Starting phenix.real_space_refine on Wed Jul 30 12:17:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6n24_9322/07_2025/6n24_9322_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n24_9322/07_2025/6n24_9322.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6n24_9322/07_2025/6n24_9322.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n24_9322/07_2025/6n24_9322.map" model { file = "/net/cci-nas-00/data/ceres_data/6n24_9322/07_2025/6n24_9322_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n24_9322/07_2025/6n24_9322_neut.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.185 sd= 1.557 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 65 5.16 5 C 8338 2.51 5 N 2060 2.21 5 O 2180 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12643 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2529 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 292} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 2527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2527 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 292} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2529 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 292} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2529 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 292} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2529 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 292} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 7.72, per 1000 atoms: 0.61 Number of scatterers: 12643 At special positions: 0 Unit cell: (94.656, 94.656, 113.152, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 65 16.00 O 2180 8.00 N 2060 7.00 C 8338 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 185 " distance=2.04 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 185 " distance=2.04 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 185 " distance=2.04 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 185 " distance=2.04 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 185 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.86 Conformation dependent library (CDL) restraints added in 1.9 seconds 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2940 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 0 sheets defined 74.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 34 through 53 removed outlier: 3.725A pdb=" N ILE A 46 " --> pdb=" O LEU A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 72 removed outlier: 3.584A pdb=" N LEU A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N MET A 61 " --> pdb=" O SER A 57 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS A 64 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 65 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 76 removed outlier: 3.626A pdb=" N ILE A 76 " --> pdb=" O ALA A 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 73 through 76' Processing helix chain 'A' and resid 77 through 94 removed outlier: 3.717A pdb=" N GLY A 83 " --> pdb=" O SER A 79 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE A 84 " --> pdb=" O PHE A 80 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR A 85 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER A 87 " --> pdb=" O GLY A 83 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 97 No H-bonds generated for 'chain 'A' and resid 95 through 97' Processing helix chain 'A' and resid 103 through 114 removed outlier: 3.757A pdb=" N ASN A 108 " --> pdb=" O ASP A 104 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU A 109 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N CYS A 112 " --> pdb=" O ASN A 108 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL A 114 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 144 removed outlier: 3.680A pdb=" N ASN A 133 " --> pdb=" O MET A 129 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N SER A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ILE A 139 " --> pdb=" O CYS A 135 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N SER A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 151 Processing helix chain 'A' and resid 154 through 160 removed outlier: 3.534A pdb=" N VAL A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 172 removed outlier: 3.766A pdb=" N LYS A 169 " --> pdb=" O PRO A 165 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS A 170 " --> pdb=" O GLU A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 197 removed outlier: 3.972A pdb=" N SER A 189 " --> pdb=" O CYS A 185 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL A 193 " --> pdb=" O SER A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 230 removed outlier: 3.518A pdb=" N ILE A 210 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU A 213 " --> pdb=" O GLY A 209 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR A 216 " --> pdb=" O ASN A 212 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 217 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 224 " --> pdb=" O GLN A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 255 removed outlier: 4.070A pdb=" N VAL A 239 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL A 240 " --> pdb=" O TYR A 236 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL A 242 " --> pdb=" O GLN A 238 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL A 244 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR A 245 " --> pdb=" O THR A 241 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE A 247 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ILE A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG A 255 " --> pdb=" O CYS A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 285 Processing helix chain 'A' and resid 285 through 296 removed outlier: 4.358A pdb=" N ASN A 296 " --> pdb=" O GLU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 319 removed outlier: 3.725A pdb=" N ASP A 312 " --> pdb=" O ASN A 308 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN A 316 " --> pdb=" O ASP A 312 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER A 318 " --> pdb=" O ASN A 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 53 removed outlier: 3.725A pdb=" N ILE B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 72 removed outlier: 3.585A pdb=" N LEU B 60 " --> pdb=" O GLU B 56 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N MET B 61 " --> pdb=" O SER B 57 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS B 64 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 65 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 76 removed outlier: 3.627A pdb=" N ILE B 76 " --> pdb=" O ALA B 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 73 through 76' Processing helix chain 'B' and resid 77 through 94 removed outlier: 3.718A pdb=" N GLY B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE B 84 " --> pdb=" O PHE B 80 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR B 85 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER B 87 " --> pdb=" O GLY B 83 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER B 91 " --> pdb=" O SER B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 97 No H-bonds generated for 'chain 'B' and resid 95 through 97' Processing helix chain 'B' and resid 103 through 114 removed outlier: 3.757A pdb=" N ASN B 108 " --> pdb=" O ASP B 104 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU B 109 " --> pdb=" O ARG B 105 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N CYS B 112 " --> pdb=" O ASN B 108 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL B 114 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 144 removed outlier: 3.680A pdb=" N ASN B 133 " --> pdb=" O MET B 129 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N SER B 136 " --> pdb=" O SER B 132 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ILE B 139 " --> pdb=" O CYS B 135 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N SER B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 151 Processing helix chain 'B' and resid 154 through 160 removed outlier: 3.534A pdb=" N VAL B 158 " --> pdb=" O MET B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 172 removed outlier: 3.766A pdb=" N LYS B 169 " --> pdb=" O PRO B 165 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS B 170 " --> pdb=" O GLU B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 197 removed outlier: 3.973A pdb=" N SER B 189 " --> pdb=" O CYS B 185 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL B 193 " --> pdb=" O SER