue: A 407 - end of helix removed outlier: 3.688A pdb=" N LYS A 415 " --> pdb=" O ASP A 411 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N MET A 416 " --> pdb=" O LEU A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 459 Processing helix chain 'A' and resid 667 through 695 removed outlier: 3.716A pdb=" N ILE A 671 " --> pdb=" O CYS A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 706 Processing helix chain 'A' and resid 724 through 743 removed outlier: 3.542A pdb=" N ASN A 728 " --> pdb=" O LYS A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 772 removed outlier: 3.624A pdb=" N ILE A 752 " --> pdb=" O LEU A 748 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE A 755 " --> pdb=" O ALA A 751 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN A 772 " --> pdb=" O VAL A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 809 Proline residue: A 802 - end of helix Processing helix chain 'A' and resid 826 through 837 removed outlier: 3.985A pdb=" N GLU A 832 " --> pdb=" O VAL A 828 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS A 835 " --> pdb=" O ARG A 831 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG A 836 " --> pdb=" O GLU A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 847 removed outlier: 3.693A pdb=" N HIS A 847 " --> pdb=" O SER A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 880 Proline residue: A 856 - end of helix Processing helix chain 'B' and resid 76 through 93 Processing helix chain 'B' and resid 99 through 119 removed outlier: 4.490A pdb=" N SER B 119 " --> pdb=" O GLU B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 147 Processing helix chain 'B' and resid 152 through 164 removed outlier: 3.922A pdb=" N ILE B 156 " --> pdb=" O TRP B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 191 removed outlier: 4.061A pdb=" N TYR B 170 " --> pdb=" O VAL B 166 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE B 171 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE B 191 " --> pdb=" O ILE B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 202 Processing helix chain 'B' and resid 204 through 216 removed outlier: 5.116A pdb=" N THR B 213 " --> pdb=" O ASN B 209 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N ARG B 214 " --> pdb=" O ARG B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 223 removed outlier: 4.093A pdb=" N VAL B 223 " --> pdb=" O ALA B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 248 removed outlier: 3.615A pdb=" N TYR B 247 " --> pdb=" O PHE B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 290 removed outlier: 3.760A pdb=" N PHE B 274 " --> pdb=" O THR B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 309 Processing helix chain 'B' and resid 318 through 343 Processing helix chain 'B' and resid 349 through 381 removed outlier: 3.538A pdb=" N SER B 381 " --> pdb=" O ALA B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 417 removed outlier: 4.014A pdb=" N SER B 397 " --> pdb=" O ASN B 393 " (cutoff:3.500A) Proline residue: B 407 - end of helix removed outlier: 3.901A pdb=" N MET B 416 " --> pdb=" O LEU B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 459 Processing helix chain 'B' and resid 667 through 695 Processing helix chain 'B' and resid 695 through 706 Processing helix chain 'B' and resid 712 through 716 Processing helix chain 'B' and resid 724 through 743 Processing helix chain 'B' and resid 748 through 771 removed outlier: 3.783A pdb=" N ILE B 755 " --> pdb=" O ALA B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 809 Proline residue: B 802 - end of helix Processing helix chain 'B' and resid 826 through 834 removed outlier: 3.710A pdb=" N GLU B 832 " --> pdb=" O VAL B 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 838 through 847 removed outlier: 3.578A pdb=" N HIS B 847 " --> pdb=" O SER B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 850 through 880 Proline residue: B 856 - end of helix Processing helix chain 'C' and resid 21 through 32 Processing helix chain 'C' and resid 35 through 50 removed outlier: 3.763A pdb=" N ASN C 50 " --> pdb=" O PHE C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 66 Processing helix chain 'C' and resid 70 through 75 Processing helix chain 'C' and resid 84 through 93 Processing helix chain 'C' and resid 102 through 112 Processing helix chain 'C' and resid 117 through 130 Processing helix chain 'C' and resid 138 through 150 Processing helix chain 'C' and resid 155 through 170 Processing helix chain 'C' and resid 179 through 188 removed outlier: 3.676A pdb=" N SER C 188 " --> pdb=" O GLU C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 197 Processing helix chain 'D' and resid 23 through 45 Processing helix chain 'D' and resid 53 through 63 Processing helix chain 'E' and resid 21 through 32 Processing helix chain 'E' and resid 35 through 50 removed outlier: 3.895A pdb=" N ASN E 50 " --> pdb=" O PHE E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 66 removed outlier: 3.516A pdb=" N ILE E 65 " --> pdb=" O ASN E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 75 Processing helix chain 'E' and resid 84 through 93 Processing helix chain 'E' and resid 102 through 112 Processing helix chain 'E' and resid 117 through 130 removed outlier: 3.845A pdb=" N ASP E 130 " --> pdb=" O PHE E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 151 Processing helix chain 'E' and resid 155 through 170 Processing helix chain 'E' and resid 179 through 188 Processing helix chain 'E' and resid 192 through 197 Processing helix chain 'F' and resid 23 through 46 removed outlier: 3.704A pdb=" N PHE F 45 " --> pdb=" O ILE F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 63 Processing helix chain 'J' and resid 179 through 184 removed outlier: 3.533A pdb=" N LEU J 183 " --> pdb=" O GLU J 179 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER J 184 " --> pdb=" O GLU J 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 179 through 184' Processing helix chain 'J' and resid 362 through 366 removed outlier: 3.598A pdb=" N ARG J 366 " --> pdb=" O PRO J 363 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 67 through 69 Processing sheet with id=AA2, first strand: chain 'E' and resid 67 through 69 Processing sheet with id=AA3, first strand: chain 'J' and resid 31 through 37 Processing sheet with id=AA4, first strand: chain 'J' and resid 42 through 43 removed outlier: 4.575A pdb=" N TYR J 43 " --> pdb=" O THR J 169 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N TYR J 148 " --> pdb=" O PHE J 168 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ILE J 170 " --> pdb=" O ILE J 146 " (cutoff:3.500A) removed outlier: 10.413A pdb=" N ILE J 146 " --> pdb=" O ILE J 170 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY J 65 " --> pdb=" O ASP J 155 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE J 66 " --> pdb=" O LEU J 102 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU J 96 " --> pdb=" O GLY J 72 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N VAL J 74 " --> pdb=" O TYR J 94 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N TYR J 94 " --> pdb=" O VAL J 74 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ALA J 76 " --> pdb=" O ASP J 92 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ASP J 92 " --> pdb=" O ALA J 76 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N LEU J 78 " --> pdb=" O LYS J 90 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LYS J 90 " --> pdb=" O LEU J 78 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N VAL J 80 " --> pdb=" O THR J 88 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N THR J 88 " --> pdb=" O VAL J 80 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LYS J 82 " --> pdb=" O ARG J 86 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ARG J 86 " --> pdb=" O LYS J 82 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'J' and resid 42 through 43 removed outlier: 4.575A pdb=" N TYR J 43 " --> pdb=" O THR J 169 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N TYR J 148 " --> pdb=" O PHE J 168 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ILE J 170 " --> pdb=" O ILE J 146 " (cutoff:3.500A) removed outlier: 10.413A pdb=" N ILE J 146 " --> pdb=" O ILE J 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'J' and resid 186 through 193 Processing sheet with id=AA7, first strand: chain 'J' and resid 214 through 216 removed outlier: 5.625A pdb=" N TYR J 215 " --> pdb=" O ALA J 332 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N GLU J 321 " --> pdb=" O ASP J 316 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ASP J 316 " --> pdb=" O GLU J 321 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N LEU J 323 " --> pdb=" O MET J 314 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N MET J 314 " --> pdb=" O LEU J 323 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N TYR J 308 " --> pdb=" O LEU J 329 " (cutoff:3.500A) removed outlier: 8.533A pdb=" N VAL J 331 " --> pdb=" O ILE J 306 " (cutoff:3.500A) removed outlier: 11.815A pdb=" N ILE J 306 " --> pdb=" O VAL J 331 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU J 256 " --> pdb=" O VAL J 249 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 214 through 216 removed outlier: 5.625A pdb=" N TYR J 215 " --> pdb=" O ALA J 332 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N GLU J 321 " --> pdb=" O ASP J 316 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ASP J 316 " --> pdb=" O GLU J 321 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N LEU J 323 " --> pdb=" O MET J 314 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N MET J 314 " --> pdb=" O LEU J 323 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N TYR J 308 " --> pdb=" O LEU J 329 " (cutoff:3.500A) removed outlier: 8.533A pdb=" N VAL J 331 " --> pdb=" O ILE J 306 " (cutoff:3.500A) removed outlier: 11.815A pdb=" N ILE J 306 " --> pdb=" O VAL J 331 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU J 237 " --> pdb=" O LYS J 268 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LYS J 268 " --> pdb=" O LEU J 237 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE J 239 " --> pdb=" O GLU J 266 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLU J 266 " --> pdb=" O ILE J 239 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU J 241 " --> pdb=" O VAL J 264 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 347 through 350 997 hydrogen bonds defined for protein. 2964 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: 2.60 Time building geometry restraints manager: 1.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2562 1.31 - 1.44: 4665 1.44 - 1.56: 9560 1.56 - 1.69: 9 1.69 - 1.82: 152 Bond restraints: 16948 Sorted by residual: bond pdb=" C21 3PE B1304 " pdb=" O21 3PE B1304 " ideal model delta sigma weight residual 1.316 1.399 -0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" C21 3PE A1304 " pdb=" O21 3PE A1304 " ideal model delta sigma weight residual 1.316 1.398 -0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" C30 PEE B1303 " pdb=" O3 PEE B1303 " ideal model delta sigma weight residual 1.327 1.400 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C30 PEE A1303 " pdb=" O3 PEE A1303 " ideal model delta sigma weight residual 1.327 1.397 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" C31 3PE A1304 " pdb=" O31 3PE A1304 " ideal model delta sigma weight residual 1.331 1.400 -0.069 2.00e-02 2.50e+03 1.19e+01 ... (remaining 16943 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.37: 22683 3.37 - 6.73: 186 6.73 - 10.10: 27 10.10 - 13.46: 4 13.46 - 16.83: 5 Bond angle restraints: 22905 Sorted by residual: angle pdb=" C ASN J 340 " pdb=" N ALA J 341 " pdb=" CA ALA J 341 " ideal model delta sigma weight residual 120.68 133.70 -13.02 1.52e+00 4.33e-01 7.34e+01 angle pdb=" N SER A 870 " pdb=" CA SER A 870 " pdb=" C SER A 870 " ideal model delta sigma weight residual 111.14 102.17 8.97 1.08e+00 8.57e-01 6.90e+01 angle pdb=" C MET A 810 " pdb=" N SER A 811 " pdb=" CA SER A 811 " ideal model delta sigma weight residual 121.61 132.79 -11.18 1.39e+00 5.18e-01 6.47e+01 angle pdb=" C GLN B 301 " pdb=" CA GLN B 301 " pdb=" CB GLN B 301 " ideal model delta sigma weight residual 116.54 109.86 6.68 1.15e+00 7.56e-01 3.37e+01 angle pdb=" O3P PEE A1303 " pdb=" P PEE A1303 " pdb=" O4P PEE A1303 " ideal model delta sigma weight residual 92.91 109.74 -16.83 3.00e+00 1.11e-01 3.15e+01 ... (remaining 22900 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.29: 9853 34.29 - 68.59: 340 68.59 - 102.88: 16 102.88 - 137.17: 1 137.17 - 171.47: 4 Dihedral angle restraints: 10214 sinusoidal: 4247 harmonic: 5967 Sorted by residual: dihedral pdb=" CA PRO J 344 " pdb=" C PRO J 344 " pdb=" N PRO J 345 " pdb=" CA PRO J 345 " ideal model delta harmonic sigma weight residual 180.00 -155.36 -24.64 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" C4 PEE A1303 " pdb=" O4P PEE A1303 " pdb=" P PEE A1303 " pdb=" O1P PEE A1303 " ideal model delta sinusoidal sigma weight residual 57.28 -131.25 -171.47 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C4 PEE B1303 " pdb=" O4P PEE B1303 " pdb=" P PEE B1303 " pdb=" O1P PEE B1303 " ideal model delta sinusoidal sigma weight residual 57.28 -141.02 -161.70 1 3.00e+01 1.11e-03 2.08e+01 ... (remaining 10211 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1798 0.038 - 0.076: 609 0.076 - 0.115: 149 0.115 - 0.153: 21 0.153 - 0.191: 3 Chirality restraints: 2580 Sorted by residual: chirality pdb=" C2 PEE A1303 " pdb=" C1 PEE A1303 " pdb=" C3 PEE A1303 " pdb=" O2 PEE A1303 " both_signs ideal model delta sigma weight residual False -2.33 -2.52 0.19 2.00e-01 2.50e+01 9.12e-01 