Starting phenix.real_space_refine on Sat Jul 4 11:50:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ik3_35504/07_2026/8ik3_35504.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ik3_35504/07_2026/8ik3_35504.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ik3_35504/07_2026/8ik3_35504.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ik3_35504/07_2026/8ik3_35504.map" model { file = "/net/cci-nas-00/data/ceres_data/8ik3_35504/07_2026/8ik3_35504.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ik3_35504/07_2026/8ik3_35504.cif" } resolution = 3.3 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= 0.015 sd= 0.069 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: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 104 5.16 5 C 13281 2.51 5 N 3731 2.21 5 O 3806 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20938 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2587 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 311} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2583 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 16, 'TRANS': 310} Chain breaks: 1 Chain: "C" Number of atoms: 2567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2567 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 309} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2569 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 309} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 2567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2567 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 309} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2569 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 309} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 2567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2567 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 309} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "H" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2569 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 309} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 90 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1, 45 Unusual residues: {'1SY': 1} Classifications: {'undetermined': 1} Conformer: "B" Number of residues, atoms: 1, 45 Unusual residues: {'1SY': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 90 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1, 45 Unusual residues: {'1SY': 1} Classifications: {'undetermined': 1} Conformer: "B" Number of residues, atoms: 1, 45 Unusual residues: {'1SY': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 90 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1, 45 Unusual residues: {'1SY': 1} Classifications: {'undetermined': 1} Conformer: "B" Number of residues, atoms: 1, 45 Unusual residues: {'1SY': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 90 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1, 45 Unusual residues: {'1SY': 1} Classifications: {'undetermined': 1} Conformer: "B" Number of residues, atoms: 1, 45 Unusual residues: {'1SY': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" C1'A1SY B 601 " occ=0.50 ... (88 atoms not shown) pdb=" P27B1SY B 601 " occ=0.50 residue: pdb=" C1'A1SY D 601 " occ=0.50 ... (88 atoms not shown) pdb=" P27B1SY D 601 " occ=0.50 residue: pdb=" C1'A1SY G 601 " occ=0.50 ... (88 atoms not shown) pdb=" P27B1SY G 601 " occ=0.50 residue: pdb=" C1'A1SY F 601 " occ=0.50 ... (88 atoms not shown) pdb=" P27B1SY F 601 " occ=0.50 Time building chain proxies: 4.76, per 1000 atoms: 0.23 Number of scatterers: 20938 At special positions: 0 Unit cell: (89.01, 168.36, 113.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 104 16.00 P 16 15.00 O 3806 8.00 N 3731 7.00 C 13281 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.85 Conformation dependent library (CDL) restraints added in 790.0 milliseconds 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4870 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 24 sheets defined 58.5% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 17 through 35 Processing helix chain 'A' and resid 39 through 70 removed outlier: 3.853A pdb=" N LEU A 47 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU A 68 " --> pdb=" O CYS A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 77 removed outlier: 3.528A pdb=" N TYR A 77 " --> pdb=" O ILE A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 89 removed outlier: 3.902A pdb=" N THR A 84 " --> pdb=" O SER A 80 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL A 85 " --> pdb=" O TYR A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 109 removed outlier: 3.737A pdb=" N TYR A 104 " --> pdb=" O LEU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 135 removed outlier: 3.652A pdb=" N LEU A 121 " --> pdb=" O PHE A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 152 removed outlier: 3.711A pdb=" N SER A 145 " --> pdb=" O PRO A 141 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ALA A 146 " --> pdb=" O ALA A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 172 removed outlier: 3.938A pdb=" N GLY A 158 " --> pdb=" O ASN A 154 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ARG A 169 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N LEU A 170 " --> pdb=" O GLY A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 186 Processing helix chain 'A' and resid 262 through 271 removed outlier: 3.789A pdb=" N GLN A 266 " --> pdb=" O ALA A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 301 removed outlier: 3.884A pdb=" N LEU A 285 " --> pdb=" O ARG A 281 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS A 289 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU A 290 " --> pdb=" O GLU A 286 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N CYS A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ARG A 293 " --> pdb=" O LYS A 289 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASP A 301 " --> pdb=" O ASP A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 337 removed outlier: 3.539A pdb=" N GLU A 328 " --> pdb=" O SER A 324 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 36 Processing helix chain 'B' and resid 39 through 70 removed outlier: 4.236A pdb=" N THR B 43 " --> pdb=" O PRO B 39 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA B 67 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLU B 68 " --> pdb=" O CYS B 64 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU B 69 " --> pdb=" O SER B 65 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 77 Processing helix chain 'B' and resid 80 through 89 removed outlier: 3.748A pdb=" N THR B 84 " --> pdb=" O SER B 80 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL B 85 " --> pdb=" O TYR B 81 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N CYS B 88 " --> pdb=" O THR B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 107 Processing helix chain 'B' and resid 117 through 135 removed outlier: 3.703A pdb=" N LEU B 121 " --> pdb=" O PHE B 117 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA B 122 " --> pdb=" O THR B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 167 removed outlier: 3.889A pdb=" N GLY B 158 " --> pdb=" O ASN B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 172 Processing helix chain 'B' and resid 174 through 186 removed outlier: 3.783A pdb=" N ARG B 178 " --> pdb=" O GLU B 174 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR B 186 " --> pdb=" O TYR B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 272 removed outlier: 3.868A pdb=" N GLN B 266 " --> pdb=" O ALA B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 301 removed outlier: 4.039A pdb=" N GLU B 286 " --> pdb=" O GLU B 282 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA B 288 " --> pdb=" O ARG B 284 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASP B 301 " --> pdb=" O ASP B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 334 removed outlier: 3.715A pdb=" N GLU B 328 " --> pdb=" O SER B 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 36 removed outlier: 3.580A pdb=" N LYS C 20 " --> pdb=" O HIS C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 70 removed outlier: 4.087A pdb=" N THR C 43 " --> pdb=" O PRO C 39 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA C 67 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N GLU C 68 " --> pdb=" O CYS C 64 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU C 69 " --> pdb=" O SER C 65 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU C 70 " --> pdb=" O LEU C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.869A pdb=" N VAL C 85 " --> pdb=" O TYR