B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 230 removed outlier: 3.518A pdb=" N ILE B 210 " --> pdb=" O LEU B 206 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU B 213 " --> pdb=" O GLY B 209 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR B 216 " --> pdb=" O ASN B 212 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B 217 " --> pdb=" O GLU B 213 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU B 224 " --> pdb=" O GLN B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 255 removed outlier: 4.070A pdb=" N VAL B 239 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL B 240 " --> pdb=" O TYR B 236 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL B 242 " --> pdb=" O GLN B 238 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL B 244 " --> pdb=" O VAL B 240 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR B 245 " --> pdb=" O THR B 241 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE B 247 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ILE B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG B 255 " --> pdb=" O CYS B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 285 Processing helix chain 'B' and resid 285 through 296 removed outlier: 4.357A pdb=" N ASN B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 319 removed outlier: 3.724A pdb=" N ASP B 312 " --> pdb=" O ASN B 308 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN B 316 " --> pdb=" O ASP B 312 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER B 318 " --> pdb=" O ASN B 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 53 removed outlier: 3.725A pdb=" N ILE C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 72 removed outlier: 3.584A pdb=" N LEU C 60 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N MET C 61 " --> pdb=" O SER C 57 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS C 64 " --> pdb=" O LEU C 60 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU C 65 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER C 71 " --> pdb=" O LEU C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 76 removed outlier: 3.626A pdb=" N ILE C 76 " --> pdb=" O ALA C 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 73 through 76' Processing helix chain 'C' and resid 77 through 94 removed outlier: 3.718A pdb=" N GLY C 83 " --> pdb=" O SER C 79 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE C 84 " --> pdb=" O PHE C 80 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR C 85 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER C 87 " --> pdb=" O GLY C 83 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N SER C 91 " --> pdb=" O SER C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 97 No H-bonds generated for 'chain 'C' and resid 95 through 97' Processing helix chain 'C' and resid 103 through 114 removed outlier: 3.757A pdb=" N ASN C 108 " --> pdb=" O ASP C 104 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU C 109 " --> pdb=" O ARG C 105 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N CYS C 112 " --> pdb=" O ASN C 108 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL C 114 " --> pdb=" O VAL C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 144 removed outlier: 3.680A pdb=" N ASN C 133 " --> pdb=" O MET C 129 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N SER C 136 " --> pdb=" O SER C 132 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ILE C 139 " --> pdb=" O CYS C 135 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N SER C 142 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 151 Processing helix chain 'C' and resid 154 through 160 removed outlier: 3.534A pdb=" N VAL C 158 " --> pdb=" O MET C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 172 removed outlier: 3.766A pdb=" N LYS C 169 " --> pdb=" O PRO C 165 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS C 170 " --> pdb=" O GLU C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 197 removed outlier: 3.972A pdb=" N SER C 189 " --> pdb=" O CYS C 185 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL C 193 " --> pdb=" O SER C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 230 removed outlier: 3.519A pdb=" N ILE C 210 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU C 213 " --> pdb=" O GLY C 209 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR C 216 " --> pdb=" O ASN C 212 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU C 217 " --> pdb=" O GLU C 213 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU C 224 " --> pdb=" O GLN C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 255 removed outlier: 4.071A pdb=" N VAL C 239 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL C 240 " --> pdb=" O TYR C 236 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL C 242 " --> pdb=" O GLN C 238 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL C 244 " --> pdb=" O VAL C 240 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR C 245 " --> pdb=" O THR C 241 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE C 247 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ILE C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG C 255 " --> pdb=" O CYS C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 285 Processing helix chain 'C' and resid 285 through 296 removed outlier: 4.358A pdb=" N ASN C 296 " --> pdb=" O GLU C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 319 removed outlier: 3.725A pdb=" N ASP C 312 " --> pdb=" O ASN C 308 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN C 316 " --> pdb=" O ASP C 312 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER C 318 " --> pdb=" O ASN C 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 53 removed outlier: 3.725A pdb=" N ILE D 46 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 72 removed outlier: 3.585A pdb=" N LEU D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N MET D 61 " --> pdb=" O SER D 57 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS D 64 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU D 65 " --> pdb=" O MET D 61 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER D 71 " --> pdb=" O LEU D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 76 removed outlier: 3.626A pdb=" N ILE D 76 " --> pdb=" O ALA D 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 73 through 76' Processing helix chain 'D' and resid 77 through 94 removed outlier: 3.717A pdb=" N GLY D 83 " --> pdb=" O SER D 79 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE D 84 " --> pdb=" O PHE D 80 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR D 85 " --> pdb=" O VAL D 81 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER D 87 " --> pdb=" O GLY D 83 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N SER D 91 " --> pdb=" O SER D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 97 No H-bonds generated for 'chain 'D' and resid 95 through 97' Processing helix chain 'D' and resid 103 through 114 removed outlier: 3.757A pdb=" N ASN D 108 " --> pdb=" O ASP D 104 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU D 109 " --> pdb=" O ARG D 105 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N CYS D 112 " --> pdb=" O ASN D 108 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL D 114 " --> pdb=" O VAL D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 144 removed outlier: 3.679A pdb=" N ASN D 133 " --> pdb=" O MET D 129 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N SER D 136 " --> pdb=" O SER D 132 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ILE D 139 " --> pdb=" O CYS D 135 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N SER D 142 " --> pdb=" O LEU D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 151 Processing helix chain 'D' and resid 154 through 160 removed outlier: 3.534A pdb=" N VAL D 158 " --> pdb=" O MET D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 172 removed outlier: 3.765A pdb=" N LYS D 169 " --> pdb=" O PRO D 165 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS D 170 " --> pdb=" O GLU D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 197 removed outlier: 3.973A pdb=" N SER D 189 " --> pdb=" O CYS D 185 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL D 193 " --> pdb=" O SER D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 230 removed outlier: 3.519A pdb=" N ILE D 210 " --> pdb=" O LEU D 206 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU D 213 " --> pdb=" O GLY D 209 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR D 216 " --> pdb=" O ASN D 212 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU D 217 " --> pdb=" O GLU D 213 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU D 224 " --> pdb=" O GLN D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 255 removed outlier: 4.071A pdb=" N VAL D 239 " --> pdb=" O VAL D 235 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL D 240 " --> pdb=" O TYR D 236 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL D 242 " --> pdb=" O GLN D 238 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL D 244 " --> pdb=" O VAL D 240 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR D 245 " --> pdb=" O THR D 241 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE D 247 " --> pdb=" O ALA D 243 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ILE D 253 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG D 255 " --> pdb=" O CYS D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 285 Processing helix chain 'D' and resid 285 through 296 removed outlier: 4.358A pdb=" N ASN D 296 " --> pdb=" O GLU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 319 removed outlier: 3.724A pdb=" N ASP D 312 " --> pdb=" O ASN D 308 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN D 316 " --> pdb=" O ASP D 312 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER D 318 " --> pdb=" O ASN D 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 34 through 53 removed outlier: 3.725A pdb=" N ILE E 46 " --> pdb=" O LEU E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 72 removed outlier: 3.584A pdb=" N LEU E 60 " --> pdb=" O GLU E 56 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N MET E 61 " --> pdb=" O SER E 57 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS E 64 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU E 65 " --> pdb=" O MET E 61 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER E 71 " --> pdb=" O LEU E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 76 removed outlier: 3.627A pdb=" N ILE E 76 " --> pdb=" O ALA E 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 73 through 76' Processing helix chain 'E' and resid 77 through 94 removed outlier: 3.718A pdb=" N GLY E 83 " --> pdb=" O SER E 79 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE E 84 " --> pdb=" O PHE E 80 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR E 85 " --> pdb=" O VAL E 81 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER E 87 " --> pdb=" O GLY E 83 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N SER E 91 " --> pdb=" O SER E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 97 No H-bonds generated for 'chain 'E' and resid 95 through 97' Processing helix chain 'E' and resid 103 through 114 removed outlier: 3.757A pdb=" N ASN E 108 " --> pdb=" O ASP E 104 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU E 109 " --> pdb=" O ARG E 105 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N CYS E 112 " --> pdb=" O ASN E 108 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL E 114 " --> pdb=" O VAL E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 144 removed outlier: 3.680A pdb=" N ASN E 133 " --> pdb=" O MET E 129 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N SER E 136 " --> pdb=" O SER E 132 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ILE E 139 " --> pdb=" O CYS E 135 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N SER E 142 " --> pdb=" O LEU E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 151 Processing helix chain 'E' and resid 154 through 160 removed outlier: 3.534A pdb=" N VAL E 158 " --> pdb=" O MET E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 172 removed outlier: 3.766A pdb=" N LYS E 169 " --> pdb=" O PRO E 165 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS E 170 " --> pdb=" O GLU E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 197 removed outlier: 3.972A pdb=" N SER E 189 " --> pdb=" O CYS E 185 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL E 193 " --> pdb=" O SER E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 230 removed outlier: 3.518A pdb=" N ILE E 210 " --> pdb=" O LEU E 206 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU E 213 " --> pdb=" O GLY E 209 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR E 216 " --> pdb=" O ASN E 212 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU E 217 " --> pdb=" O GLU E 213 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU E 224 " --> pdb=" O GLN E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 255 removed outlier: 4.071A pdb=" N VAL E 239 " --> pdb=" O VAL E 235 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL E 240 " --> pdb=" O TYR E 236 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL E 242 " --> pdb=" O GLN E 238 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL E 244 " --> pdb=" O VAL E 240 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR E 245 " --> pdb=" O THR E 241 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE E 247 " --> pdb=" O ALA E 243 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ILE E 253 " --> pdb=" O LEU E 249 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG E 255 " --> pdb=" O CYS E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 285 Processing helix chain 'E' and resid 285 through 296 removed outlier: 4.356A pdb=" N ASN E 296 " --> pdb=" O GLU E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 319 removed outlier: 3.724A pdb=" N ASP E 312 " --> pdb=" O ASN E 308 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN E 316 " --> pdb=" O ASP E 312 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER E 318 " --> pdb=" O ASN E 314 " (cutoff:3.500A) 615 hydrogen bonds defined for protein. 1845 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: 3.18 Time building geometry restraints manager: 3.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3884 1.34 - 1.46: 3433 1.46 - 1.58: 5580 1.58 - 1.70: 0 1.70 - 1.82: 100 Bond restraints: 12997 Sorted by residual: bond pdb=" CB TRP D 229 " pdb=" CG TRP D 229 " ideal model delta sigma weight residual 1.498 1.457 0.041 3.10e-02 1.04e+03 1.76e+00 bond pdb=" CB TRP B 229 " pdb=" CG TRP B 229 " ideal model delta sigma weight residual 1.498 1.457 0.041 3.10e-02 1.04e+03 1.73e+00 bond pdb=" CB TRP E 229 " pdb=" CG TRP E 229 " ideal model delta sigma weight residual 1.498 1.457 0.041 3.10e-02 1.04e+03 1.72e+00 bond pdb=" CB TRP A 229 " pdb=" CG TRP A 229 " ideal model delta sigma weight residual 1.498 1.458 0.040 3.10e-02 1.04e+03 1.70e+00 bond pdb=" CB TRP C 229 " pdb=" CG TRP C 229 " ideal model delta sigma weight residual 1.498 1.458 0.040 3.10e-02 1.04e+03 1.68e+00 ... (remaining 12992 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 16907 1.73 - 3.46: 659 3.46 - 5.18: 74 5.18 - 6.91: 20 6.91 - 8.64: 5 Bond angle restraints: 17665 Sorted by residual: angle pdb=" C LEU C 271 " pdb=" N PHE C 272 " pdb=" CA PHE C 272 " ideal model delta sigma weight residual 121.54 127.63 -6.09 1.91e+00 2.74e-01 1.02e+01 angle pdb=" C LEU A 271 " pdb=" N PHE A 272 " pdb=" CA PHE A 272 " ideal model delta sigma weight residual 121.54 127.62 -6.08 1.91e+00 2.74e-01 1.01e+01 angle pdb=" C LEU D 271 " pdb=" N PHE D 272 " pdb=" CA PHE D 272 " ideal model delta sigma weight residual 121.54 127.60 -6.06 1.91e+00 2.74e-01 1.01e+01 angle pdb=" C LEU E 271 " pdb=" N PHE E 272 " pdb=" CA PHE E 272 " ideal model delta sigma weight residual 121.54 127.59 -6.05 1.91e+00 2.74e-01 1.00e+01 angle pdb=" C LEU B 271 " pdb=" N PHE B 272 " pdb=" CA PHE B 272 " ideal model delta sigma weight residual 121.54 127.58 -6.04 1.91e+00 2.74e-01 9.99e+00 ... (remaining 17660 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.48: 6516 8.48 - 16.95: 852 16.95 - 25.43: 139 25.43 - 33.91: 55 33.91 - 42.38: 65 Dihedral angle restraints: 7627 sinusoidal: 3077 harmonic: 4550 Sorted by residual: dihedral pdb=" CA TYR A 97 " pdb=" C TYR A 97 " pdb=" N GLU A 98 " pdb=" CA GLU A 98 " ideal model delta harmonic sigma weight residual 180.00 154.05 25.95 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA TYR C 97 " pdb=" C TYR C 97 " pdb=" N GLU C 98 " pdb=" CA GLU C 98 " ideal model delta harmonic sigma weight residual 180.00 154.07 25.93 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA TYR B 97 " pdb=" C TYR B 97 " pdb=" N GLU B 98 " pdb=" CA GLU B 98 " ideal model delta harmonic sigma weight residual 180.00 154.07 25.93 0 5.00e+00 4.00e-02 2.69e+01 ... (remaining 7624 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 