chirality pdb=" CG LEU F 30 " pdb=" CB LEU F 30 " pdb=" CD1 LEU F 30 " pdb=" CD2 LEU F 30 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.18 2.00e-01 2.50e+01 8.54e-01 chirality pdb=" CA ILE J 338 " pdb=" N ILE J 338 " pdb=" C ILE J 338 " pdb=" CB ILE J 338 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.79e-01 ... (remaining 2577 not shown) Planarity restraints: 2843 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1305 " 0.202 2.00e-02 2.50e+03 1.67e-01 3.49e+02 pdb=" C7 NAG B1305 " -0.055 2.00e-02 2.50e+03 pdb=" C8 NAG B1305 " 0.146 2.00e-02 2.50e+03 pdb=" N2 NAG B1305 " -0.272 2.00e-02 2.50e+03 pdb=" O7 NAG B1305 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1305 " 0.115 2.00e-02 2.50e+03 9.50e-02 1.13e+02 pdb=" C7 NAG A1305 " -0.032 2.00e-02 2.50e+03 pdb=" C8 NAG A1305 " 0.087 2.00e-02 2.50e+03 pdb=" N2 NAG A1305 " -0.151 2.00e-02 2.50e+03 pdb=" O7 NAG A1305 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 395 " 0.087 5.00e-02 4.00e+02 1.28e-01 2.62e+01 pdb=" N PRO A 396 " -0.221 5.00e-02 4.00e+02 pdb=" CA PRO A 396 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO A 396 " 0.070 5.00e-02 4.00e+02 ... (remaining 2840 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.11: 4 2.11 - 2.81: 4491 2.81 - 3.51: 23112 3.51 - 4.20: 34922 4.20 - 4.90: 64703 Nonbonded interactions: 127232 Sorted by model distance: nonbonded pdb=" OD1 ASP C 171 " pdb="CA CA C 302 " model vdw 1.415 2.510 nonbonded pdb=" ND2 ASN A 209 " pdb=" C3 NAG A1305 " model vdw 1.424 3.550 nonbonded pdb=" ND2 ASN B 209 " pdb=" C3 NAG B1305 " model vdw 1.467 3.550 nonbonded pdb=" OE1 GLU C 182 " pdb="CA CA C 302 " model vdw 1.981 2.510 nonbonded pdb=" OE2 GLU C 182 " pdb="CA CA C 302 " model vdw 2.124 2.510 ... (remaining 127227 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' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.360 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6639 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 : 0.004 0.140 16951 Z= 0.214 Angle : 0.778 16.825 22909 Z= 0.402 Chirality : 0.041 0.191 2580 Planarity : 0.006 0.167 2843 Dihedral : 17.183 171.469 6340 Min Nonbonded Distance : 1.415 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.28 % Allowed : 23.12 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.19), residues: 2005 helix: 2.08 (0.15), residues: 1157 sheet: 0.95 (0.38), residues: 169 loop : -0.83 (0.24), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 64 TYR 0.032 0.001 TYR B 245 PHE 0.025 0.001 PHE A 376 TRP 0.018 0.001 TRP A 668 HIS 0.002 0.001 HIS A 731 Details of bonding type rmsd covalent geometry : bond 0.00368 (16948) covalent geometry : angle 0.77824 (22905) SS BOND : bond 0.00303 ( 2) SS BOND : angle 0.20502 ( 4) hydrogen bonds : bond 0.13196 ( 975) hydrogen bonds : angle 5.18175 ( 2964) Misc. bond : bond 0.14049 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 175 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 426 ARG cc_start: 0.6409 (mmm-85) cc_final: 0.5115 (mmt180) REVERT: A 451 MET cc_start: 0.4165 (tpt) cc_final: 0.3650 (tmm) REVERT: A 783 ARG cc_start: 0.6486 (mtt90) cc_final: 0.4234 (ptt-90) REVERT: A 826 TYR cc_start: 0.7461 (p90) cc_final: 0.6969 (p90) REVERT: A 836 ARG cc_start: 0.5039 (mtt90) cc_final: 0.3789 (mtm-85) REVERT: B 831 ARG cc_start: 0.6385 (mtm180) cc_final: 0.6039 (ttp-170) REVERT: F 30 LEU cc_start: 0.6673 (OUTLIER) cc_final: 0.6347 (mm) REVERT: J 314 MET cc_start: 0.1850 (mpp) cc_final: 0.1541 (mtt) outliers start: 5 outliers final: 2 residues processed: 180 average time/residue: 0.1348 time to fit residues: 36.4940 Evaluate side-chains 164 residues out of total 1819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 161 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain J residue 129 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 8.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.0670 overall best weight: 0.8722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN A 731 HIS A 736 GLN A 753 ASN B 879 ASN C 50 ASN ** C 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5208 r_free = 0.5208 target = 0.265486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.5180 r_free = 0.5180 target = 0.262270 restraints weight = 19908.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4891 r_free = 0.4891 target = 0.241494 restraints weight = 38739.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4855 r_free = 0.4855 target = 0.237547 restraints weight = 43262.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4859 r_free = 0.4859 target = 0.238121 restraints weight = 39225.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4856 r_free = 0.4856 target = 0.237933 restraints weight = 31784.678| |-----------------------------------------------------------------------------| r_work (final): 0.4887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6251 moved from start: 0.0809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16951 Z= 0.128 Angle : 0.547 8.177 22909 Z= 0.282 Chirality : 0.040 0.169 2580 Planarity : 0.004 0.065 2843 Dihedral : 10.507 178.341 2442 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.11 % Allowed : 20.75 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.19), residues: 2005 helix: 2.13 (0.15), residues: 1199 sheet: 1.16 (0.39), residues: 169 loop : -0.73 (0.25), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 105 TYR 0.025 0.001 TYR B 245 PHE 0.021 0.001 PHE E 105 TRP 0.013 0.001 TRP A 152 HIS 0.004 0.001 HIS A 404 Details of bonding type rmsd covalent geometry : bond 0.00286 (16948) covalent geometry : angle 0.54713 (22905) SS BOND : bond 0.00333 ( 2) SS BOND : angle 0.84330 ( 4) hydrogen bonds : bond 0.04177 ( 975) hydrogen bonds : angle 4.01082 ( 2964) Misc. bond : bond 0.00128 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 178 time to evaluate : 0.615 Fit side-chains revert: symmetry clash REVERT: A 245 TYR cc_start: 0.5142 (OUTLIER) cc_final: 0.3763 (t80) REVERT: A 451 MET cc_start: 0.4240 (tpt) cc_final: 0.3535 (tmm) REVERT: A 689 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7352 (tt) REVERT: A 735 ASN cc_start: 0.8132 (OUTLIER) cc_final: 0.7907 (t0) REVERT: A 783 ARG cc_start: 0.6516 (mtt90) cc_final: 0.4746 (ptt-90) REVERT: B 181 ASN cc_start: 0.8205 (OUTLIER) cc_final: 0.7747 (m-40) REVERT: B 740 TRP cc_start: 0.7319 (m-10) cc_final: 0.6949 (m-10) REVERT: J 44 TYR cc_start: 0.4526 (OUTLIER) cc_final: 0.3982 (m-10) REVERT: J 314 MET cc_start: 0.2994 (mpp) cc_final: 0.2428 (mtt) outliers start: 55 outliers final: 28 residues processed: 221 average time/residue: 0.1269 time to fit residues: 42.8961 Evaluate side-chains 195 residues out of total 1819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 162 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 735 ASN Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 