C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 105 removed outlier: 3.932A pdb=" N PHE C 105 " --> pdb=" O LEU C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 108 No H-bonds generated for 'chain 'C' and resid 106 through 108' Processing helix chain 'C' and resid 117 through 135 removed outlier: 3.641A pdb=" N LEU C 121 " --> pdb=" O PHE C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 152 removed outlier: 3.897A pdb=" N ALA C 146 " --> pdb=" O ALA C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 167 removed outlier: 3.863A pdb=" N GLY C 158 " --> pdb=" O ASN C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 172 Processing helix chain 'C' and resid 174 through 186 Processing helix chain 'C' and resid 262 through 272 removed outlier: 3.776A pdb=" N GLN C 266 " --> pdb=" O ALA C 262 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER C 272 " --> pdb=" O LEU C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 301 removed outlier: 4.080A pdb=" N LEU C 285 " --> pdb=" O ARG C 281 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N CYS C 292 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ARG C 293 " --> pdb=" O LYS C 289 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ASP C 301 " --> pdb=" O ASP C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 335 removed outlier: 3.641A pdb=" N GLU C 328 " --> pdb=" O SER C 324 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N HIS C 332 " --> pdb=" O GLU C 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 36 Processing helix chain 'D' and resid 39 through 70 removed outlier: 3.693A pdb=" N THR D 43 " --> pdb=" O PRO D 39 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU D 44 " --> pdb=" O PRO D 40 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU D 58 " --> pdb=" O LEU D 54 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU D 59 " --> pdb=" O GLN D 55 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU D 60 " --> pdb=" O LEU D 56 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ASN D 61 " --> pdb=" O GLY D 57 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU D 68 " --> pdb=" O CYS D 64 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU D 70 " --> pdb=" O LEU D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 77 Processing helix chain 'D' and resid 80 through 89 removed outlier: 3.522A pdb=" N ALA D 87 " --> pdb=" O ARG D 83 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N CYS D 88 " --> pdb=" O THR D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 109 removed outlier: 3.501A pdb=" N SER D 108 " --> pdb=" O TYR D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 135 removed outlier: 3.759A pdb=" N LEU D 121 " --> pdb=" O PHE D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 151 removed outlier: 4.246A pdb=" N ALA D 146 " --> pdb=" O ALA D 142 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU D 149 " --> pdb=" O SER D 145 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY D 151 " --> pdb=" O VAL D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 172 removed outlier: 4.207A pdb=" N GLY D 158 " --> pdb=" O ASN D 154 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ARG D 169 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N LEU D 170 " --> pdb=" O GLY D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 186 removed outlier: 3.866A pdb=" N THR D 181 " --> pdb=" O ALA D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 272 removed outlier: 3.809A pdb=" N GLN D 266 " --> pdb=" O ALA D 262 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER D 272 " --> pdb=" O LEU D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 301 removed outlier: 4.095A pdb=" N GLU D 286 " --> pdb=" O GLU D 282 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA D 288 " --> pdb=" O ARG D 284 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N CYS D 292 " --> pdb=" O ALA D 288 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG D 293 " --> pdb=" O LYS D 289 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASP D 301 " --> pdb=" O ASP D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 335 removed outlier: 3.788A pdb=" N GLU D 328 " --> pdb=" O SER D 324 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLN D 335 " --> pdb=" O ARG D 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 36 Processing helix chain 'E' and resid 39 through 70 removed outlier: 4.213A pdb=" N THR E 43 " --> pdb=" O PRO E 39 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA E 67 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N GLU E 68 " --> pdb=" O CYS E 64 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU E 69 " --> pdb=" O SER E 65 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU E 70 " --> pdb=" O LEU E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 73 No H-bonds generated for 'chain 'E' and resid 71 through 73' Processing helix chain 'E' and resid 81 through 90 removed outlier: 4.127A pdb=" N VAL E 85 " --> pdb=" O TYR E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 105 removed outlier: 3.757A pdb=" N PHE E 105 " --> pdb=" O LEU E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 108 No H-bonds generated for 'chain 'E' and resid 106 through 108' Processing helix chain 'E' and resid 117 through 135 removed outlier: 3.771A pdb=" N LEU E 121 " --> pdb=" O PHE E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 152 Processing helix chain 'E' and resid 154 through 167 removed outlier: 3.721A pdb=" N GLY E 158 " --> pdb=" O ASN E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 172 Processing helix chain 'E' and resid 174 through 186 Processing helix chain 'E' and resid 262 through 272 removed outlier: 3.562A pdb=" N GLN E 266 " --> pdb=" O ALA E 262 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER E 272 " --> pdb=" O LEU E 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 301 removed outlier: 3.614A pdb=" N LEU E 285 " --> pdb=" O ARG E 281 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N CYS E 292 " --> pdb=" O ALA E 288 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG E 293 " --> pdb=" O LYS E 289 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ASP E 301 " --> pdb=" O ASP E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 307 No H-bonds generated for 'chain 'E' and resid 305 through 307' Processing helix chain 'E' and resid 324 through 335 removed outlier: 3.809A pdb=" N GLN E 335 " --> pdb=" O ARG E 331 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 36 Processing helix chain 'G' and resid 39 through 70 removed outlier: 4.089A pdb=" N LEU G 58 " --> pdb=" O LEU G 54 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU G 59 " --> pdb=" O GLN G 55 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU G 60 " --> pdb=" O LEU G 56 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ASN G 61 " --> pdb=" O GLY G 57 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU G 68 " --> pdb=" O CYS G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 77 Processing helix chain 'G' and resid 80 through 87 Processing helix chain 'G' and resid 93 through 109 removed outlier: 3.547A pdb=" N LEU G 109 " --> pdb=" O PHE G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 135 removed outlier: 3.566A pdb=" N LEU G 121 " --> pdb=" O PHE G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 151 removed outlier: 3.838A pdb=" N ALA G 146 " --> pdb=" O ALA G 142 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU G 149 " --> pdb=" O SER G 145 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY G 151 " --> pdb=" O VAL G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 172 removed outlier: 4.533A pdb=" N ARG G 169 " --> pdb=" O ILE G 165 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N LEU G 170 " --> pdb=" O GLY G 166 " (cutoff:3.500A) Processing helix chain 'G' and resid 174 through 186 removed outlier: 3.701A pdb=" N ARG G 178 " --> pdb=" O GLU G 174 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N THR G 181 " --> pdb=" O ALA G 177 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN G 184 " --> pdb=" O ARG G 180 " (cutoff:3.500A) Processing helix chain 'G' and resid 262 through 272 removed outlier: 3.739A pdb=" N GLN G 266 " --> pdb=" O ALA G 262 " (cutoff:3.500A) Processing helix chain 'G' and resid 282 through 301 removed outlier: 3.865A pdb=" N GLU G 286 " --> pdb=" O GLU G 282 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N CYS G 292 " --> pdb=" O ALA G 288 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG G 293 " --> pdb=" O LYS G 289 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASP G 301 " --> pdb=" O ASP G 297 " (cutoff:3.500A) Processing helix chain 'G' and resid 324 through 335 removed outlier: 3.811A pdb=" N GLU G 328 " --> pdb=" O SER G 324 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN G 335 " --> pdb=" O ARG G 331 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 36 Processing helix chain 'F' and resid 39 through 70 removed outlier: 3.927A pdb=" N THR F 43 " --> pdb=" O PRO F 39 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA F 67 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLU F 68 " --> pdb=" O CYS F 64 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU F 69 " --> pdb=" O SER F 65 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU F 70 " --> pdb=" O LEU F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 73 No H-bonds generated for 'chain 'F' and resid 71 through 73' Processing helix chain 'F' and resid 80 through 89 removed outlier: 4.537A pdb=" N THR F 84 " --> pdb=" O SER F 80 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL F 85 " --> pdb=" O TYR F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 105 Processing helix chain 'F' and resid 106 through 108 No H-bonds generated for 'chain 'F' and resid 106 through 108' Processing helix chain 'F' and resid 117 through 135 removed outlier: 3.631A pdb=" N LEU F 121 " --> pdb=" O PHE F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 152 Processing helix chain 'F' and resid 154 through 167 removed outlier: 3.690A pdb=" N GLY F 158 " --> pdb=" O ASN F 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 172 Processing helix chain 'F' and resid 174 through 186 Processing helix chain 'F' and resid 262 through 274 removed outlier: 3.740A pdb=" N GLN F 266 " --> pdb=" O ALA F 262 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLN F 273 " --> pdb=" O PHE F 269 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N TYR F 274 " --> pdb=" O ALA F 270 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 301 removed outlier: 3.798A pdb=" N CYS F 292 " --> pdb=" O ALA F 288 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG F 293 " --> pdb=" O LYS F 289 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASP F 301 " --> pdb=" O ASP F 297 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 307 No H-bonds generated for 'chain 'F' and resid 305 through 307' Processing helix chain 'F' and resid 324 through 335 removed outlier: 3.703A pdb=" N GLU F 328 " --> pdb=" O SER F 324 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N HIS F 332 " --> pdb=" O GLU F 328 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN F 335 " --> pdb=" O ARG F 331 " (cutoff:3.500A) Processing helix chain 'H' and resid 17 through 36 Processing helix chain 'H' and resid 39 through 70 removed outlier: 3.778A pdb=" N THR H 43 " --> pdb=" O PRO H 39 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU H 58 " --> pdb=" O LEU H 54 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU H 59 " --> pdb=" O GLN H 55 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LEU H 60 " --> pdb=" O LEU H 56 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ASN H 61 " --> pdb=" O GLY H 57 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU H 68 " --> pdb=" O CYS H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 77 Processing helix chain 'H' and resid 80 through 89 removed outlier: 3.716A pdb=" N CYS H 88 " --> pdb=" O THR H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 109 removed outlier: 3.508A pdb=" N SER H 108 " --> pdb=" O TYR H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 135 removed outlier: 3.640A pdb=" N LEU H 121 " --> pdb=" O PHE H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 151 removed outlier: 3.504A pdb=" N SER H 145 " --> pdb=" O PRO H 141 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA H 146 " --> pdb=" O ALA H 142 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY H 151 " --> pdb=" O VAL H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 154 through 172 removed outlier: 4.207A pdb=" N GLY H 158 " --> pdb=" O ASN H 154 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ARG H 169 " --> pdb=" O ILE H 165 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N LEU H 170 " --> pdb=" O GLY H 166 " (cutoff:3.500A) Processing helix chain 'H' and resid 175 through 186 removed outlier: 3.806A pdb=" N THR H 181 " --> pdb=" O ALA H 177 " (cutoff:3.500A) Processing helix chain 'H' and resid 262 through 272 removed outlier: 3.551A pdb=" N GLN H 266 " --> pdb=" O ALA H 262 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER H 272 " --> pdb=" O LEU H 268 " (cutoff:3.500A) Processing helix chain 'H' and resid 282 through 302 removed outlier: 3.675A pdb=" N GLU H 286 " --> pdb=" O GLU H 282 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA H 288 " --> pdb=" O ARG H 284 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N CYS H 292 " --> pdb=" O ALA H 288 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG H 293 " --> pdb=" O LYS H 289 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ASP H 301 " --> pdb=" O ASP H 297 " (cutoff:3.500A) Processing helix chain 'H' and resid 324 through 335 removed outlier: 3.814A pdb=" N GLU H 328 " --> pdb=" O SER H 324 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLN H 335 " --> pdb=" O ARG H 331 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 259 through 260 removed outlier: 3.879A pdb=" N ARG A 310 " --> pdb=" O LEU A 198 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ILE A 200 " --> pdb=" O ARG A 310 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR A 314 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 219 through 224 removed outlier: 6.337A pdb=" N ILE A 219 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N LEU A 248 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N PHE A 221 " --> pdb=" O GLU A 246 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N GLU A 246 " --> pdb=" O PHE A 221 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASP A 223 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N TYR A 245 " --> pdb=" O THR A 256 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N THR A 256 " --> pdb=" O TYR A 245 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU A 247 " --> pdb=" O ALA A 254 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 228 through 232 removed outlier: 6.847A pdb=" N ARG A 232 " --> pdb=" O LYS A 236 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N LYS A 236 " --> pdb=" O ARG A 232 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 259 through 260 removed outlier: 3.857A pdb=" N TYR B 314 " --> pdb=" O LEU B 202 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 219 through 224 removed outlier: 7.058A pdb=" N ILE B 244 " --> pdb=" O LEU B 222 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N TYR B 245 " --> pdb=" O THR B 256 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N THR B 256 " --> pdb=" O TYR B 245 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N LEU B 247 " --> pdb=" O ALA B 254 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 228 through 232 removed outlier: 6.948A pdb=" N ARG B 232 " --> pdb=" O LYS B 236 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N LYS B 236 " --> pdb=" O ARG B 232 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 259 through 260 removed outlier: 3.867A pdb=" N TYR C 314 " --> pdb=" O LEU C 202 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 219 through 224 removed outlier: 3.609A pdb=" N ARG C 220 " --> pdb=" O GLU C 246 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ILE C 244 " --> pdb=" O LEU C 222 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N TYR C 245 " --> pdb=" O THR C 256 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N THR C 256 " --> pdb=" O TYR C 245 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LEU C 247 " --> pdb=" O ALA C 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 228 through 232 removed outlier: 6.979A pdb=" N ARG C 232 " --> pdb=" O LYS C 236 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N LYS C 236 " --> pdb=" O ARG C 232 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 259 through 260 removed outlier: 3.646A pdb=" N TYR D 314 " --> pdb=" O LEU D 202 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 220 through 224 removed outlier: 3.510A pdb=" N ARG D 220 " --> pdb=" O GLU D 246 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE D 244 " --> pdb=" O LEU D 222 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N TYR D 245 " --> pdb=" O THR D 256 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N