853 0.034 - 0.069: 767 0.069 - 0.103: 252 0.103 - 0.138: 60 0.138 - 0.172: 18 Chirality restraints: 1950 Sorted by residual: chirality pdb=" CG LEU C 258 " pdb=" CB LEU C 258 " pdb=" CD1 LEU C 258 " pdb=" CD2 LEU C 258 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.40e-01 chirality pdb=" CG LEU B 258 " pdb=" CB LEU B 258 " pdb=" CD1 LEU B 258 " pdb=" CD2 LEU B 258 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.31e-01 chirality pdb=" CG LEU D 258 " pdb=" CB LEU D 258 " pdb=" CD1 LEU D 258 " pdb=" CD2 LEU D 258 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.25e-01 ... (remaining 1947 not shown) Planarity restraints: 2194 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 227 " -0.010 2.00e-02 2.50e+03 1.34e-02 3.61e+00 pdb=" CG TYR A 227 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR A 227 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR A 227 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR A 227 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 227 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 227 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 227 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 227 " 0.010 2.00e-02 2.50e+03 1.33e-02 3.54e+00 pdb=" CG TYR D 227 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR D 227 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR D 227 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR D 227 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR D 227 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR D 227 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR D 227 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 227 " -0.010 2.00e-02 2.50e+03 1.33e-02 3.54e+00 pdb=" CG TYR B 227 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR B 227 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR B 227 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR B 227 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 227 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 227 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 227 " 0.000 2.00e-02 2.50e+03 ... (remaining 2191 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 4220 2.85 - 3.36: 11420 3.36 - 3.87: 20563 3.87 - 4.39: 24194 4.39 - 4.90: 40721 Nonbonded interactions: 101118 Sorted by model distance: nonbonded pdb=" OD2 ASP D 104 " pdb=" NH2 ARG E 218 " model vdw 2.332 3.120 nonbonded pdb=" OD2 ASP C 104 " pdb=" NH2 ARG D 218 " model vdw 2.338 3.120 nonbonded pdb=" OE1 GLU B 63 " pdb=" OH TYR B 264 " model vdw 2.344 3.040 nonbonded pdb=" OE1 GLU D 63 " pdb=" OH TYR D 264 " model vdw 2.345 3.040 nonbonded pdb=" OE1 GLU A 63 " pdb=" OH TYR A 264 " model vdw 2.345 3.040 ... (remaining 101113 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 28 through 176 or (resid 177 and (name N or name CA or nam \ e C or name O or name CB )) or resid 178 through 339)) selection = chain 'B' selection = (chain 'C' and (resid 28 through 176 or (resid 177 and (name N or name CA or nam \ e C or name O or name CB )) or resid 178 through 339)) selection = (chain 'D' and (resid 28 through 176 or (resid 177 and (name N or name CA or nam \ e C or name O or name CB )) or resid 178 through 339)) selection = (chain 'E' and (resid 28 through 176 or (resid 177 and (name N or name CA or nam \ e C or name O or name CB )) or resid 178 through 339)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 29.530 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.050 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:14.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 13002 Z= 0.305 Angle : 0.780 8.639 17675 Z= 0.425 Chirality : 0.052 0.172 1950 Planarity : 0.006 0.041 2194 Dihedral : 9.044 42.382 4672 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.29 % Allowed : 1.87 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.07 (0.13), residues: 1510 helix: -4.24 (0.07), residues: 1070 sheet: None (None), residues: 0 loop : -2.69 (0.26), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 309 HIS 0.009 0.003 HIS C 326 PHE 0.019 0.002 PHE D 181 TYR 0.032 0.003 TYR A 227 ARG 0.005 0.001 ARG E 125 Details of bonding type rmsd hydrogen bonds : bond 0.29357 ( 615) hydrogen bonds : angle 8.96505 ( 1845) SS BOND : bond 0.01113 ( 5) SS BOND : angle 2.28892 ( 10) covalent geometry : bond 0.00713 (12997) covalent geometry : angle 0.77818 (17665) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 315 time to evaluate : 1.592 Fit side-chains revert: symmetry clash REVERT: A 29 TYR cc_start: 0.7773 (m-80) cc_final: 0.7349 (p90) REVERT: A 41 SER cc_start: 0.9494 (m) cc_final: 0.9277 (p) REVERT: A 61 MET cc_start: 0.8042 (ttm) cc_final: 0.6989 (tpt) REVERT: A 94 TRP cc_start: 0.7886 (t-100) cc_final: 0.6634 (m100) REVERT: A 259 ASP cc_start: 0.8548 (t0) cc_final: 0.8328 (t0) REVERT: A 312 ASP cc_start: 0.8234 (m-30) cc_final: 0.7799 (m-30) REVERT: A 316 GLN cc_start: 0.8765 (tm-30) cc_final: 0.8487 (tm-30) REVERT: A 328 ASP cc_start: 0.7487 (t70) cc_final: 0.7213 (t70) REVERT: B 29 TYR cc_start: 0.7789 (m-80) cc_final: 0.7119 (p90) REVERT: B 41 SER cc_start: 0.9506 (m) cc_final: 0.9302 (p) REVERT: B 61 MET cc_start: 0.7949 (ttm) cc_final: 0.7724 (ttm) REVERT: B 94 TRP cc_start: 0.7796 (t-100) cc_final: 0.6604 (m100) REVERT: B 220 GLN cc_start: 0.8558 (mt0) cc_final: 0.8309 (mt0) REVERT: B 259 ASP cc_start: 0.8635 (t0) cc_final: 0.8115 (t0) REVERT: B 293 GLN cc_start: 0.8504 (tt0) cc_final: 0.7939 (mt0) REVERT: B 316 GLN cc_start: 0.8812 (tm-30) cc_final: 0.8491 (tm-30) REVERT: B 328 ASP cc_start: 0.7324 (t70) cc_final: 0.7096 (t70) REVERT: C 29 TYR cc_start: 0.7696 (m-80) cc_final: 0.7249 (p90) REVERT: C 41 SER cc_start: 0.9439 (m) cc_final: 0.9200 (p) REVERT: C 60 LEU cc_start: 0.9159 (tt) cc_final: 0.8949 (mt) REVERT: C 61 MET cc_start: 0.7860 (ttm) cc_final: 0.6846 (tpt) REVERT: C 94 TRP cc_start: 0.7734 (t-100) cc_final: 0.6636 (m100) REVERT: C 259 ASP cc_start: 0.8622 (t0) cc_final: 0.8332 (t0) REVERT: C 316 GLN cc_start: 0.8697 (tm-30) cc_final: 0.8357 (tm-30) REVERT: C 328 ASP cc_start: 0.7453 (t70) cc_final: 0.7121 (t70) REVERT: D 29 TYR cc_start: 0.7812 (m-80) cc_final: 0.7132 (p90) REVERT: D 61 MET cc_start: 0.8044 (ttm) cc_final: 0.7090 (tpt) REVERT: D 94 TRP cc_start: 0.7839 (t-100) cc_final: 0.6526 (m100) REVERT: D 259 ASP cc_start: 0.8606 (t0) cc_final: 0.8063 (t0) REVERT: D 293 GLN cc_start: 0.8413 (tt0) cc_final: 0.8135 (tt0) REVERT: D 312 ASP cc_start: 0.8306 (m-30) cc_final: 0.7903 (m-30) REVERT: D 328 ASP cc_start: 0.7296 (t70) cc_final: 0.6985 (t0) REVERT: E 29 TYR cc_start: 0.7740 (m-80) cc_final: 0.7113 (p90) REVERT: E 30 LYS cc_start: 0.8313 (ttmt) cc_final: 0.8086 (mttp) REVERT: E 41 SER cc_start: 0.9479 (m) cc_final: 0.9269 (p) REVERT: E 61 MET cc_start: 0.8051 (ttm) cc_final: 0.7117 (tpt) REVERT: E 64 LYS cc_start: 0.9061 (mttt) cc_final: 0.8802 (mttm) REVERT: E 94 TRP cc_start: 0.7850 (t-100) cc_final: 0.6508 (m100) REVERT: E 259 ASP cc_start: 0.8594 (t0) cc_final: 0.8095 (t0) REVERT: E 293 GLN cc_start: 0.8317 (tt0) cc_final: 0.7887 (mt0) REVERT: E 312 ASP cc_start: 0.8166 (m-30) cc_final: 0.7831 (m-30) REVERT: E 316 GLN cc_start: 0.8844 (tm-30) cc_final: 0.8506 (tm-30) REVERT: E 328 ASP cc_start: 0.7595 (t70) cc_final: 0.7326 (t0) outliers start: 4 outliers final: 2 residues processed: 318 average time/residue: 1.2865 time to fit residues: 444.4422 Evaluate side-chains 133 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 131 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain E residue 230 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 60 optimal weight: 20.0000 chunk 117 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 296 ASN C 58 GLN C 293 GLN C 296 ASN D 58 GLN D 296 ASN E 238 GLN E 296 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.088989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.064130 restraints weight = 25405.321| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 3.60 r_work: 0.2596 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13002 Z= 0.152 Angle : 0.610 7.895 17675 Z= 0.322 Chirality : 0.043 0.165 1950 Planarity : 0.005 0.033 2194 Dihedral : 4.696 25.047 1704 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.81 % Allowed : 11.16 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.53 (0.18), residues: 1510 helix: -2.03 (0.12), residues: 1090 sheet: None (None), residues: 0 loop : -2.69 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 94 HIS 0.002 0.001 HIS D 326 