702 ILE Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 771 CYS Chi-restraints excluded: chain B residue 833 ILE Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 50 ASN Chi-restraints excluded: chain C residue 52 HIS Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain E residue 28 TYR Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain J residue 44 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 140 optimal weight: 0.5980 chunk 34 optimal weight: 4.9990 chunk 154 optimal weight: 0.9980 chunk 153 optimal weight: 0.8980 chunk 86 optimal weight: 9.9990 chunk 172 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 chunk 141 optimal weight: 0.0670 chunk 99 optimal weight: 0.6980 chunk 129 optimal weight: 0.0050 chunk 122 optimal weight: 3.9990 overall best weight: 0.4532 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 HIS B 352 GLN B 420 HIS C 59 GLN D 56 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5217 r_free = 0.5217 target = 0.266629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.5178 r_free = 0.5178 target = 0.262456 restraints weight = 20165.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4879 r_free = 0.4879 target = 0.245194 restraints weight = 43817.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4846 r_free = 0.4846 target = 0.239249 restraints weight = 42575.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4849 r_free = 0.4849 target = 0.239683 restraints weight = 41605.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4842 r_free = 0.4842 target = 0.238777 restraints weight = 31343.230| |-----------------------------------------------------------------------------| r_work (final): 0.4872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6272 moved from start: 0.1065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16951 Z= 0.102 Angle : 0.482 7.082 22909 Z= 0.250 Chirality : 0.039 0.169 2580 Planarity : 0.004 0.051 2843 Dihedral : 9.781 174.860 2440 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.37 % Allowed : 21.65 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.19), residues: 2005 helix: 2.31 (0.15), residues: 1198 sheet: 1.21 (0.39), residues: 169 loop : -0.68 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 105 TYR 0.022 0.001 TYR B 245 PHE 0.018 0.001 PHE E 105 TRP 0.010 0.001 TRP A 668 HIS 0.003 0.000 HIS A 404 Details of bonding type rmsd covalent geometry : bond 0.00217 (16948) covalent geometry : angle 0.48219 (22905) SS BOND : bond 0.00232 ( 2) SS BOND : angle 0.51087 ( 4) hydrogen bonds : bond 0.03581 ( 975) hydrogen bonds : angle 3.81534 ( 2964) Misc. bond : bond 0.00061 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 177 time to evaluate : 0.566 Fit side-chains revert: symmetry clash REVERT: A 92 LYS cc_start: 0.6791 (tptt) cc_final: 0.6462 (tppt) REVERT: A 426 ARG cc_start: 0.6403 (OUTLIER) cc_final: 0.5165 (mmt180) REVERT: A 689 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7392 (tt) REVERT: A 783 ARG cc_start: 0.6441 (mtt90) cc_final: 0.4646 (ptt-90) REVERT: B 181 ASN cc_start: 0.8206 (OUTLIER) cc_final: 0.7735 (m-40) REVERT: B 327 MET cc_start: 0.6440 (mmt) cc_final: 0.6111 (mmt) REVERT: B 416 MET cc_start: 0.6567 (mmm) cc_final: 0.6242 (mmt) REVERT: E 79 LEU cc_start: 0.6228 (mp) cc_final: 0.5542 (mt) REVERT: J 44 TYR cc_start: 0.4435 (OUTLIER) cc_final: 0.3895 (m-10) REVERT: J 314 MET cc_start: 0.3034 (mpp) cc_final: 0.2416 (mtt) outliers start: 42 outliers final: 21 residues processed: 208 average time/residue: 0.1184 time to fit residues: 37.7926 Evaluate side-chains 189 residues out of total 1819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 164 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain A residue 426 ARG Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 771 CYS Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 52 HIS Chi-restraints excluded: chain C residue 59 GLN Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain E residue 28 TYR Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain J residue 44 TYR Chi-restraints excluded: chain J residue 54 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 87 optimal weight: 8.9990 chunk 188 optimal weight: 50.0000 chunk 12 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 195 optimal weight: 0.0470 chunk 53 optimal weight: 7.9990 chunk 156 optimal weight: 9.9990 chunk 155 optimal weight: 0.9980 chunk 187 optimal weight: 6.9990 chunk 167 optimal weight: 30.0000 overall best weight: 1.1880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 ASN A 731 HIS ** B 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 420 HIS C 57 ASN C 59 GLN D 56 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5192 r_free = 0.5192 target = 0.263435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.5160 r_free = 0.5160 target = 0.259711 restraints weight = 19936.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4868 r_free = 0.4868 target = 0.238817 restraints weight = 42151.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4840 r_free = 0.4840 target = 0.235786 restraints weight = 46413.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4839 r_free = 0.4839 target = 0.235951 restraints weight = 40786.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4838 r_free = 0.4838 target = 0.235856 restraints weight = 31468.041| |-----------------------------------------------------------------------------| r_work (final): 0.4876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6279 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16951 Z= 0.133 Angle : 0.515 13.856 22909 Z= 0.264 Chirality : 0.040 0.143 2580 Planarity : 0.004 0.051 2843 Dihedral : 9.710 177.533 2440 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.62 % Allowed : 21.71 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.19), residues: 2005 helix: 2.16 (0.15), residues: 1196 sheet: 1.29 (0.40), residues: 169 loop : -0.72 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 105 TYR 0.019 0.001 TYR A 245 PHE 0.021 0.001 PHE E 105 TRP 0.014 0.001 TRP B 740 HIS 0.005 0.001 HIS E 198 Details of bonding type rmsd covalent geometry : bond 0.00314 (16948) covalent geometry : angle 0.51480 (22905) SS BOND : bond 0.00522 ( 2) SS BOND : angle 0.28496 ( 4) hydrogen bonds : bond 0.03773 ( 975) hydrogen bonds : angle 3.79945 ( 2964) Misc. bond : bond 0.00080 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 170 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 245 TYR cc_start: 0.5295 (OUTLIER) cc_final: 0.3879 (t80) REVERT: A 268 MET cc_start: 0.6635 (tpp) cc_final: 0.6417 (tpp) REVERT: A 369 PHE cc_start: 0.7041 (t80) cc_final: 0.6710 (t80) REVERT: A 451 MET cc_start: 0.4312 (tpt) cc_final: 0.3367 (tmm) REVERT: A 689 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7409 (tt) REVERT: A 783 