THR D 256 " --> pdb=" O TYR D 245 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LEU D 247 " --> pdb=" O ALA D 254 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 228 through 232 removed outlier: 6.626A pdb=" N ARG D 232 " --> pdb=" O LYS D 236 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N LYS D 236 " --> pdb=" O ARG D 232 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 259 through 260 removed outlier: 6.096A pdb=" N LEU E 198 " --> pdb=" O ARG E 310 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N ILE E 312 " --> pdb=" O LEU E 198 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE E 200 " --> pdb=" O ILE E 312 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N TYR E 314 " --> pdb=" O ILE E 200 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU E 202 " --> pdb=" O TYR E 314 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 219 through 224 removed outlier: 6.949A pdb=" N ILE E 244 " --> pdb=" O LEU E 222 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N TYR E 245 " --> pdb=" O THR E 256 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N THR E 256 " --> pdb=" O TYR E 245 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N LEU E 247 " --> pdb=" O ALA E 254 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 228 through 232 removed outlier: 6.972A pdb=" N ARG E 232 " --> pdb=" O LYS E 236 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N LYS E 236 " --> pdb=" O ARG E 232 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 259 through 260 Processing sheet with id=AB8, first strand: chain 'G' and resid 220 through 224 removed outlier: 3.544A pdb=" N ARG G 220 " --> pdb=" O GLU G 246 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N ILE G 244 " --> pdb=" O LEU G 222 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N TYR G 245 " --> pdb=" O THR G 256 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N THR G 256 " --> pdb=" O TYR G 245 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LEU G 247 " --> pdb=" O ALA G 254 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 228 through 232 removed outlier: 6.433A pdb=" N GLN G 228 " --> pdb=" O VAL G 239 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N VAL G 239 " --> pdb=" O GLN G 228 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N GLY G 230 " --> pdb=" O ASP G 237 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 259 through 260 removed outlier: 3.549A pdb=" N TYR F 314 " --> pdb=" O LEU F 202 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 219 through 224 removed outlier: 7.399A pdb=" N ILE F 244 " --> pdb=" O LEU F 222 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N TYR F 245 " --> pdb=" O THR F 256 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N THR F 256 " --> pdb=" O TYR F 245 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N LEU F 247 " --> pdb=" O ALA F 254 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 228 through 232 removed outlier: 7.046A pdb=" N ARG F 232 " --> pdb=" O LYS F 236 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N LYS F 236 " --> pdb=" O ARG F 232 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 259 through 260 removed outlier: 3.643A pdb=" N TYR H 314 " --> pdb=" O LEU H 202 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 220 through 224 removed outlier: 5.924A pdb=" N PHE H 221 " --> pdb=" O GLU H 246 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N GLU H 246 " --> pdb=" O PHE H 221 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N TYR H 245 " --> pdb=" O THR H 256 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N THR H 256 " --> pdb=" O TYR H 245 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LEU H 247 " --> pdb=" O ALA H 254 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 228 through 232 removed outlier: 6.464A pdb=" N ARG H 232 " --> pdb=" O LYS H 236 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N LYS H 236 " --> pdb=" O ARG H 232 " (cutoff:3.500A) 1071 hydrogen bonds defined for protein. 3165 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.11 Time building geometry restraints manager: 2.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3299 1.31 - 1.44: 5848 1.44 - 1.56: 12123 1.56 - 1.69: 3 1.69 - 1.81: 158 Bond restraints: 21431 Sorted by residual: bond pdb=" C36A1SY G 601 " pdb=" N42A1SY G 601 " ideal model delta sigma weight residual 1.357 1.494 -0.137 2.00e-02 2.50e+03 4.71e+01 bond pdb=" C40B1SY G 601 " pdb=" N39B1SY G 601 " ideal model delta sigma weight residual 1.304 1.441 -0.137 2.00e-02 2.50e+03 4.67e+01 bond pdb=" C36A1SY F 601 " pdb=" N42A1SY F 601 " ideal model delta sigma weight residual 1.357 1.493 -0.136 2.00e-02 2.50e+03 4.64e+01 bond pdb=" C36B1SY G 601 " pdb=" N42B1SY G 601 " ideal model delta sigma weight residual 1.357 1.493 -0.136 2.00e-02 2.50e+03 4.63e+01 bond pdb=" C40A1SY F 601 " pdb=" N39A1SY F 601 " ideal model delta sigma weight residual 1.304 1.440 -0.136 2.00e-02 2.50e+03 4.63e+01 ... (remaining 21426 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.80: 28879 3.80 - 7.59: 200 7.59 - 11.39: 47 11.39 - 15.18: 33 15.18 - 18.98: 20 Bond angle restraints: 29179 Sorted by residual: angle pdb=" O19A1SY F 601 " pdb=" P18A1SY F 601 " pdb=" O44A1SY F 601 " ideal model delta sigma weight residual 123.21 104.23 18.98 3.00e+00 1.11e-01 4.00e+01 angle pdb=" O19B1SY G 601 " pdb=" P18B1SY G 601 " pdb=" O44B1SY G 601 " ideal model delta sigma weight residual 123.21 104.28 18.93 3.00e+00 1.11e-01 3.98e+01 angle pdb=" O19A1SY G 601 " pdb=" P18A1SY G 601 " pdb=" O44A1SY G 601 " ideal model delta sigma weight residual 123.21 104.49 18.72 3.00e+00 1.11e-01 3.89e+01 angle pdb=" O19B1SY F 601 " pdb=" P18B1SY F 601 " pdb=" O44B1SY F 601 " ideal model delta sigma weight residual 123.21 104.52 18.69 3.00e+00 1.11e-01 3.88e+01 angle pdb=" O19A1SY B 601 " pdb=" P18A1SY B 601 " pdb=" O44A1SY B 601 " ideal model delta sigma weight residual 123.21 104.70 18.51 3.00e+00 1.11e-01 3.81e+01 ... (remaining 29174 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.03: 12795 35.03 - 70.07: 301 70.07 - 105.10: 49 105.10 - 140.14: 1 140.14 - 175.17: 15 Dihedral angle restraints: 13161 sinusoidal: 5563 harmonic: 7598 Sorted by residual: dihedral pdb=" C3'B1SY G 601 " pdb=" O28B1SY G 601 " pdb=" P27B1SY G 601 " pdb=" O29B1SY G 601 " ideal model delta sinusoidal sigma weight residual 344.19 169.02 175.17 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C3'A1SY F 601 " pdb=" O28A1SY F 601 " pdb=" P27A1SY F 601 " pdb=" O29A1SY F 601 " ideal model delta sinusoidal sigma weight residual 344.19 171.19 173.00 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C3'B1SY F 601 " pdb=" O28B1SY F 601 " pdb=" P27B1SY F 601 " pdb=" O29B1SY F 601 " ideal model delta sinusoidal sigma weight residual 344.19 172.04 172.15 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 13158 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2404 0.040 - 0.081: 646 0.081 - 0.121: 169 0.121 - 0.162: 28 0.162 - 0.202: 24 Chirality restraints: 3271 Sorted by residual: chirality pdb=" C24B1SY F 601 " pdb=" C22B1SY F 601 " pdb=" C25B1SY F 601 " pdb=" O31B1SY F 601 " both_signs ideal model delta sigma weight residual False -2.43 -2.63 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" C2'B1SY F 601 " pdb=" C1'B1SY F 601 " pdb=" C3'B1SY F 601 " pdb=" O2'B1SY F 601 " both_signs ideal model delta sigma weight residual False -2.74 -2.54 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" C4'B1SY B 601 " pdb=" C16B1SY B 601 " pdb=" C3'B1SY B 601 " pdb=" O4'B1SY B 601 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 3268 not shown) Planarity restraints: 3691 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 216 " -0.085 5.00e-02 4.00e+02 1.26e-01 2.55e+01 pdb=" N PRO C 217 " 0.218 5.00e-02 4.00e+02 pdb=" CA PRO C 217 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO C 217 " -0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 216 " 0.032 5.00e-02 4.00e+02 4.79e-02 3.68e+00 pdb=" N PRO B 217 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 217 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 217 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR D 164 " 0.008 2.00e-02 2.50e+03 1.52e-02 2.31e+00 pdb=" C TYR D 164 " -0.026 2.00e-02 2.50e+03 pdb=" O TYR D 164 " 0.010 2.00e-02 2.50e+03 pdb=" N ILE D 165 " 0.009 2.00e-02 2.50e+03 ... (remaining 3688 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 373 2.70 - 3.25: 19667 3.25 - 3.80: 30766 3.80 - 4.35: 38119 4.35 - 4.90: 66653 Nonbonded interactions: 155578 Sorted by model distance: nonbonded pdb=" OE1 