PHE 0.022 0.001 PHE B 272 TYR 0.012 0.001 TYR B 43 ARG 0.005 0.001 ARG C 223 Details of bonding type rmsd hydrogen bonds : bond 0.04999 ( 615) hydrogen bonds : angle 4.46065 ( 1845) SS BOND : bond 0.00211 ( 5) SS BOND : angle 1.09678 ( 10) covalent geometry : bond 0.00341 (12997) covalent geometry : angle 0.60951 (17665) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 172 time to evaluate : 1.388 Fit side-chains REVERT: A 29 TYR cc_start: 0.8076 (m-80) cc_final: 0.7172 (t80) REVERT: A 61 MET cc_start: 0.8106 (ttm) cc_final: 0.6993 (tpt) REVERT: A 94 TRP cc_start: 0.7430 (t-100) cc_final: 0.6791 (m100) REVERT: A 230 ILE cc_start: 0.5976 (mm) cc_final: 0.5535 (pt) REVERT: A 316 GLN cc_start: 0.8325 (tm-30) cc_final: 0.7795 (tm-30) REVERT: A 320 MET cc_start: 0.8087 (ttt) cc_final: 0.7856 (ttm) REVERT: B 29 TYR cc_start: 0.7987 (m-80) cc_final: 0.6995 (t80) REVERT: B 61 MET cc_start: 0.8224 (ttm) cc_final: 0.7339 (tpt) REVERT: B 94 TRP cc_start: 0.7336 (t-100) cc_final: 0.6586 (m100) REVERT: B 293 GLN cc_start: 0.7839 (tt0) cc_final: 0.7536 (mt0) REVERT: B 316 GLN cc_start: 0.8472 (tm-30) cc_final: 0.8021 (tm-30) REVERT: C 29 TYR cc_start: 0.7975 (m-80) cc_final: 0.7272 (p90) REVERT: C 30 LYS cc_start: 0.8222 (ttmt) cc_final: 0.7944 (mttt) REVERT: C 61 MET cc_start: 0.8015 (ttm) cc_final: 0.7010 (tpt) REVERT: C 94 TRP cc_start: 0.7332 (t-100) cc_final: 0.6775 (m100) REVERT: C 316 GLN cc_start: 0.8303 (tm-30) cc_final: 0.7953 (tm-30) REVERT: D 29 TYR cc_start: 0.8066 (m-80) cc_final: 0.7180 (p90) REVERT: D 61 MET cc_start: 0.8161 (ttm) cc_final: 0.7886 (ttm) REVERT: D 94 TRP cc_start: 0.7301 (t-100) cc_final: 0.6701 (m100) REVERT: D 293 GLN cc_start: 0.7764 (tt0) cc_final: 0.7394 (mt0) REVERT: D 316 GLN cc_start: 0.8050 (tm-30) cc_final: 0.7781 (tm-30) REVERT: E 61 MET cc_start: 0.8276 (ttm) cc_final: 0.7286 (tpt) REVERT: E 64 LYS cc_start: 0.8463 (mttt) cc_final: 0.8260 (mttm) REVERT: E 94 TRP cc_start: 0.7296 (t-100) cc_final: 0.6546 (m100) REVERT: E 293 GLN cc_start: 0.7562 (tt0) cc_final: 0.7250 (mt0) REVERT: E 316 GLN cc_start: 0.8526 (tm-30) cc_final: 0.8121 (tm-30) outliers start: 39 outliers final: 7 residues processed: 205 average time/residue: 1.1497 time to fit residues: 259.0158 Evaluate side-chains 145 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 138 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 294 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 19 optimal weight: 0.9980 chunk 117 optimal weight: 8.9990 chunk 58 optimal weight: 9.9990 chunk 64 optimal weight: 0.9990 chunk 144 optimal weight: 0.0970 chunk 138 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 72 optimal weight: 7.9990 chunk 20 optimal weight: 20.0000 chunk 102 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.091196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.066377 restraints weight = 25398.036| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 3.59 r_work: 0.2638 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13002 Z= 0.097 Angle : 0.522 10.183 17675 Z= 0.263 Chirality : 0.040 0.156 1950 Planarity : 0.004 0.027 2194 Dihedral : 4.200 24.091 1700 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.81 % Allowed : 12.31 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.20), residues: 1510 helix: -0.85 (0.15), residues: 1085 sheet: None (None), residues: 0 loop : -2.64 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 229 HIS 0.002 0.000 HIS D 326 PHE 0.013 0.001 PHE B 272 TYR 0.008 0.001 TYR C 97 ARG 0.006 0.000 ARG C 223 Details of bonding type rmsd hydrogen bonds : bond 0.03710 ( 615) hydrogen bonds : angle 3.91218 ( 1845) SS BOND : bond 0.00127 ( 5) SS BOND : angle 0.60418 ( 10) covalent geometry : bond 0.00207 (12997) covalent geometry : angle 0.52222 (17665) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 158 time to evaluate : 1.563 Fit side-chains REVERT: A 43 TYR cc_start: 0.7777 (t80) cc_final: 0.7438 (t80) REVERT: A 61 MET cc_start: 0.8127 (ttm) cc_final: 0.6962 (tpt) REVERT: A 94 TRP cc_start: 0.7599 (t-100) cc_final: 0.6921 (m100) REVERT: A 256 GLN cc_start: 0.8980 (mm-40) cc_final: 0.8697 (mm-40) REVERT: A 316 GLN cc_start: 0.8223 (tm-30) cc_final: 0.7858 (tm-30) REVERT: B 29 TYR cc_start: 0.8022 (m-80) cc_final: 0.7025 (t80) REVERT: B 54 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8856 (mm) REVERT: B 61 MET cc_start: 0.8171 (ttm) cc_final: 0.7277 (tpt) REVERT: B 94 TRP cc_start: 0.7432 (t-100) cc_final: 0.6915 (t60) REVERT: B 229 TRP cc_start: 0.7271 (t60) cc_final: 0.7018 (t60) REVERT: B 230 ILE cc_start: 0.5821 (mm) cc_final: 0.5439 (pt) REVERT: B 293 GLN cc_start: 0.7813 (tt0) cc_final: 0.7522 (mt0) REVERT: B 316 GLN cc_start: 0.8549 (tm-30) cc_final: 0.8252 (tm-30) REVERT: C 29 TYR cc_start: 0.7993 (m-80) cc_final: 0.7278 (p90) REVERT: C 30 LYS cc_start: 0.8196 (ttmt) cc_final: 0.7970 (mptt) REVERT: C 54 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8849 (mm) REVERT: C 58 GLN cc_start: 0.8359 (tt0) cc_final: 0.7930 (mt0) REVERT: C 61 MET cc_start: 0.8083 (ttm) cc_final: 0.7062 (tpt) REVERT: C 94 TRP cc_start: 0.7420 (t-100) cc_final: 0.6832 (m100) REVERT: C 289 LYS cc_start: 0.7220 (mmmm) cc_final: 0.6862 (mptt) REVERT: C 316 GLN cc_start: 0.8297 (tm-30) cc_final: 0.8010 (tm-30) REVERT: D 29 TYR cc_start: 0.8166 (m-80) cc_final: 0.7132 (t80) REVERT: D 58 GLN cc_start: 0.8430 (tt0) cc_final: 0.8061 (mt0) REVERT: D 61 MET cc_start: 0.8121 (ttm) cc_final: 0.7088 (tpt) REVERT: D 94 TRP cc_start: 0.7447 (t-100) cc_final: 0.6802 (m100) REVERT: D 107 MET cc_start: 0.7839 (OUTLIER) cc_final: 0.7579 (ptp) REVERT: D 230 ILE cc_start: 0.5953 (mm) cc_final: 0.5664 (pt) REVERT: D 256 GLN cc_start: 0.8898 (mm-40) cc_final: 0.8689 (mm-40) REVERT: D 293 GLN cc_start: 0.7677 (tt0) cc_final: 0.7342 (mt0) REVERT: D 316 GLN cc_start: 0.8049 (tm-30) cc_final: 0.7841 (tm-30) REVERT: E 54 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8638 (mm) REVERT: E 61 MET cc_start: 0.8300 (ttm) cc_final: 0.7379 (tpt) REVERT: E 94 TRP cc_start: 0.7301 (t-100) cc_final: 0.6690 (m100) REVERT: E 293 GLN cc_start: 0.7546 (tt0) cc_final: 0.7218 (mt0) REVERT: E 316 GLN cc_start: 0.8554 (tm-30) cc_final: 0.8188 (tm-30) outliers start: 39 outliers final: 6 residues processed: 184 average time/residue: 1.1051 time to fit residues: 223.8755 Evaluate side-chains 144 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 134 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 249 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 118 optimal weight: 10.0000 chunk 68 optimal weight: 0.6980 chunk 31 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 110 optimal weight: 20.0000 chunk 93 optimal weight: 6.9990 chunk 23 optimal weight: 0.5980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN B 256 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.098016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.072572 restraints weight = 24814.526| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 3.46 r_work: 0.2784 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 13002 Z= 0.111 Angle : 0.520 10.181 17675 Z= 0.259 Chirality : 0.040 0.135 1950 Planarity : 0.004 0.052 2194 Dihedral : 3.970 22.939 1700 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.59 % Allowed : 13.10 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.22), residues: 1510 helix: -0.19 (0.16), residues: 1085 sheet: None (None), residues: 0 loop : -2.49 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 229 HIS 0.001 0.000 HIS D 326 PHE 0.012 0.001 PHE B 272 TYR 0.031 0.001 TYR B 43 ARG 0.004 0.000 ARG C 223 Details of bonding type rmsd hydrogen bonds : bond 0.03459 ( 615) hydrogen bonds : angle 3.72556 ( 1845) SS BOND : bond 0.00187 ( 5) SS BOND : angle 0.72885 ( 10) covalent geometry : bond 0.00257 (12997) covalent geometry : angle 0.51944 (17665) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 142 time to evaluate : 1.406 Fit side-chains REVERT: A 61 MET cc_start: 0.8097 (ttm) cc_final: 0.6951 (tpt) REVERT: A 94 TRP cc_start: 0.7547 (t-100) cc_final: 0.6883 (m100) REVERT: A 258 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8423 (mm) REVERT: A 316 GLN cc_start: 0.8407 (tm-30) cc_final: 0.7939 (tm-30) REVERT: B 29 TYR cc_start: 0.8062 (m-80) cc_final: 0.6991 (t80) REVERT: B 54 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8856 (mm) REVERT: B 61 MET cc_start: 0.8181 (ttm) cc_final: 0.7281 (tpt) REVERT: B 94 TRP cc_start: 0.7474 (t-100) cc_final: 0.6878 (t60) REVERT: B 154 