ARG cc_start: 0.6500 (mtt90) cc_final: 0.4714 (ptt-90) REVERT: B 181 ASN cc_start: 0.8241 (OUTLIER) cc_final: 0.7740 (m-40) REVERT: B 327 MET cc_start: 0.6500 (mmt) cc_final: 0.6200 (mmt) REVERT: B 415 LYS cc_start: 0.6977 (OUTLIER) cc_final: 0.6764 (mtpt) REVERT: B 416 MET cc_start: 0.6520 (mmm) cc_final: 0.6319 (mmt) REVERT: E 114 GLU cc_start: 0.6786 (OUTLIER) cc_final: 0.4942 (pm20) REVERT: J 44 TYR cc_start: 0.4534 (OUTLIER) cc_final: 0.3973 (m-10) REVERT: J 314 MET cc_start: 0.3098 (mpp) cc_final: 0.2460 (mtt) outliers start: 64 outliers final: 42 residues processed: 221 average time/residue: 0.1184 time to fit residues: 40.6096 Evaluate side-chains 213 residues out of total 1819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 165 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain A residue 426 ARG Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 415 LYS Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 702 ILE Chi-restraints excluded: chain B residue 733 ILE Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 771 CYS Chi-restraints excluded: chain B residue 833 ILE Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 52 HIS Chi-restraints excluded: chain C residue 59 GLN Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 28 TYR Chi-restraints excluded: chain E residue 114 GLU Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain J residue 44 TYR Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 338 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 89 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 74 optimal weight: 4.9990 chunk 1 optimal weight: 30.0000 chunk 121 optimal weight: 4.9990 chunk 144 optimal weight: 0.9990 chunk 28 optimal weight: 0.4980 chunk 49 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 HIS ** B 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 420 HIS C 59 GLN D 56 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5202 r_free = 0.5202 target = 0.264774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.5171 r_free = 0.5171 target = 0.261240 restraints weight = 19962.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4854 r_free = 0.4854 target = 0.239217 restraints weight = 42300.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4828 r_free = 0.4828 target = 0.235185 restraints weight = 43829.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4827 r_free = 0.4827 target = 0.235526 restraints weight = 44421.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4826 r_free = 0.4826 target = 0.235389 restraints weight = 32869.875| |-----------------------------------------------------------------------------| r_work (final): 0.4860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6302 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16951 Z= 0.104 Angle : 0.476 9.837 22909 Z= 0.246 Chirality : 0.039 0.142 2580 Planarity : 0.004 0.051 2843 Dihedral : 9.570 179.569 2440 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.00 % Allowed : 23.29 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.19), residues: 2005 helix: 2.26 (0.15), residues: 1201 sheet: 1.33 (0.40), residues: 169 loop : -0.70 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 105 TYR 0.019 0.001 TYR B 245 PHE 0.019 0.001 PHE E 105 TRP 0.015 0.001 TRP B 740 HIS 0.002 0.000 HIS A 404 Details of bonding type rmsd covalent geometry : bond 0.00233 (16948) covalent geometry : angle 0.47604 (22905) SS BOND : bond 0.00325 ( 2) SS BOND : angle 0.31462 ( 4) hydrogen bonds : bond 0.03460 ( 975) hydrogen bonds : angle 3.71216 ( 2964) Misc. bond : bond 0.00053 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 178 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 245 TYR cc_start: 0.4930 (OUTLIER) cc_final: 0.3543 (t80) REVERT: A 268 MET cc_start: 0.6472 (tpp) cc_final: 0.6261 (tpp) REVERT: A 369 PHE cc_start: 0.6996 (t80) cc_final: 0.6733 (t80) REVERT: A 689 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7582 (tt) REVERT: A 783 ARG cc_start: 0.6481 (mtt90) cc_final: 0.4682 (ptt-90) REVERT: A 826 TYR cc_start: 0.7539 (p90) cc_final: 0.7220 (p90) REVERT: B 181 ASN cc_start: 0.8122 (OUTLIER) cc_final: 0.7667 (m-40) REVERT: B 327 MET cc_start: 0.6429 (mmt) cc_final: 0.6132 (mmt) REVERT: B 415 LYS cc_start: 0.6966 (OUTLIER) cc_final: 0.6752 (mtpt) REVERT: B 740 TRP cc_start: 0.7219 (m-10) cc_final: 0.6827 (m-10) REVERT: E 53 LYS cc_start: 0.6827 (tttm) cc_final: 0.6615 (tttm) REVERT: E 114 GLU cc_start: 0.6736 (OUTLIER) cc_final: 0.4914 (pm20) REVERT: J 44 TYR cc_start: 0.4473 (OUTLIER) cc_final: 0.3908 (m-10) REVERT: J 314 MET cc_start: 0.3069 (mpp) cc_final: 0.2431 (mtt) outliers start: 53 outliers final: 40 residues processed: 221 average time/residue: 0.1252 time to fit residues: 42.5042 Evaluate side-chains 216 residues out of total 1819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 170 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain A residue 426 ARG Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain B residue 162 HIS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 373 CYS Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 415 LYS Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 771 CYS Chi-restraints excluded: chain B residue 833 ILE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 28 TYR Chi-restraints excluded: chain E residue 114 GLU Chi-restraints excluded: chain E residue 169 GLU Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain J residue 44 TYR Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 213 THR Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 338 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 90 optimal weight: 0.0870 chunk 169 optimal weight: 0.0970 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 168 optimal weight: 20.0000 chunk 32 optimal weight: 0.7980 chunk 158 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 105 optimal weight: 0.4980 overall best weight: 0.4556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 HIS A 439 ASN A 731 HIS B 420 HIS B 735 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5215 r_free = 0.5215 target = 0.266508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.5187 r_free = 0.5187 target = 0.263182 restraints weight = 19893.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4863 r_free = 0.4863 target = 0.241565 restraints weight = 39426.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4834 r_free = 0.4834 target = 0.237965 restraints weight = 42045.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4834 r_free = 0.4834 target = 0.237928 restraints weight = 34823.