GLU A 69 " pdb=" OH TYR A 77 " model vdw 2.148 3.040 nonbonded pdb=" OE1 GLU D 69 " pdb=" OH TYR D 77 " model vdw 2.150 3.040 nonbonded pdb=" O LEU C 98 " pdb=" OG SER C 102 " model vdw 2.163 3.040 nonbonded pdb=" O SER F 127 " pdb=" ND2 ASN F 131 " model vdw 2.178 3.120 nonbonded pdb=" O ALA A 302 " pdb=" OG SER A 305 " model vdw 2.180 3.040 ... (remaining 155573 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 106 or (resid 107 and (name N or name CA or name \ C or name O or name CB )) or resid 108 or resid 116 through 335)) selection = (chain 'B' and (resid 4 through 37 or (resid 38 and (name N or name CA or name C \ or name O or name CB )) or resid 39 through 106 or (resid 107 and (name N or na \ me CA or name C or name O or name CB )) or resid 108 through 335)) selection = (chain 'C' and (resid 4 through 37 or (resid 38 and (name N or name CA or name C \ or name O or name CB )) or resid 39 through 335)) selection = (chain 'D' and (resid 4 through 106 or (resid 107 and (name N or name CA or name \ C or name O or name CB )) or resid 108 or resid 116 through 335)) selection = (chain 'E' and (resid 4 through 37 or (resid 38 and (name N or name CA or name C \ or name O or name CB )) or resid 39 through 335)) selection = (chain 'F' and (resid 4 through 37 or (resid 38 and (name N or name CA or name C \ or name O or name CB )) or resid 39 through 335)) selection = (chain 'G' and (resid 4 through 106 or (resid 107 and (name N or name CA or name \ C or name O or name CB )) or resid 108 or resid 116 through 335)) selection = (chain 'H' and (resid 4 through 106 or (resid 107 and (name N or name CA or name \ C or name O or name CB )) or resid 108 or resid 116 through 335)) } 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=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.520 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: 0.000 Extract box with map and model: 0.470 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 18.050 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 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 : 0.009 0.137 21431 Z= 0.459 Angle : 1.028 18.981 29179 Z= 0.419 Chirality : 0.043 0.202 3271 Planarity : 0.005 0.126 3691 Dihedral : 17.386 175.169 8291 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.09 % Allowed : 0.32 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.17), residues: 2579 helix: 1.88 (0.15), residues: 1361 sheet: 0.74 (0.55), residues: 106 loop : -1.00 (0.18), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 180 TYR 0.017 0.001 TYR B 261 PHE 0.022 0.002 PHE C 279 TRP 0.010 0.001 TRP C 82 HIS 0.006 0.001 HIS D 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00944 / 0.46 (21431) covalent geometry : angle 1.02767 / 0.42 (29179) hydrogen bonds : bond 0.15977 / 10.54 ( 1071) hydrogen bonds : angle 5.99015 / 4.27 ( 3165) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 217 time to evaluate : 0.759 Fit side-chains revert: symmetry clash REVERT: A 107 TYR cc_start: 0.8361 (t80) cc_final: 0.7930 (t80) REVERT: B 107 TYR cc_start: 0.7500 (t80) cc_final: 0.6871 (t80) REVERT: E 74 HIS cc_start: 0.6700 (t70) cc_final: 0.6382 (t70) REVERT: G 221 PHE cc_start: 0.6498 (t80) cc_final: 0.5806 (t80) REVERT: G 269 PHE cc_start: 0.6787 (t80) cc_final: 0.6448 (t80) REVERT: H 120 MET cc_start: 0.7847 (mmt) cc_final: 0.7543 (mmm) outliers start: 2 outliers final: 1 residues processed: 218 average time/residue: 0.1506 time to fit residues: 51.2599 Evaluate side-chains 150 residues out of total 2211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 149 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 185 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 50.0000 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 16 HIS B 218 ASN E 307 ASN G 42 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.198184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.142687 restraints weight = 35694.262| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 6.04 r_work: 0.3103 rms_B_bonded: 5.92 restraints_weight: 2.0000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3099 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3099 r_free = 0.3099 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3099 r_free = 0.3099 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (12 function evaluations) r_final: 0.3099 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.0941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 21431 Z= 0.110 Angle : 0.527 6.890 29179 Z= 0.262 Chirality : 0.037 0.213 3271 Planarity : 0.004 0.077 3691 Dihedral : 14.887 177.394 3442 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.64 % Allowed : 6.94 % Favored : 92.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.18), residues: 2579 helix: 2.16 (0.15), residues: 1372 sheet: 0.59 (0.52), residues: 119 loop : -0.85 (0.19), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 281 TYR 0.014 0.001 TYR B 261 PHE 0.015 0.001 PHE C 291 TRP 0.009 0.001 TRP B 82 HIS 0.006 0.001 HIS E 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (21431) covalent geometry : angle 0.52687 / 0.26 (29179) hydrogen bonds : bond 0.04267 / 2.89 ( 1071) hydrogen bonds : angle 4.35283 / 3.09 ( 3165) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 174 time to evaluate : 0.821 Fit side-chains revert: symmetry clash REVERT: A 116 PRO cc_start: 0.8021 (Cg_exo) cc_final: 0.7576 (Cg_endo) REVERT: A 301 ASP cc_start: 0.8031 (t0) cc_final: 0.7677 (t0) REVERT: B 107 TYR cc_start: 0.7371 (t80) cc_final: 0.6852 (t80) REVERT: C 310 ARG cc_start: 0.7940 (mmt-90) cc_final: 0.7526 (mpt180) REVERT: C 325 LEU cc_start: 0.8294 (tt) cc_final: 0.8090 (tt) REVERT: E 74 HIS cc_start: 0.7654 (t70) cc_final: 0.7387 (t70) REVERT: E 332 HIS cc_start: 0.7174 (m-70) cc_final: 0.6668 (m-70) REVERT: G 221 PHE cc_start: 0.5573 (t80) cc_final: 0.5052 (t80) REVERT: G 269 PHE cc_start: 0.6651 (t80) cc_final: 0.6409 (t80) REVERT: H 120 MET cc_start: 0.7719 (mmt) cc_final: 0.7439 (mmm) outliers start: 14 outliers final: 12 residues processed: 182 average time/residue: 0.1598 time to fit residues: 44.3672 Evaluate side-chains 163 residues out of total 2211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 151 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 249 GLU Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain F residue 64 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 212 optimal weight: 0.4980 chunk 86 optimal weight: 0.7980 chunk 143 optimal weight: 9.9990 chunk 147 optimal weight: 9.9990 chunk 134 optimal weight: 10.0000 chunk 129 optimal weight: 20.0000 chunk 108 optimal weight: 8.9990 chunk 17 optimal weight: 0.7980 chunk 252 optimal weight: 10.0000 chunk 50 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 overall best weight: 1.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 307 ASN G 42 HIS F 252 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.197658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.153188 restraints weight = 50405.692| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 6.55 r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3880 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3880 r_free = 0.3880 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3880 r_free = 0.3880 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3880 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 21431 Z= 0.110 Angle : 0.487 6.670 29179 Z= 0.243 Chirality : 0.037 0.191 3271 Planarity : 0.004 0.064 3691 Dihedral : 14.593 176.624 3440 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.95 % Allowed : 9.62 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.17), residues: 2579 helix: 2.31 (0.15), residues: 1371 sheet: 0.56 (0.55), residues: 106 loop : -0.88 (0.18), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 220 TYR 0.012 0.001 TYR A 107 PHE 0.013 0.001 PHE E 221 TRP 0.008 0.001 TRP B 161 HIS 0.004 0.001 HIS D 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (21431) covalent geometry : angle 0.48658 / 0.24 (29179) hydrogen bonds : bond 0.03926 / 2.66 ( 1071) hydrogen bonds : angle 4.06308 / 2.89 ( 3165) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 167 time to evaluate : 0.765 Fit side-chains REVERT: A 116 PRO cc_start: 0.8009 (Cg_exo) cc_final: 0.7604 (Cg_endo) REVERT: A 301 ASP cc_start: 0.7856 (t0) cc_final: 0.7422 (t0) REVERT: B 107 TYR cc_start: 0.7443 (t80) cc_final: 0.6867 (t80) REVERT: B 211 ASN cc_start: 0.8331 (t0) cc_final: 0.7929 (t0) REVERT: C 310 ARG cc_start: 0.7779 (mmt-90) cc_final: 0.7325 (mpt180) REVERT: C 325 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8082 (tt) REVERT: E 74 HIS cc_start: 0.6873 (t70) cc_final: 0.6629 (t70) REVERT: G 221 PHE cc_start: 0.5831 (t80) cc_final: 0.5538 (t80) REVERT: H 120 MET cc_start: 0.7930 (mmt) cc_final: 0.7625 (mmm) outliers start: 21 outliers final: 14 residues processed: 179 average time/residue: 0.1490 time to fit residues: 41.3033 Evaluate side-chains 168 residues out of total 2211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 153 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 64 CYS Chi-restraints excluded: chain H residue 263 THR Chi-restraints excluded: chain H residue 295 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 42 optimal weight: 8.9990 chunk 213 optimal weight: 8.9990 chunk 13 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 241 optimal weight: 50.0000 chunk 162 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 117 optimal weight: 6.9990 chunk 145 optimal weight: 10.0000 chunk 67 optimal weight: 7.