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.8495 (mmp) REVERT: B 293 GLN cc_start: 0.7752 (tt0) cc_final: 0.7453 (mt0) REVERT: B 316 GLN cc_start: 0.8479 (tm-30) cc_final: 0.8120 (tm-30) REVERT: C 54 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8820 (mm) REVERT: C 58 GLN cc_start: 0.8380 (tt0) cc_final: 0.7982 (mt0) REVERT: C 61 MET cc_start: 0.8082 (ttm) cc_final: 0.6970 (tpt) REVERT: C 94 TRP cc_start: 0.7369 (t-100) cc_final: 0.6765 (m100) REVERT: C 258 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8374 (mm) REVERT: C 316 GLN cc_start: 0.8038 (tm-30) cc_final: 0.7784 (tm-30) REVERT: D 29 TYR cc_start: 0.8230 (m-80) cc_final: 0.7136 (t80) REVERT: D 58 GLN cc_start: 0.8465 (tt0) cc_final: 0.7996 (mt0) REVERT: D 61 MET cc_start: 0.8087 (ttm) cc_final: 0.7017 (tpt) REVERT: D 94 TRP cc_start: 0.7382 (t-100) cc_final: 0.6794 (m100) REVERT: D 107 MET cc_start: 0.7805 (OUTLIER) cc_final: 0.7546 (ptp) REVERT: D 256 GLN cc_start: 0.8901 (mm-40) cc_final: 0.8514 (mm-40) REVERT: D 293 GLN cc_start: 0.7714 (tt0) cc_final: 0.7367 (mt0) REVERT: E 54 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8601 (mm) REVERT: E 58 GLN cc_start: 0.8419 (tt0) cc_final: 0.8028 (mt0) REVERT: E 61 MET cc_start: 0.8287 (ttm) cc_final: 0.7344 (tpt) REVERT: E 94 TRP cc_start: 0.7328 (t-100) cc_final: 0.6711 (m100) REVERT: E 262 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8228 (mmmm) REVERT: E 293 GLN cc_start: 0.7441 (tt0) cc_final: 0.7129 (mt0) REVERT: E 316 GLN cc_start: 0.8499 (tm-30) cc_final: 0.8178 (tm-30) outliers start: 36 outliers final: 9 residues processed: 170 average time/residue: 1.0407 time to fit residues: 195.6359 Evaluate side-chains 142 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 262 LYS Chi-restraints excluded: chain E residue 294 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 139 optimal weight: 8.9990 chunk 72 optimal weight: 8.9990 chunk 82 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 146 optimal weight: 8.9990 chunk 148 optimal weight: 0.8980 chunk 136 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 143 optimal weight: 5.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN B 238 GLN D 267 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.089111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.064281 restraints weight = 25341.423| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 3.57 r_work: 0.2595 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13002 Z= 0.136 Angle : 0.525 10.440 17675 Z= 0.261 Chirality : 0.041 0.161 1950 Planarity : 0.003 0.030 2194 Dihedral : 3.911 21.840 1700 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.74 % Allowed : 13.03 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.22), residues: 1510 helix: 0.20 (0.16), residues: 1090 sheet: None (None), residues: 0 loop : -2.26 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 229 HIS 0.002 0.000 HIS D 326 PHE 0.013 0.001 PHE A 248 TYR 0.024 0.001 TYR D 43 ARG 0.004 0.000 ARG C 223 Details of bonding type rmsd hydrogen bonds : bond 0.03487 ( 615) hydrogen bonds : angle 3.69198 ( 1845) SS BOND : bond 0.00184 ( 5) SS BOND : angle 0.85259 ( 10) covalent geometry : bond 0.00327 (12997) covalent geometry : angle 0.52474 (17665) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 137 time to evaluate : 1.490 Fit side-chains REVERT: A 61 MET cc_start: 0.8104 (ttm) cc_final: 0.6947 (tpt) REVERT: A 94 TRP cc_start: 0.7513 (t-100) cc_final: 0.6829 (m100) REVERT: A 316 GLN cc_start: 0.8175 (tm-30) cc_final: 0.7927 (tm-30) REVERT: B 29 TYR cc_start: 0.8108 (m-80) cc_final: 0.6980 (t80) REVERT: B 43 TYR cc_start: 0.7698 (t80) cc_final: 0.7260 (t80) REVERT: B 54 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8849 (mm) REVERT: B 61 MET cc_start: 0.8236 (ttm) cc_final: 0.7319 (tpt) REVERT: B 94 TRP cc_start: 0.7396 (t-100) cc_final: 0.6783 (t60) REVERT: B 154 MET cc_start: 0.8728 (mmp) cc_final: 0.8454 (mmp) REVERT: B 293 GLN cc_start: 0.7642 (tt0) cc_final: 0.7354 (mt0) REVERT: B 316 GLN cc_start: 0.8470 (tm-30) cc_final: 0.8148 (tm-30) REVERT: C 54 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8799 (mm) REVERT: C 58 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.8005 (mt0) REVERT: C 61 MET cc_start: 0.8079 (ttm) cc_final: 0.7007 (tpt) REVERT: C 92 ARG cc_start: 0.6143 (OUTLIER) cc_final: 0.5765 (tmm-80) REVERT: C 94 TRP cc_start: 0.7400 (t-100) cc_final: 0.6837 (m100) REVERT: C 316 GLN cc_start: 0.7875 (tm-30) cc_final: 0.7560 (tm-30) REVERT: D 29 TYR cc_start: 0.8310 (m-80) cc_final: 0.7151 (t80) REVERT: D 30 LYS cc_start: 0.3621 (mptt) cc_final: 0.3166 (mptt) REVERT: D 58 GLN cc_start: 0.8461 (tt0) cc_final: 0.7968 (mt0) REVERT: D 61 MET cc_start: 0.8153 (ttm) cc_final: 0.7145 (tpt) REVERT: D 94 TRP cc_start: 0.7405 (t-100) cc_final: 0.6759 (m100) REVERT: D 107 MET cc_start: 0.7749 (OUTLIER) cc_final: 0.7462 (ptp) REVERT: D 256 GLN cc_start: 0.8953 (mm-40) cc_final: 0.8654 (mm-40) REVERT: D 293 GLN cc_start: 0.7740 (tt0) cc_final: 0.7373 (mt0) REVERT: E 54 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8622 (mm) REVERT: E 58 GLN cc_start: 0.8413 (tt0) cc_final: 0.8039 (mt0) REVERT: E 61 MET cc_start: 0.8267 (ttm) cc_final: 0.7334 (tpt) REVERT: E 92 ARG cc_start: 0.6790 (OUTLIER) cc_final: 0.6558 (tmt170) REVERT: E 94 TRP cc_start: 0.7361 (t-100) cc_final: 0.6732 (m100) REVERT: E 262 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8209 (mmmm) REVERT: E 293 GLN cc_start: 0.7468 (tt0) cc_final: 0.7168 (mt0) REVERT: E 316 GLN cc_start: 0.8416 (tm-30) cc_final: 0.8146 (tm-30) outliers start: 38 outliers final: 8 residues processed: 165 average time/residue: 1.1363 time to fit residues: 206.9841 Evaluate side-chains 144 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 1.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 58 GLN Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 92 ARG Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 262 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 114 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 chunk 115 optimal weight: 0.9980 chunk 32 optimal weight: 8.9990 chunk 137 optimal weight: 7.9990 chunk 83 optimal weight: 10.0000 chunk 145 optimal weight: 7.9990 chunk 124 optimal weight: 0.9980 chunk 129 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 256 GLN C 267 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.096266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.070569 restraints weight = 25295.703| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 3.50 r_work: 0.2750 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 13002 Z= 0.149 Angle : 0.543 10.672 17675 Z= 0.266 Chirality : 0.042 0.160 1950 Planarity : 0.003 0.032 2194 Dihedral : 3.930 20.724 1700 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.45 % Allowed : 14.18 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.22), residues: 1510 helix: 0.41 (0.16), residues: 1090 sheet: None (None), residues: 0 loop : -2.18 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 229 HIS 0.002 0.000 HIS D 326 PHE 0.013 0.001 PHE A 248 TYR 0.030 0.001 TYR C 43 ARG 0.003 0.000 ARG C 223 Details of bonding type rmsd hydrogen bonds : bond 0.03543 ( 615) hydrogen bonds : angle 3.67374 ( 1845) SS BOND : bond 0.00219 ( 5) SS BOND : angle 0.86670 ( 10) covalent geometry : bond 0.00356 (12997) covalent geometry : angle 0.54272 (17665) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 136 time to evaluate : 1.610 Fit side-chains revert: symmetry clash REVERT: A 61 MET cc_start: 0.8060 (ttm) cc_final: 0.6958 (tpt) REVERT: A 94 TRP cc_start: 0.7492 (t-100) cc_final: 0.6863 (m100) REVERT: A 229 TRP cc_start: 0.7324 (t60) cc_final: 0.7021 (p-90) REVERT: A 316 GLN cc_start: 0.8091 (tm-30) cc_final: 0.7886 (tm-30) REVERT: B 29 TYR cc_start: 0.8213 (m-80) cc_final: 0.7097 (t80) REVERT: B 61 MET cc_start: 0.8234 (ttm) cc_final: 0.7349 (tpt) REVERT: B 94 TRP cc_start: 0.7362 (t-100) cc_final: 0.6787 (t60) REVERT: B 154 MET cc_start: 0.8723 (mmp) cc_final: 0.8519 (mmp) REVERT: B 293 GLN cc_start: 0.7648 (tt0) cc_final: 0.7369 (mt0) REVERT: B 316 GLN cc_start: 0.8448 (tm-30) cc_final: 0.8186 (tm-30) REVERT: C 54 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8792 (mm) REVERT: C 58 GLN cc_start: 0.8390 (tt0) cc_final: 0.7937 (mt0) REVERT: C 92 ARG cc_start: 0.6030 (OUTLIER) cc_final: 0.5681 (tmm-80) REVERT: C 94 TRP cc_start: 0.7317 (t-100) cc_final: 0.6771 (m100) REVERT: C 316 GLN cc_start: 0.7869 (tm-30) cc_final: 0.7625 (tm-30) REVERT: D 29 TYR cc_start: 0.8340 (m-80) cc_final: 0.7176 (t80) REVERT: D 58 GLN cc_start: 0.8496 (tt0) cc_final: 0.8063 (mt0) REVERT: D 61 MET cc_start: 0.8143 (ttm) cc_final: 0.7119 (tpt) REVERT: D 94 TRP cc_start: 0.7412 (t-100) cc_final: 0.6785 (m100) REVERT: D 107 MET cc_start: 0.7684 (OUTLIER) cc_final: 0.7425 (ptp) REVERT: D 293 GLN cc_start: 0.7711 (tt0) cc_final: 0.7354 (mt0) REVERT: E 54 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8604 (mm) REVERT: E 58 GLN cc_start: 0.8419 (tt0) cc_final: 0.8014 (mt0) REVERT: E 61 MET cc_start: 0.8253 (ttm) cc_final: 0.7320 (tpt) REVERT: E 94 TRP cc_start: 0.7382 (t-100) cc_final: 0.6815 (m100) REVERT: E 262 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8219 (mmmm) REVERT: E 293 GLN cc_start: 0.7472 (tt0) cc_final: 0.7181 (mt0) REVERT: E 316 GLN cc_start: 0.8393 (tm-30) cc_final: 0.8137 (tm-30) outliers start: 34 outliers final: 10 residues processed: 159 average time/residue: 1.0943 time to fit residues: 192.1092 Evaluate side-chains 147 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 262 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 27 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 chunk 115 optimal weight: 10.0000 chunk 123 optimal weight: 20.0000 chunk 16 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 132 optimal weight: 9.9990 chunk 88 optimal weight: 6.9990 chunk 68 optimal weight: 0.0010 chunk 40 optimal weight: 1.9990 overall best weight: 2.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.095414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.071111 restraints weight = 24957.132| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 3.34 r_work: 0.2754 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13002 Z= 0.136 Angle : 0.535 11.325 17675 Z= 0.263 Chirality : 0.042 0.138 1950 Planarity : 0.003 0.036 2194 Dihedral : 3.883 19.909 1700 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.30 % Allowed : 15.12 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.22), residues: 1510 helix: 0.51 (0.16), residues: 1115 sheet: None (None), residues: 0 loop : -2.17 (0.29), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 229 HIS 0.002 0.000 HIS D 326 PHE 0.013 0.001 PHE A 248 TYR 0.012 0.001 TYR E 97 ARG 0.004 0.000 ARG E 92 Details of bonding type rmsd hydrogen bonds : bond 0.03440 ( 615) hydrogen bonds : angle 3.62689 ( 1845) SS BOND : bond 0.00200 ( 5) SS BOND : angle 0.77984 ( 10) covalent geometry : bond 0.00326 (12997) covalent geometry : angle 0.53453 (17665) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 3.273 Fit side-chains revert: symmetry clash REVERT: A 61 MET cc_start: 0.8041 (ttm) cc_final: 0.6942 (tpt) REVERT: A 94 TRP cc_start: 0.7477 (t-100) cc_final: 0.6842 (m100) REVERT: A 316 GLN cc_start: 0.8096 (tm-30) cc_final: 0.7893 (tm-30) REVERT: B 29 TYR cc_start: 0.8243 (m-80) cc_final: 0.7089 (t80) REVERT: B 61 MET cc_start: 0.8264 (ttm) cc_final: 0.7349 (tpt) REVERT: B 94 TRP cc_start: 0.7357 (t-100) cc_final: 0.6759 (t60) REVERT: B 293 GLN cc_start: 0.7620 (tt0) cc_final: 0.7361 (mt0) REVERT: B 316 GLN cc_start: 0.8394 (tm-30) cc_final: 0.8039 (tm-30) REVERT: C 54 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8809 (mm) REVERT: C 58 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7919 (mt0) REVERT: C 92 ARG cc_start: 0.6035 (OUTLIER) cc_final: 0.5663 (tmm-80) REVERT: C 94 TRP cc_start: 0.7337 (t-100) cc_final: 0.6804 (m100) REVERT: C 316 GLN cc_start: 0.7883 (tm-30) cc_final: 0.7637 (tm-30) REVERT: D 29 TYR cc_start: 0.8307 (m-80) cc_final: 0.7155 (t80) REVERT: D 58 GLN cc_start: 0.8526 (tt0) cc_final: 0.8030 (mt0) REVERT: D 61 MET cc_start: 0.8151 (ttm) cc_final: 0.7123 (tpt) REVERT: D 94 TRP cc_start: 0.7397 (t-100) cc_final: 0.6718 (m100) REVERT: D 107 MET cc_start: 0.7631 (OUTLIER) cc_final: 0.7364 (ptp) REVERT: E 54 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8624 (mm) REVERT: E 58 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.8058 (mt0) REVERT: E 61 MET cc_start: 0.8305 (ttm) cc_final: 0.7358 (tpt) REVERT: E 94 TRP cc_start: 0.7340 (t-100) cc_final: 0.6634 (m100) REVERT: E 262 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8226 (mmmm) REVERT: E 293 GLN cc_start: 0.7474 (tt0) cc_final: 0.7187 (mt0) REVERT: E 316 GLN cc_start: 0.8401 (tm-30) cc_final: 0.8140 (tm-30) outliers start: 32 outliers final: 10 residues processed: 157 average time/residue: 1.1506 time to fit residues: 199.8736 Evaluate side-chains 146 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 58 GLN Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 58 GLN Chi-restraints excluded: chain E residue 107 MET Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 262 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 116 optimal weight: 8.9990 chunk 128 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 142 optimal weight: 0.7980 chunk 126 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 100 optimal weight: 7.9990 chunk 46 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.096424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.070983 restraints weight = 25041.315| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 3.46 r_work: 0.2745 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13002 Z= 0.129 Angle : 0.546 11.729 17675 Z= 0.264 Chirality : 0.041 0.136 1950 Planarity : 0.003 0.037 2194 Dihedral : 3.841 19.194 1700 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.80 % Allowed : 15.98 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.22), residues: 1510 helix: 0.63 (0.16), residues: 1115 sheet: None (None), residues: 0 loop : -2.09 (0.29), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 229 HIS 0.002 0.000 HIS D 326 PHE 0.012 0.001 PHE A 248 TYR 0.019 0.001 TYR C 43 ARG 0.004 0.000 ARG A 92 Details of bonding type rmsd hydrogen bonds : bond 0.03384 ( 615) hydrogen bonds : angle 3.59648 ( 1845) SS BOND : bond 0.00197 ( 5) SS BOND : angle 0.73690 ( 10) covalent geometry : bond 0.00310 (12997) covalent geometry : angle 0.54554 (17665) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 1.491 Fit side-chains revert: symmetry clash REVERT: A 61 MET cc_start: 0.8040 (ttm) cc_final: 0.6949 (tpt) REVERT: A 94 TRP cc_start: 0.7467 (t-100) cc_final: 0.6798 (m100) REVERT: A 100 ILE cc_start: 0.7891 (mm) cc_final: 0.7202 (pt) REVERT: A 229 TRP cc_start: 0.7349 (t60) cc_final: 0.7130 (p-90) REVERT: A 316 GLN cc_start: 0.8090 (tm-30) cc_final: 0.7879 (tm-30) REVERT: B 61 MET cc_start: 0.8262 (ttm) cc_final: 0.7351 (tpt) REVERT: B 94 TRP cc_start: 0.7289 (t-100) cc_final: 0.6661 (t60) REVERT: B 293 GLN cc_start: 0.7610 (tt0) cc_final: 0.7355 (mt0) REVERT: B 316 GLN cc_start: 0.8296 (tm-30) cc_final: 0.8004 (tm-30) REVERT: C 54 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8802 (mm) REVERT: C 58 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.7933 (mt0) REVERT: C 92 ARG cc_start: 0.6034 (OUTLIER) cc_final: 0.5574 (tmm-80) REVERT: C 94 TRP cc_start: 0.7343 (t-100) cc_final: 0.6819 (m100) REVERT: C 316 GLN cc_start: 0.7865 (tm-30) cc_final: 0.7637 (tm-30) REVERT: D 29 TYR cc_start: 0.8302 (m-80) cc_final: 0.7159 (t80) REVERT: D 58 GLN cc_start: 0.8521 (tt0) cc_final: 0.8022 (mt0) REVERT: D 61 MET cc_start: 0.8150 (ttm) cc_final: 0.7125 (tpt) REVERT: D 94 TRP cc_start: 0.7401 (t-100) cc_final: 0.6705 (m100) REVERT: D 107 MET cc_start: 0.7613 (OUTLIER) cc_final: 0.7344 (ptp) REVERT: E 54 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8614 (mm) REVERT: E 58 GLN cc_start: 0.8504 (tt0) cc_final: 0.8079 (mt0) REVERT: E 61 MET cc_start: 0.8256 (ttm) cc_final: 0.7318 (tpt) REVERT: E 94 TRP cc_start: 0.7284 (t-100) cc_final: 0.6569 (m100) REVERT: E 107 MET cc_start: 0.7167 (OUTLIER) cc_final: 0.6872 (ptp) REVERT: E 262 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8228 (mmmm) REVERT: E 293 GLN cc_start: 0.7471 (tt0) cc_final: 0.7176 (mt0) REVERT: E 316 GLN cc_start: 0.8405 (tm-30) cc_final: 0.8144 (tm-30) outliers start: 25 outliers final: 10 residues processed: 157 average time/residue: 1.1374 time to fit residues: 197.1927 Evaluate side-chains 147 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 58 GLN Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 107 MET Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 262 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 20 optimal weight: 8.9990 chunk 108 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 135 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 137 optimal