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4834 r_free = 0.4834 target = 0.237937 restraints weight = 28116.146| |-----------------------------------------------------------------------------| r_work (final): 0.4863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6298 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16951 Z= 0.095 Angle : 0.464 11.277 22909 Z= 0.238 Chirality : 0.039 0.139 2580 Planarity : 0.004 0.052 2843 Dihedral : 9.271 177.366 2440 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.26 % Allowed : 23.57 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.19), residues: 2005 helix: 2.38 (0.15), residues: 1202 sheet: 1.37 (0.40), residues: 169 loop : -0.66 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 105 TYR 0.018 0.001 TYR B 245 PHE 0.022 0.001 PHE J 265 TRP 0.017 0.001 TRP A 152 HIS 0.003 0.000 HIS A 404 Details of bonding type rmsd covalent geometry : bond 0.00205 (16948) covalent geometry : angle 0.46445 (22905) SS BOND : bond 0.00218 ( 2) SS BOND : angle 0.30760 ( 4) hydrogen bonds : bond 0.03194 ( 975) hydrogen bonds : angle 3.61810 ( 2964) Misc. bond : bond 0.00040 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 180 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LYS cc_start: 0.6693 (tptt) cc_final: 0.6230 (tppt) REVERT: A 96 GLN cc_start: 0.6377 (mm110) cc_final: 0.5862 (mm110) REVERT: A 419 TYR cc_start: 0.6614 (OUTLIER) cc_final: 0.6361 (p90) REVERT: A 451 MET cc_start: 0.3847 (tpt) cc_final: 0.3272 (tmm) REVERT: A 689 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7404 (tt) REVERT: A 783 ARG cc_start: 0.6401 (mtt90) cc_final: 0.4617 (ptt-90) REVERT: A 826 TYR cc_start: 0.7526 (p90) cc_final: 0.7119 (p90) REVERT: B 327 MET cc_start: 0.6478 (mmt) cc_final: 0.6179 (mmt) REVERT: B 740 TRP cc_start: 0.7142 (m-10) cc_final: 0.6720 (m-10) REVERT: E 114 GLU cc_start: 0.6621 (OUTLIER) cc_final: 0.4913 (pm20) REVERT: J 314 MET cc_start: 0.3071 (mpp) cc_final: 0.2450 (mtt) outliers start: 40 outliers final: 25 residues processed: 209 average time/residue: 0.1100 time to fit residues: 36.4356 Evaluate side-chains 197 residues out of total 1819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 169 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 419 TYR Chi-restraints excluded: chain A residue 426 ARG Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain B residue 162 HIS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 771 CYS Chi-restraints excluded: chain B residue 841 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 41 ARG Chi-restraints excluded: chain E residue 114 GLU Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain J residue 213 THR Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 338 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 119 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 183 optimal weight: 40.0000 chunk 9 optimal weight: 2.9990 chunk 109 optimal weight: 0.5980 chunk 24 optimal weight: 4.9990 chunk 91 optimal weight: 0.0050 chunk 10 optimal weight: 0.5980 chunk 194 optimal weight: 8.9990 chunk 120 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 HIS ** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 420 HIS ** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5212 r_free = 0.5212 target = 0.266122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.5185 r_free = 0.5185 target = 0.262846 restraints weight = 19935.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4893 r_free = 0.4893 target = 0.241989 restraints weight = 42672.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4859 r_free = 0.4859 target = 0.238055 restraints weight = 46516.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4855 r_free = 0.4855 target = 0.238167 restraints weight = 44089.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4852 r_free = 0.4852 target = 0.237850 restraints weight = 35075.011| |-----------------------------------------------------------------------------| r_work (final): 0.4898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6241 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16951 Z= 0.097 Angle : 0.467 10.617 22909 Z= 0.239 Chirality : 0.039 0.142 2580 Planarity : 0.004 0.054 2843 Dihedral : 9.098 175.995 2440 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.83 % Allowed : 23.35 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.19), residues: 2005 helix: 2.40 (0.15), residues: 1203 sheet: 1.42 (0.40), residues: 169 loop : -0.62 (0.25), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 105 TYR 0.016 0.001 TYR B 245 PHE 0.019 0.001 PHE A 376 TRP 0.017 0.001 TRP A 152 HIS 0.003 0.000 HIS A 404 Details of bonding type rmsd covalent geometry : bond 0.00215 (16948) covalent geometry : angle 0.46750 (22905) SS BOND : bond 0.00280 ( 2) SS BOND : angle 0.28627 ( 4) hydrogen bonds : bond 0.03201 ( 975) hydrogen bonds : angle 3.59598 ( 2964) Misc. bond : bond 0.00044 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 171 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 245 TYR cc_start: 0.4923 (OUTLIER) cc_final: 0.3537 (t80) REVERT: A 419 TYR cc_start: 0.6688 (OUTLIER) cc_final: 0.6420 (p90) REVERT: A 451 MET cc_start: 0.4081 (tpt) cc_final: 0.3417 (tmm) REVERT: A 689 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7396 (tt) REVERT: A 783 ARG cc_start: 0.6456 (mtt90) cc_final: 0.4750 (ptt-90) REVERT: A 826 TYR cc_start: 0.7566 (p90) cc_final: 0.7187 (p90) REVERT: B 181 ASN cc_start: 0.8159 (OUTLIER) cc_final: 0.7376 (m-40) REVERT: B 327 MET cc_start: 0.6493 (mmt) cc_final: 0.6230 (mmt) REVERT: B 419 TYR cc_start: 0.5103 (t80) cc_final: 0.4819 (t80) REVERT: B 740 TRP cc_start: 0.7234 (m-10) cc_final: 0.6834 (m-10) REVERT: E 79 LEU cc_start: 0.6222 (mp) cc_final: 0.5318 (mp) REVERT: E 114 GLU cc_start: 0.6619 (OUTLIER) cc_final: 0.4893 (pm20) outliers start: 50 outliers final: 32 residues processed: 212 average time/residue: 0.1159 time to fit residues: 38.3277 Evaluate side-chains 204 residues out of total 1819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 167 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 419 TYR Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain B residue 162 HIS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 771 CYS Chi-restraints excluded: chain B residue 841 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 114 GLU Chi-restraints excluded: chain E residue 169 GLU Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain J residue 213 THR Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 338 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 89 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 28 optimal weight: 9.9990 chunk 101 optimal weight: 0.0040 chunk 21 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 142 optimal weight: 5.9990 chunk 152 optimal weight: 0.7980 chunk 164 optimal weight: 3.9990 chunk 156 optimal weight: 7.9990 overall best weight: 0.