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 307 ASN G 42 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.194058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.148737 restraints weight = 48015.502| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 6.48 r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3830 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3830 r_free = 0.3830 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3830 r_free = 0.3830 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3830 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 21431 Z= 0.199 Angle : 0.576 6.744 29179 Z= 0.285 Chirality : 0.040 0.198 3271 Planarity : 0.005 0.059 3691 Dihedral : 14.630 169.545 3440 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.59 % Allowed : 11.62 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.17), residues: 2579 helix: 2.10 (0.15), residues: 1367 sheet: 0.33 (0.55), residues: 106 loop : -1.02 (0.18), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 284 TYR 0.015 0.001 TYR B 106 PHE 0.020 0.002 PHE C 279 TRP 0.008 0.001 TRP B 161 HIS 0.006 0.001 HIS C 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.20 (21431) covalent geometry : angle 0.57631 / 0.29 (29179) hydrogen bonds : bond 0.05219 / 3.56 ( 1071) hydrogen bonds : angle 4.19904 / 3.00 ( 3165) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 169 time to evaluate : 0.791 Fit side-chains REVERT: A 301 ASP cc_start: 0.8048 (t0) cc_final: 0.7725 (t0) REVERT: B 107 TYR cc_start: 0.7533 (t80) cc_final: 0.6978 (t80) REVERT: B 211 ASN cc_start: 0.8360 (t0) cc_final: 0.7995 (t0) REVERT: B 222 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8078 (tt) REVERT: C 310 ARG cc_start: 0.7814 (mmt-90) cc_final: 0.7485 (mpt180) REVERT: D 185 HIS cc_start: 0.6567 (t-90) cc_final: 0.5984 (m170) REVERT: D 301 ASP cc_start: 0.7979 (t0) cc_final: 0.7754 (m-30) REVERT: E 287 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.7177 (mp10) REVERT: G 221 PHE cc_start: 0.5893 (t80) cc_final: 0.5538 (t80) REVERT: G 269 PHE cc_start: 0.6873 (t80) cc_final: 0.6649 (t80) REVERT: H 120 MET cc_start: 0.7956 (mmt) cc_final: 0.7663 (mmm) outliers start: 35 outliers final: 24 residues processed: 194 average time/residue: 0.1572 time to fit residues: 46.9743 Evaluate side-chains 180 residues out of total 2211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 287 GLN Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 64 CYS Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 261 TYR Chi-restraints excluded: chain H residue 263 THR Chi-restraints excluded: chain H residue 295 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 112 optimal weight: 0.9990 chunk 53 optimal weight: 7.9990 chunk 133 optimal weight: 20.0000 chunk 229 optimal weight: 5.9990 chunk 50 optimal weight: 0.6980 chunk 33 optimal weight: 9.9990 chunk 196 optimal weight: 9.9990 chunk 149 optimal weight: 40.0000 chunk 150 optimal weight: 30.0000 chunk 228 optimal weight: 20.0000 chunk 180 optimal weight: 0.0570 overall best weight: 3.1504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 184 GLN E 307 ASN G 42 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.195293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.149506 restraints weight = 35397.665| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 4.95 r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3839 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3839 r_free = 0.3839 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3839 r_free = 0.3839 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3839 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21431 Z= 0.148 Angle : 0.519 7.090 29179 Z= 0.258 Chirality : 0.038 0.213 3271 Planarity : 0.004 0.054 3691 Dihedral : 14.458 166.231 3440 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.81 % Allowed : 12.89 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.20 (0.17), residues: 2579 helix: 2.21 (0.15), residues: 1367 sheet: 0.37 (0.56), residues: 106 loop : -1.03 (0.18), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 331 TYR 0.013 0.001 TYR G 167 PHE 0.014 0.001 PHE C 291 TRP 0.010 0.001 TRP B 161 HIS 0.005 0.001 HIS D 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (21431) covalent geometry : angle 0.51853 / 0.26 (29179) hydrogen bonds : bond 0.04366 / 2.98 ( 1071) hydrogen bonds : angle 4.02102 / 2.87 ( 3165) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 163 time to evaluate : 0.790 Fit side-chains REVERT: A 301 ASP cc_start: 0.7748 (t0) cc_final: 0.7490 (t0) REVERT: B 107 TYR cc_start: 0.7575 (t80) cc_final: 0.7040 (t80) REVERT: B 211 ASN cc_start: 0.8311 (t0) cc_final: 0.7993 (t0) REVERT: B 222 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8152 (tt) REVERT: B 225 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8255 (mp) REVERT: C 310 ARG cc_start: 0.7666 (mmt-90) cc_final: 0.7384 (mpt180) REVERT: D 185 HIS cc_start: 0.6450 (t-90) cc_final: 0.5831 (m170) REVERT: D 301 ASP cc_start: 0.7845 (t0) cc_final: 0.7643 (m-30) REVERT: E 287 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.6971 (mp10) REVERT: G 224 LYS cc_start: 0.5472 (mmtm) cc_final: 0.5001 (mtpt) REVERT: H 120 MET cc_start: 0.7879 (mmt) cc_final: 0.7598 (mmm) outliers start: 40 outliers final: 25 residues processed: 190 average time/residue: 0.1414 time to fit residues: 41.9721 Evaluate side-chains 183 residues out of total 2211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 155 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain E residue 64 CYS Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 287 GLN Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 171 ILE Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 64 CYS Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 261 TYR Chi-restraints excluded: chain H residue 263 THR Chi-restraints excluded: chain H residue 295 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 11 optimal weight: 6.9990 chunk 127 optimal weight: 9.9990 chunk 42 optimal weight: 9.9990 chunk 209 optimal weight: 0.6980 chunk 198 optimal weight: 20.0000 chunk 31 optimal weight: 20.0000 chunk 241 optimal weight: 50.0000 chunk 206 optimal weight: 10.0000 chunk 205 optimal weight: 10.0000 chunk 36 optimal weight: 0.9980 chunk 137 optimal weight: 50.0000 overall best weight: 5.