weight: 0.7980 chunk 127 optimal weight: 7.9990 chunk 8 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 238 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.093834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.068291 restraints weight = 24996.997| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 3.43 r_work: 0.2776 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13002 Z= 0.105 Angle : 0.526 11.029 17675 Z= 0.257 Chirality : 0.040 0.157 1950 Planarity : 0.003 0.030 2194 Dihedral : 3.740 18.065 1700 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.58 % Allowed : 16.56 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.22), residues: 1510 helix: 0.83 (0.16), residues: 1110 sheet: None (None), residues: 0 loop : -2.03 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 229 HIS 0.002 0.000 HIS C 326 PHE 0.011 0.001 PHE A 248 TYR 0.013 0.001 TYR B 29 ARG 0.003 0.000 ARG A 92 Details of bonding type rmsd hydrogen bonds : bond 0.03160 ( 615) hydrogen bonds : angle 3.52049 ( 1845) SS BOND : bond 0.00135 ( 5) SS BOND : angle 0.57802 ( 10) covalent geometry : bond 0.00251 (12997) covalent geometry : angle 0.52586 (17665) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 1.454 Fit side-chains revert: symmetry clash REVERT: A 61 MET cc_start: 0.8052 (ttm) cc_final: 0.6949 (tpt) REVERT: A 94 TRP cc_start: 0.7438 (t-100) cc_final: 0.6799 (m100) REVERT: A 100 ILE cc_start: 0.7854 (mm) cc_final: 0.7160 (pt) REVERT: A 180 LYS cc_start: 0.7736 (OUTLIER) cc_final: 0.7529 (mttp) REVERT: A 229 TRP cc_start: 0.7228 (t60) cc_final: 0.6991 (p-90) REVERT: A 316 GLN cc_start: 0.8033 (tm-30) cc_final: 0.7827 (tm-30) REVERT: B 61 MET cc_start: 0.8244 (ttm) cc_final: 0.7283 (tpt) REVERT: B 94 TRP cc_start: 0.7383 (t-100) cc_final: 0.6753 (t60) REVERT: B 293 GLN cc_start: 0.7579 (tt0) cc_final: 0.7316 (mt0) REVERT: B 316 GLN cc_start: 0.8061 (tm-30) cc_final: 0.7838 (tm-30) REVERT: C 54 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8788 (mm) REVERT: C 58 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7886 (mt0) REVERT: C 92 ARG cc_start: 0.5968 (OUTLIER) cc_final: 0.5502 (tmm-80) REVERT: C 94 TRP cc_start: 0.7371 (t-100) cc_final: 0.6808 (m100) REVERT: D 29 TYR cc_start: 0.8324 (m-80) cc_final: 0.7142 (t80) REVERT: D 30 LYS cc_start: 0.3691 (mptt) cc_final: 0.3343 (mptt) REVERT: D 58 GLN cc_start: 0.8450 (tt0) cc_final: 0.7979 (mt0) REVERT: D 61 MET cc_start: 0.8152 (ttm) cc_final: 0.7122 (tpt) REVERT: D 94 TRP cc_start: 0.7411 (t-100) cc_final: 0.6742 (m100) REVERT: D 107 MET cc_start: 0.7595 (OUTLIER) cc_final: 0.7300 (ptp) REVERT: E 54 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8597 (mm) REVERT: E 58 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.8064 (mt0) REVERT: E 61 MET cc_start: 0.8232 (ttm) cc_final: 0.7316 (tpt) REVERT: E 94 TRP cc_start: 0.7282 (t-100) cc_final: 0.6539 (m100) REVERT: E 262 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8234 (mmmm) REVERT: E 293 GLN cc_start: 0.7473 (tt0) cc_final: 0.7195 (mt0) REVERT: E 316 GLN cc_start: 0.8406 (tm-30) cc_final: 0.8149 (tm-30) outliers start: 22 outliers final: 10 residues processed: 155 average time/residue: 1.1017 time to fit residues: 189.8956 Evaluate side-chains 151 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 LYS Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 58 GLN Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 58 GLN Chi-restraints excluded: chain E residue 107 MET Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 262 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 93 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 36 optimal weight: 20.0000 chunk 44 optimal weight: 7.9990 chunk 58 optimal weight: 0.3980 chunk 108 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 127 optimal weight: 6.9990 chunk 85 optimal weight: 0.9980 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.092351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.066807 restraints weight = 24972.280| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 3.41 r_work: 0.2758 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13002 Z= 0.142 Angle : 0.563 12.557 17675 Z= 0.273 Chirality : 0.042 0.160 1950 Planarity : 0.003 0.043 2194 Dihedral : 3.762 17.587 1700 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.37 % Allowed : 17.49 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.22), residues: 1510 helix: 0.87 (0.16), residues: 1110 sheet: None (None), residues: 0 loop : -2.04 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP C 229 HIS 0.002 0.000 HIS D 326 PHE 0.011 0.001 PHE A 248 TYR 0.017 0.001 TYR C 43 ARG 0.003 0.000 ARG B 126 Details of bonding type rmsd hydrogen bonds : bond 0.03371 ( 615) hydrogen bonds : angle 3.58414 ( 1845) SS BOND : bond 0.00227 ( 5) SS BOND : angle 0.84293 ( 10) covalent geometry : bond 0.00346 (12997) covalent geometry : angle 0.56260 (17665) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.8020 (ttm) cc_final: 0.6940 (tpt) REVERT: A 94 TRP cc_start: 0.7437 (t-100) cc_final: 0.6835 (m100) REVERT: A 100 ILE cc_start: 0.7878 (mm) cc_final: 0.7212 (pt) REVERT: A 316 GLN cc_start: 0.7984 (tm-30) cc_final: 0.7770 (tm-30) REVERT: B 61 MET cc_start: 0.8242 (ttm) cc_final: 0.7286 (tpt) REVERT: B 94 TRP cc_start: 0.7216 (t-100) cc_final: 0.6718 (t60) REVERT: B 293 GLN cc_start: 0.7607 (tt0) cc_final: 0.7342 (mt0) REVERT: C 54 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8797 (mm) REVERT: C 58 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.7928 (mt0) REVERT: C 92 ARG cc_start: 0.5979 (OUTLIER) cc_final: 0.5508 (tmm-80) REVERT: C 94 TRP cc_start: 0.7347 (t-100) cc_final: 0.6795 (m100) REVERT: D 29 TYR cc_start: 0.8322 (m-80) cc_final: 0.7142 (t80) REVERT: D 58 GLN cc_start: 0.8441 (tt0) cc_final: 0.7979 (mt0) REVERT: D 61 MET cc_start: 0.8134 (ttm) cc_final: 0.7110 (tpt) REVERT: D 94 TRP cc_start: 0.7383 (t-100) cc_final: 0.6702 (m100) REVERT: D 107 MET cc_start: 0.7570 (OUTLIER) cc_final: 0.7288 (ptp) REVERT: E 54 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8589 (mm) REVERT: E 58 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.8024 (mt0) REVERT: E 61 MET cc_start: 0.8234 (ttm) cc_final: 0.7332 (tpt) REVERT: E 94 TRP cc_start: 0.7278 (t-100) cc_final: 0.6523 (m100) REVERT: E 107 MET cc_start: 0.7140 (OUTLIER) cc_final: 0.6834 (ptp) REVERT: E 262 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8159 (mmmm) REVERT: E 293 GLN cc_start: 0.7489 (tt0) cc_final: 0.7212 (mt0) REVERT: E 316 GLN cc_start: 0.8419 (tm-30) cc_final: 0.8162 (tm-30) outliers start: 19 outliers final: 9 residues processed: 147 average time/residue: 1.1258 time to fit residues: 182.6218 Evaluate side-chains 148 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 58 GLN Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 58 GLN Chi-restraints excluded: chain E residue 107 MET Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 262 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 59 optimal weight: 5.9990 chunk 79 optimal weight: 9.9990 chunk 98 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 145 optimal weight: 10.0000 chunk 85 optimal weight: 8.9990 chunk 99 optimal weight: 0.9990 chunk 36 optimal weight: 20.0000 chunk 8 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 238 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.094941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.069968 restraints weight = 25160.457| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 3.46 r_work: 0.2755 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13002 Z= 0.143 Angle : 0.568 12.605 17675 Z= 0.276 Chirality : 0.042 0.169 1950 Planarity : 0.003 0.042 2194 Dihedral : 3.768 17.193 1700 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.44 % Allowed : 17.57 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.22), residues: 1510 helix: 0.91 (0.16), residues: 1110 sheet: None (None), residues: 0 loop : -2.03 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 229 HIS 0.002 0.000 HIS D 326 PHE 0.012 0.001 PHE A 248 TYR 0.011 0.001 TYR B 29 ARG 0.003 0.000 ARG C 196 Details of bonding type rmsd hydrogen bonds : bond 0.03394 ( 615) hydrogen bonds : angle 3.58777 ( 1845) SS BOND : bond 0.00223 ( 5) SS BOND : angle 0.83466 ( 10) covalent geometry : bond 0.00348 (12997) covalent geometry : angle 0.56828 (17665) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7104.47 seconds wall clock time: 123 minutes 5.65 seconds (7385.65 seconds total)