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 420 HIS A 731 HIS ** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 420 HIS ** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 879 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5199 r_free = 0.5199 target = 0.264473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.5171 r_free = 0.5171 target = 0.261288 restraints weight = 19881.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4931 r_free = 0.4931 target = 0.243403 restraints weight = 35333.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4894 r_free = 0.4894 target = 0.239669 restraints weight = 49040.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4895 r_free = 0.4895 target = 0.240022 restraints weight = 46742.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4894 r_free = 0.4894 target = 0.239937 restraints weight = 34804.427| |-----------------------------------------------------------------------------| r_work (final): 0.4938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6139 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16951 Z= 0.111 Angle : 0.481 10.159 22909 Z= 0.247 Chirality : 0.040 0.144 2580 Planarity : 0.004 0.075 2843 Dihedral : 8.977 172.902 2440 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.83 % Allowed : 23.40 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.19), residues: 2005 helix: 2.32 (0.15), residues: 1203 sheet: 1.44 (0.40), residues: 169 loop : -0.60 (0.25), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 41 TYR 0.019 0.001 TYR B 245 PHE 0.026 0.001 PHE A 369 TRP 0.024 0.001 TRP A 152 HIS 0.005 0.001 HIS A 420 Details of bonding type rmsd covalent geometry : bond 0.00259 (16948) covalent geometry : angle 0.48130 (22905) SS BOND : bond 0.00395 ( 2) SS BOND : angle 0.33660 ( 4) hydrogen bonds : bond 0.03374 ( 975) hydrogen bonds : angle 3.60141 ( 2964) Misc. bond : bond 0.00055 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 177 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 245 TYR cc_start: 0.5117 (OUTLIER) cc_final: 0.3741 (t80) REVERT: A 419 TYR cc_start: 0.6585 (OUTLIER) cc_final: 0.6285 (p90) REVERT: A 451 MET cc_start: 0.4298 (tpt) cc_final: 0.3528 (tmm) REVERT: A 689 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7447 (tt) REVERT: A 783 ARG cc_start: 0.6414 (mtt90) cc_final: 0.4742 (ptt-90) REVERT: A 826 TYR cc_start: 0.7695 (p90) cc_final: 0.7276 (p90) REVERT: A 836 ARG cc_start: 0.4577 (mtt90) cc_final: 0.4286 (mtm110) REVERT: B 181 ASN cc_start: 0.8187 (OUTLIER) cc_final: 0.7804 (m-40) REVERT: B 327 MET cc_start: 0.6535 (mmt) cc_final: 0.6220 (mmt) REVERT: B 419 TYR cc_start: 0.4813 (t80) cc_final: 0.4583 (t80) REVERT: B 740 TRP cc_start: 0.7302 (m-10) cc_final: 0.6873 (m-10) REVERT: E 79 LEU cc_start: 0.6292 (mp) cc_final: 0.5740 (mp) REVERT: E 114 GLU cc_start: 0.6627 (OUTLIER) cc_final: 0.4930 (pm20) REVERT: J 178 MET cc_start: 0.2742 (mpp) cc_final: 0.1490 (mmm) outliers start: 50 outliers final: 35 residues processed: 219 average time/residue: 0.1177 time to fit residues: 40.1662 Evaluate side-chains 214 residues out of total 1819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 174 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 419 TYR Chi-restraints excluded: chain A residue 426 ARG Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain B residue 162 HIS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 373 CYS Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 833 ILE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 114 GLU Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain J residue 213 THR Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 338 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 172 optimal weight: 20.0000 chunk 40 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 187 optimal weight: 20.0000 chunk 77 optimal weight: 1.9990 chunk 113 optimal weight: 0.2980 chunk 121 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 146 optimal weight: 9.9990 chunk 92 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN A 731 HIS ** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 420 HIS ** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5199 r_free = 0.5199 target = 0.264580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.5176 r_free = 0.5176 target = 0.261798 restraints weight = 19959.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4868 r_free = 0.4868 target = 0.239435 restraints weight = 38947.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4836 r_free = 0.4836 target = 0.236030 restraints weight = 47105.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4838 r_free = 0.4838 target = 0.236563 restraints weight = 40874.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4834 r_free = 0.4834 target = 0.236202 restraints weight = 34430.932| |-----------------------------------------------------------------------------| r_work (final): 0.4864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6298 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16951 Z= 0.109 Angle : 0.485 10.001 22909 Z= 0.250 Chirality : 0.040 0.142 2580 Planarity : 0.004 0.064 2843 Dihedral : 8.913 170.776 2440 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.37 % Allowed : 24.08 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.19), residues: 2005 helix: 2.32 (0.15), residues: 1203 sheet: 1.48 (0.40), residues: 168 loop : -0.55 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 105 TYR 0.019 0.001 TYR B 245 PHE 0.019 0.001 PHE A 779 TRP 0.024 0.001 TRP A 152 HIS 0.003 0.001 HIS A 731 Details of bonding type rmsd covalent geometry : bond 0.00251 (16948) covalent geometry : angle 0.48454 (22905) SS BOND : bond 0.00363 ( 2) SS BOND : angle 0.33748 ( 4) hydrogen bonds : bond 0.03365 ( 975) hydrogen bonds : angle 3.59763 ( 2964) Misc. bond : bond 0.00034 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 179 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 245 TYR cc_start: 0.5009 (OUTLIER) cc_final: 0.3653 (t80) REVERT: A 419 TYR cc_start: 0.6775 (OUTLIER) cc_final: 0.6487 (p90) REVERT: A 451 MET cc_start: 0.4259 (tpt) cc_final: 0.3501 (tmm) REVERT: A 689 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7379 (tt) REVERT: A 783 ARG cc_start: 0.6427 (mtt90) cc_final: 0.4709 (ptt-90) REVERT: A 826 TYR cc_start: 0.7680 (p90) cc_final: 0.7275 (p90) REVERT: A 836 ARG cc_start: 0.4725 (mtt90) cc_final: 0.4289 (mtm110) REVERT: B 181 ASN cc_start: 0.8196 (OUTLIER) cc_final: 0.7834 (m-40) REVERT: B 327 MET cc_start: 0.6611 (mmt) cc_final: 0.6346 (mmt) REVERT: B 419 TYR cc_start: 0.4857 (t80) cc_final: 0.4565 (t80) REVERT: B 740 TRP cc_start: 0.7276 (m-10) cc_final: 0.6800 (m-10) REVERT: E 79 LEU cc_start: 0.6293 (mp) cc_final: 0.5723 (mp) REVERT: E 114 GLU cc_start: 0.6642 (OUTLIER) cc_final: 0.4936 (pm20) REVERT: J 155 ASP cc_start: 0.5496 (p0) cc_final: 0.5230 (t70) REVERT: J 178 MET cc_start: 0.2886 (mpp) cc_final: 0.1671 (mmm) REVERT: J 314 MET cc_start: 0.3253 (mpp) cc_final: 0.2618 (mtt) outliers start: 42 outliers final: 31 residues processed: 214 average time/residue: 0.1167 time to fit residues: 38.8345 Evaluate side-chains 211 residues out of total 1819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 175 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 419 TYR Chi-restraints excluded: chain A residue 426 ARG Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain B residue 162 HIS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 373 CYS Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 833 ILE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain E residue 114 GLU Chi-restraints excluded: chain J residue 213 THR Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 338 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 35 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 117 optimal weight: 0.0030 chunk 169 optimal weight: 1.9990 chunk 139 optimal weight: 7.9990 chunk 74 optimal weight: 0.0970 chunk 47 optimal weight: 0.9990 chunk 106 optimal weight: 0.0000 overall best weight: 0.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 HIS ** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 420 HIS ** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5215 r_free = 0.5215 target = 0.266513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.4838 r_free = 0.4838 target = 0.239616 restraints weight = 20003.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4829 r_free = 0.4829 target = 0.237890 restraints weight = 31429.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4828 r_free = 0.4828 target = 0.237608 restraints weight = 30907.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4825 r_free = 0.4825 target = 0.237064 restraints weight = 28151.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4826 r_free = 0.4826 target = 0.237120 restraints weight = 24401.330| |-----------------------------------------------------------------------------| r_work (final): 0.4849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6329 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 16951 Z= 0.097 Angle : 0.476 10.097 22909 Z= 0.244 Chirality : 0.039 0.143 2580 Planarity : 0.004 0.055 2843 Dihedral : 8.776 170.574 2438 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.75 % Allowed : 24.53 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.19), residues: 2005 helix: 2.49 (0.15), residues: 1201 sheet: 1.50 (0.40), residues: 168 loop : -0.52 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 105 TYR 0.019 0.001 TYR B 245 PHE 0.028 0.001 PHE A 369 TRP 0.023 0.001 TRP A 152 HIS 0.003 0.000 HIS A 404 Details of bonding type rmsd covalent geometry : bond 0.00212 (16948) covalent geometry : angle 0.47634 (22905) SS BOND : bond 0.00180 ( 2) SS BOND : angle 0.36844 ( 4) hydrogen bonds : bond 0.03095 ( 975) hydrogen bonds : angle 3.54248 ( 2964) Misc. bond : bond 0.00016 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 173 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 TRP cc_start: 0.6457 (m-10) cc_final: 0.6215 (m-10) REVERT: A 419 TYR cc_start: 0.6728 (OUTLIER) cc_final: 0.6445 (p90) REVERT: A 451 MET cc_start: 0.4179 (tpt) cc_final: 0.3571 (tmm) REVERT: A 689 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7445 (tt) REVERT: A 783 ARG cc_start: 0.6469 (mtt90) cc_final: 0.4760 (ptt-90) REVERT: A 826 TYR cc_start: 0.7519 (p90) cc_final: 0.7071 (p90) REVERT: A 836 ARG cc_start: 0.4621 (mtt90) cc_final: 0.4211 (mtm110) REVERT: B 181 ASN cc_start: 0.8154 (OUTLIER) cc_final: 0.7837 (m-40) REVERT: B 419 TYR cc_start: 0.4813 (t80) cc_final: 0.4484 (t80) REVERT: B 740 TRP cc_start: 0.7104 (m-10) cc_final: 0.6790 (m-10) REVERT: E 79 LEU cc_start: 0.6202 (mp) cc_final: 0.5643 (mp) REVERT: E 114 GLU cc_start: 0.6602 (OUTLIER) cc_final: 0.4892 (pm20) REVERT: J 155 ASP cc_start: 0.6194 (p0) cc_final: 0.5590 (t70) REVERT: J 178 MET cc_start: 0.2901 (mpp) cc_final: 0.1728 (mmm) REVERT: J 314 MET cc_start: 0.3181 (mpp) cc_final: 0.2554 (mtt) outliers start: 31 outliers final: 24 residues processed: 199 average time/residue: 0.1175 time to fit residues: 36.6330 Evaluate side-chains 197 residues out of total 1819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 169 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 419 TYR Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain B residue 162 HIS Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain E residue 114 GLU Chi-restraints excluded: chain J residue 213 THR Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 338 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 85 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 154 optimal weight: 0.3980 chunk 50 optimal weight: 0.5980 chunk 73 optimal weight: 0.9990 chunk 173 optimal weight: 20.0000 chunk 160 optimal weight: 0.0670 chunk 29 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 HIS ** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 420 HIS ** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5207 r_free = 0.5207 target = 0.265477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.5184 r_free = 0.5184 target = 0.262758 restraints weight = 19883.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4792 r_free = 0.4792 target = 0.237141 restraints weight = 39238.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4778 r_free = 0.4778 target = 0.235155 restraints weight = 41674.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4772 r_free = 0.4772 target = 0.234144 restraints weight = 36147.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4773 r_free = 0.4773 target = 0.234113 restraints weight = 30965.681| |-----------------------------------------------------------------------------| r_work (final): 0.4780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6468 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16951 Z= 0.101 Angle : 0.481 9.876 22909 Z= 0.246 Chirality : 0.039 0.142 2580 Planarity : 0.004 0.055 2843 Dihedral : 8.707 167.852 2438 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.87 % Allowed : 24.42 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.19), residues: 2005 helix: 2.45 (0.15), residues: 1201 sheet: 1.52 (0.40), residues: 168 loop : -0.50 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 105 TYR 0.018 0.001 TYR B 245 PHE 0.020 0.001 PHE A 376 TRP 0.022 0.001 TRP A 152 HIS 0.003 0.000 HIS A 404 Details of bonding type rmsd covalent geometry : bond 0.00228 (16948) covalent geometry : angle 0.48141 (22905) SS BOND : bond 0.00311 ( 2) SS BOND : angle 0.32883 ( 4) hydrogen bonds : bond 0.03166 ( 975) hydrogen bonds : angle 3.54226 ( 2964) Misc. bond : bond 0.00018 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2423.03 seconds wall clock time: 42 minutes 41.61 seconds (2561.61 seconds total)