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 185 HIS ** C 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 307 ASN G 42 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.192639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.148311 restraints weight = 49398.832| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 6.61 r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3828 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3828 r_free = 0.3828 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3828 r_free = 0.3828 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3828 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 21431 Z= 0.243 Angle : 0.616 7.547 29179 Z= 0.303 Chirality : 0.042 0.207 3271 Planarity : 0.005 0.054 3691 Dihedral : 14.684 168.705 3440 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.00 % Allowed : 13.93 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.17), residues: 2579 helix: 1.94 (0.15), residues: 1365 sheet: 0.23 (0.56), residues: 100 loop : -1.11 (0.18), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 284 TYR 0.016 0.002 TYR A 107 PHE 0.019 0.002 PHE C 279 TRP 0.010 0.001 TRP C 161 HIS 0.006 0.001 HIS C 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00585 / 0.24 (21431) covalent geometry : angle 0.61608 / 0.30 (29179) hydrogen bonds : bond 0.05584 / 3.81 ( 1071) hydrogen bonds : angle 4.25464 / 3.04 ( 3165) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 156 time to evaluate : 0.824 Fit side-chains REVERT: B 107 TYR cc_start: 0.7631 (t80) cc_final: 0.7140 (t80) REVERT: B 211 ASN cc_start: 0.8367 (t0) cc_final: 0.7996 (t0) REVERT: B 222 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8075 (tt) REVERT: B 225 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8248 (mp) REVERT: B 290 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8269 (tt) REVERT: C 310 ARG cc_start: 0.7887 (mmt-90) cc_final: 0.7537 (mpt180) REVERT: E 225 LEU cc_start: 0.6637 (OUTLIER) cc_final: 0.6055 (mt) REVERT: E 287 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.7101 (mp10) REVERT: G 269 PHE cc_start: 0.6890 (t80) cc_final: 0.6664 (t80) REVERT: F 222 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7667 (mt) REVERT: H 120 MET cc_start: 0.8002 (mmt) cc_final: 0.7713 (mmm) outliers start: 44 outliers final: 33 residues processed: 190 average time/residue: 0.1511 time to fit residues: 44.9540 Evaluate side-chains 190 residues out of total 2211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 151 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 205 ASP Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain E residue 64 CYS Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 287 GLN Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 171 ILE Chi-restraints excluded: chain G residue 286 GLU Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 64 CYS Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain F residue 335 GLN Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 261 TYR Chi-restraints excluded: chain H residue 263 THR Chi-restraints excluded: chain H residue 295 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 53 optimal weight: 6.9990 chunk 110 optimal weight: 0.9980 chunk 174 optimal weight: 2.9990 chunk 90 optimal weight: 0.0870 chunk 38 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 162 optimal weight: 10.0000 chunk 226 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 190 optimal weight: 10.0000 chunk 220 optimal weight: 3.9990 overall best weight: 2.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 307 ASN G 42 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.195100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.144721 restraints weight = 34463.541| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 7.22 r_work: 0.3053 rms_B_bonded: 6.18 restraints_weight: 2.0000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3045 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3045 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21431 Z= 0.130 Angle : 0.508 8.178 29179 Z= 0.253 Chirality : 0.037 0.229 3271 Planarity : 0.004 0.050 3691 Dihedral : 14.394 164.105 3440 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.91 % Allowed : 14.66 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.17), residues: 2579 helix: 2.20 (0.15), residues: 1367 sheet: 0.47 (0.61), residues: 90 loop : -1.07 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 331 TYR 0.020 0.001 TYR E 199 PHE 0.014 0.001 PHE C 291 TRP 0.011 0.001 TRP G 161 HIS 0.005 0.001 HIS D 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (21431) covalent geometry : angle 0.50795 / 0.25 (29179) hydrogen bonds : bond 0.04160 / 2.85 ( 1071) hydrogen bonds : angle 3.96541 / 2.83 ( 3165) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 158 time to evaluate : 0.880 Fit side-chains REVERT: A 196 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7352 (mm-40) REVERT: A 301 ASP cc_start: 0.8372 (t0) cc_final: 0.8117 (t0) REVERT: B 107 TYR cc_start: 0.7495 (t80) cc_final: 0.7066 (t80) REVERT: B 211 ASN cc_start: 0.8315 (t0) cc_final: 0.7815 (t0) REVERT: B 222 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8132 (tt) REVERT: B 225 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8201 (mp) REVERT: C 310 ARG cc_start: 0.7917 (mmt-90) cc_final: 0.7418 (mpt180) REVERT: D 185 HIS cc_start: 0.6377 (t-90) cc_final: 0.5351 (m170) REVERT: E 225 LEU cc_start: 0.5752 (OUTLIER) cc_final: 0.5529 (mt) REVERT: E 287 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.6965 (mp10) REVERT: E 332 HIS cc_start: 0.7940 (t70) cc_final: 0.7099 (m90) REVERT: F 222 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7488 (mt) REVERT: F 224 LYS cc_start: 0.6316 (mmtm) cc_final: 0.5808 (mtpt) REVERT: H 120 MET cc_start: 0.7779 (mmt) cc_final: 0.7496 (mmm) outliers start: 42 outliers final: 28 residues processed: 189 average time/residue: 0.1541 time to fit residues: 45.6052 Evaluate side-chains 186 residues out of total 2211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 152 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 196 GLN Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain E residue 64 CYS Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 287 GLN Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 171 ILE Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain F residue 335 GLN Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 261 TYR Chi-restraints excluded: chain H residue 263 THR Chi-restraints excluded: chain H residue 295 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 70 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 201 optimal weight: 2.9990 chunk 56 optimal weight: 9.9990 chunk 32 optimal weight: 0.4980 chunk 181 optimal weight: 0.0980 chunk 5 optimal weight: 6.9990 chunk 195 optimal weight: 0.3980 chunk 118 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 48 optimal weight: 8.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 307 ASN G 42 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.196796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.149468 restraints weight = 38060.935| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 5.36 r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3839 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3839 r_free = 0.3839 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3839 r_free = 0.3839 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3839 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 21431 Z= 0.098 Angle : 0.474 8.699 29179 Z= 0.235 Chirality : 0.036 0.239 3271 Planarity : 0.004 0.052 3691 Dihedral : 14.126 158.122 3440 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.63 % Allowed : 15.38 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.18), residues: 2579 helix: 2.40 (0.15), residues: 1369 sheet: 0.86 (0.92), residues: 42 loop : -1.03 (0.18), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 331 TYR 0.018 0.001 TYR E 199 PHE 0.013 0.001 PHE C 291 TRP 0.011 0.001 TRP B 161 HIS 0.004 0.001 HIS G 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (21431) covalent geometry : angle 0.47449 / 0.24 (29179) hydrogen bonds : bond 0.03396 / 2.32 ( 1071) hydrogen bonds : angle 3.76266 / 2.69 ( 3165) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 163 time to evaluate : 0.856 Fit side-chains REVERT: A 196 GLN cc_start: 0.7646 (OUTLIER) cc_final: 0.7360 (mm-40) REVERT: B 107 TYR cc_start: 0.7589 (t80) cc_final: 0.7110 (t80) REVERT: B 211 ASN cc_start: 0.8360 (t0) cc_final: 0.7993 (t0) REVERT: B 222 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.8060 (tt) REVERT: B 290 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8366 (tt) REVERT: C 310 ARG cc_start: 0.7672 (mmt-90) cc_final: 0.7307 (mpt180) REVERT: D 185 HIS cc_start: 0.6575 (t-90) cc_final: 0.5638 (m170) REVERT: E 225 LEU cc_start: 0.6526 (OUTLIER) cc_final: 0.5772 (mt) REVERT: E 287 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.6865 (mp10) REVERT: F 222 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7539 (mt) REVERT: H 120 MET cc_start: 0.7946 (mmt) cc_final: 0.7668 (mmm) outliers start: 36 outliers final: 22 residues processed: 191 average time/residue: 0.1526 time to fit residues: 45.3323 Evaluate side-chains 180 residues out of total 2211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 196 GLN Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain E residue 64 CYS Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 287 GLN Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 171 ILE Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 261 TYR Chi-restraints excluded: chain H residue 263 THR Chi-restraints excluded: chain H residue 295 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 30.0000 chunk 8 optimal weight: 0.7980 chunk 228 optimal weight: 9.9990 chunk 223 optimal weight: 6.9990 chunk 189 optimal weight: 0.2980 chunk 106 optimal weight: 9.9990 chunk 85 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 166 optimal weight: 8.9990 chunk 110 optimal weight: 0.0770 chunk 194 optimal weight: 10.0000 overall best weight: 2.2342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 307 ASN G 42 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.196146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.143486 restraints weight = 31556.699| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 6.46 r_work: 0.3095 rms_B_bonded: 5.82 restraints_weight: 2.0000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3086 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3085 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21431 Z= 0.119 Angle : 0.499 8.449 29179 Z= 0.247 Chirality : 0.037 0.232 3271 Planarity : 0.004 0.051 3691 Dihedral : 14.130 158.403 3440 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.72 % Allowed : 15.34 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.17), residues: 2579 helix: 2.39 (0.15), residues: 1369 sheet: 0.81 (0.92), residues: 42 loop : -1.01 (0.18), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 220 TYR 0.019 0.001 TYR B 104 PHE 0.014 0.001 PHE C 291 TRP 0.011 0.001 TRP B 161 HIS 0.015 0.001 HIS E 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (21431) covalent geometry : angle 0.49935 / 0.25 (29179) hydrogen bonds : bond 0.03716 / 2.54 ( 1071) hydrogen bonds : angle 3.78874 / 2.71 ( 3165) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 155 time to evaluate : 0.686 Fit side-chains REVERT: A 196 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.7693 (mm-40) REVERT: A 308 ASN cc_start: 0.8061 (OUTLIER) cc_final: 0.7644 (t0) REVERT: B 107 TYR cc_start: 0.7483 (t80) cc_final: 0.7072 (t80) REVERT: B 211 ASN cc_start: 0.8329 (t0) cc_final: 0.7829 (t0) REVERT: B 290 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8673 (tt) REVERT: C 310 ARG cc_start: 0.7862 (mmt-90) cc_final: 0.7415 (mpt180) REVERT: D 301 ASP cc_start: 0.8629 (t0) cc_final: 0.7855 (m-30) REVERT: E 225 LEU cc_start: 0.5659 (OUTLIER) cc_final: 0.5395 (mt) REVERT: E 287 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.6920 (mp10) REVERT: F 214 MET cc_start: 0.7629 (tmm) cc_final: 0.6920 (mmt) REVERT: F 222 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7290 (mt) REVERT: F 224 LYS cc_start: 0.6594 (mtpt) cc_final: 0.6305 (mmtm) REVERT: H 120 MET cc_start: 0.7757 (mmt) cc_final: 0.7467 (mmm) outliers start: 38 outliers final: 27 residues processed: 184 average time/residue: 0.1500 time to fit residues: 43.3528 Evaluate side-chains 185 residues out of total 2211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 152 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 196 GLN Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 308 ASN Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain E residue 64 CYS Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 287 GLN Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain E residue 307 ASN Chi-restraints excluded: chain G residue 171 ILE Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain F residue 335 GLN Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 261 TYR Chi-restraints excluded: chain H residue 263 THR Chi-restraints excluded: chain H residue 295 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 132 optimal weight: 30.0000 chunk 98 optimal weight: 0.9980 chunk 48 optimal weight: 7.9990 chunk 221 optimal weight: 30.0000 chunk 31 optimal weight: 5.9990 chunk 35 optimal weight: 0.1980 chunk 199 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 181 optimal weight: 0.2980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 307 ASN G 42 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.197580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.146285 restraints weight = 34822.896| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 7.31 r_work: 0.3098 rms_B_bonded: 6.17 restraints_weight: 2.0000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3094 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3094 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 21431 Z= 0.090 Angle : 0.477 10.652 29179 Z= 0.236 Chirality : 0.036 0.243 3271 Planarity : 0.004 0.051 3691 Dihedral : 14.015 156.369 3440 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.23 % Allowed : 15.88 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.18), residues: 2579 helix: 2.49 (0.15), residues: 1369 sheet: 0.94 (0.94), residues: 42 loop : -0.97 (0.18), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 220 TYR 0.020 0.001 TYR E 199 PHE 0.014 0.001 PHE C 291 TRP 0.011 0.001 TRP B 161 HIS 0.004 0.000 HIS G 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00196 / 0.09 (21431) covalent geometry : angle 0.47677 / 0.24 (29179) hydrogen bonds : bond 0.03204 / 2.19 ( 1071) hydrogen bonds : angle 3.67642 / 2.63 ( 3165) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 162 time to evaluate : 0.767 Fit side-chains REVERT: A 196 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7688 (mm-40) REVERT: B 107 TYR cc_start: 0.7501 (t80) cc_final: 0.7094 (t80) REVERT: B 211 ASN cc_start: 0.8321 (t0) cc_final: 0.7814 (t0) REVERT: B 290 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8630 (tt) REVERT: C 310 ARG cc_start: 0.7839 (mmt-90) cc_final: 0.7398 (mpt180) REVERT: D 185 HIS cc_start: 0.6426 (t-90) cc_final: 0.5447 (m170) REVERT: E 225 LEU cc_start: 0.5625 (OUTLIER) cc_final: 0.5353 (mt) REVERT: E 287 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.6882 (mp10) REVERT: E 332 HIS cc_start: 0.7930 (t70) cc_final: 0.7031 (m90) REVERT: F 214 MET cc_start: 0.7620 (tmm) cc_final: 0.6912 (mmt) REVERT: F 222 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7271 (mt) REVERT: F 224 LYS cc_start: 0.6566 (mtpt) cc_final: 0.6200 (mmtm) REVERT: H 120 MET cc_start: 0.7726 (mmt) cc_final: 0.7437 (mmm) REVERT: H 332 HIS cc_start: 0.7037 (t70) cc_final: 0.6639 (m-70) outliers start: 27 outliers final: 20 residues processed: 181 average time/residue: 0.1475 time to fit residues: 41.5579 Evaluate side-chains 183 residues out of total 2211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 GLN Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain D residue 106 TYR Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain E residue 64 CYS Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 287 GLN Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain E residue 307 ASN Chi-restraints excluded: chain G residue 171 ILE Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 261 TYR Chi-restraints excluded: chain H residue 263 THR Chi-restraints excluded: chain H residue 295 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 68 optimal weight: 9.9990 chunk 151 optimal weight: 20.0000 chunk 181 optimal weight: 7.9990 chunk 57 optimal weight: 0.9990 chunk 237 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 191 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 243 optimal weight: 20.0000 chunk 115 optimal weight: 6.9990 chunk 110 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 HIS E 307 ASN G 42 HIS F 335 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.192923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.148683 restraints weight = 48937.299| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 6.64 r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3834 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3834 r_free = 0.3834 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3834 r_free = 0.3834 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3834 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 21431 Z= 0.235 Angle : 0.627 9.662 29179 Z= 0.307 Chirality : 0.042 0.217 3271 Planarity : 0.005 0.054 3691 Dihedral : 14.429 162.791 3440 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.54 % Allowed : 15.61 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.17), residues: 2579 helix: 2.09 (0.15), residues: 1368 sheet: 0.27 (0.56), residues: 100 loop : -0.97 (0.18), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 284 TYR 0.020 0.002 TYR E 199 PHE 0.018 0.002 PHE C 279 TRP 0.012 0.001 TRP C 161 HIS 0.006 0.001 HIS D 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00565 / 0.23 (21431) covalent geometry : angle 0.62742 / 0.31 (29179) hydrogen bonds : bond 0.05392 / 3.67 ( 1071) hydrogen bonds : angle 4.11475 / 2.95 ( 3165) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4450.29 seconds wall clock time: 77 minutes 2.80 seconds (4622.80 seconds total)