Starting phenix.real_space_refine on Thu Sep 26 06:17:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n24_9322/09_2024/6n24_9322_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n24_9322/09_2024/6n24_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n24_9322/09_2024/6n24_9322.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n24_9322/09_2024/6n24_9322.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n24_9322/09_2024/6n24_9322_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n24_9322/09_2024/6n24_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-5461/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: 7.66, 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: 2.89 Conformation dependent library (CDL) restraints added in 1.5 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: 1.25 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: 3.12 Time building geometry restraints manager: 3.40 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: 0.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 28.580 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.490 ------------------------------------------------------------------------------- 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 12997 Z= 0.450 Angle : 0.778 8.639 17665 Z= 0.424 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 *********************** 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 fitting. rotamer outliers: 4 poor density : 315 time to evaluate : 1.525 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: 1.2094 time to fit residues: 417.5515 Evaluate side-chains 133 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 131 time to evaluate : 1.505 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 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 12997 Z= 0.215 Angle : 0.610 7.895 17665 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 *********************** 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 fitting. rotamer outliers: 39 poor density : 172 time to evaluate : 1.472 Fit side-chains REVERT: A 29 TYR cc_start: 0.7804 (m-80) cc_final: 0.7241 (t80) REVERT: A 61 MET cc_start: 0.8025 (ttm) cc_final: 0.6915 (tpt) REVERT: A 94 TRP cc_start: 0.7496 (t-100) cc_final: 0.6864 (m100) REVERT: A 230 ILE cc_start: 0.7285 (mm) cc_final: 0.6777 (pt) REVERT: A 293 GLN cc_start: 0.8254 (tt0) cc_final: 0.7989 (tm-30) REVERT: A 316 GLN cc_start: 0.8782 (tm-30) cc_final: 0.8327 (tm-30) REVERT: B 29 TYR cc_start: 0.7793 (m-80) cc_final: 0.7077 (t80) REVERT: B 61 MET cc_start: 0.7977 (ttm) cc_final: 0.7150 (tpt) REVERT: B 94 TRP cc_start: 0.7463 (t-100) cc_final: 0.6704 (m100) REVERT: B 289 LYS cc_start: 0.8097 (mmmt) cc_final: 0.7808 (mmpt) REVERT: B 293 GLN cc_start: 0.8410 (tt0) cc_final: 0.8020 (mt0) REVERT: B 316 GLN cc_start: 0.8842 (tm-30) cc_final: 0.8459 (tm-30) REVERT: B 320 MET cc_start: 0.9137 (OUTLIER) cc_final: 0.8934 (ttm) REVERT: C 29 TYR cc_start: 0.7721 (m-80) cc_final: 0.7254 (p90) REVERT: C 30 LYS cc_start: 0.8268 (ttmt) cc_final: 0.8047 (mttt) REVERT: C 41 SER cc_start: 0.9626 (m) cc_final: 0.9416 (p) REVERT: C 61 MET cc_start: 0.7912 (ttm) cc_final: 0.6972 (tpt) REVERT: C 94 TRP cc_start: 0.7500 (t-100) cc_final: 0.6872 (m100) REVERT: C 316 GLN cc_start: 0.8661 (tm-30) cc_final: 0.8317 (tm-30) REVERT: D 29 TYR cc_start: 0.7748 (m-80) cc_final: 0.7147 (p90) REVERT: D 61 MET cc_start: 0.8010 (ttm) cc_final: 0.7674 (ttm) REVERT: D 94 TRP cc_start: 0.7408 (t-100) cc_final: 0.6762 (m100) REVERT: D 289 LYS cc_start: 0.7986 (mmmt) cc_final: 0.7745 (mmtp) REVERT: D 293 GLN cc_start: 0.8386 (tt0) cc_final: 0.7891 (mt0) REVERT: E 61 MET cc_start: 0.8039 (ttm) cc_final: 0.7130 (tpt) REVERT: E 64 LYS cc_start: 0.9082 (mttt) cc_final: 0.8869 (mttm) REVERT: E 94 TRP cc_start: 0.7429 (t-100) cc_final: 0.6628 (m100) REVERT: E 289 LYS cc_start: 0.8063 (mmmt) cc_final: 0.7817 (mptt) REVERT: E 293 GLN cc_start: 0.8208 (tt0) cc_final: 0.7772 (mt0) REVERT: E 316 GLN cc_start: 0.8895 (tm-30) cc_final: 0.8564 (tm-30) outliers start: 39 outliers final: 7 residues processed: 205 average time/residue: 1.1313 time to fit residues: 254.8736 Evaluate side-chains 146 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 138 time to evaluate : 1.495 ------------------------------------------------------------------------------- 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 320 MET 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 75 optimal weight: 1.9990 chunk 42 optimal weight: 9.9990 chunk 113 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 136 optimal weight: 5.9990 chunk 147 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 135 optimal weight: 10.0000 chunk 46 optimal weight: 0.7980 chunk 109 optimal weight: 9.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN A 316 GLN B 178 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12997 Z= 0.178 Angle : 0.540 9.979 17665 Z= 0.275 Chirality : 0.042 0.167 1950 Planarity : 0.004 0.028 2194 Dihedral : 4.288 24.327 1700 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.17 % Allowed : 11.81 % Favored : 85.03 % 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: -2.20 (0.20), residues: 1510 helix: -0.88 (0.15), residues: 1085 sheet: None (None), residues: 0 loop : -2.69 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 229 HIS 0.002 0.000 HIS D 326 PHE 0.015 0.001 PHE B 272 TYR 0.009 0.001 TYR C 43 ARG 0.005 0.000 ARG C 223 *********************** 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 fitting. rotamer outliers: 44 poor density : 153 time to evaluate : 1.618 Fit side-chains REVERT: A 61 MET cc_start: 0.8056 (ttm) cc_final: 0.6999 (tpt) REVERT: A 94 TRP cc_start: 0.7613 (t-100) cc_final: 0.6897 (m100) REVERT: B 29 TYR cc_start: 0.7829 (m-80) cc_final: 0.7046 (t80) REVERT: B 61 MET cc_start: 0.7958 (ttm) cc_final: 0.7177 (tpt) REVERT: B 94 TRP cc_start: 0.7549 (t-100) cc_final: 0.6756 (m100) REVERT: B 230 ILE cc_start: 0.6952 (mm) cc_final: 0.6725 (mm) REVERT: B 293 GLN cc_start: 0.8330 (tt0) cc_final: 0.7982 (mt0) REVERT: B 316 GLN cc_start: 0.8900 (tm-30) cc_final: 0.8500 (tm-30) REVERT: C 29 TYR cc_start: 0.7773 (m-80) cc_final: 0.7263 (p90) REVERT: C 30 LYS cc_start: 0.8237 (ttmt) cc_final: 0.8005 (mttt) REVERT: C 54 LEU cc_start: 0.9525 (OUTLIER) cc_final: 0.9292 (mm) REVERT: C 61 MET cc_start: 0.7835 (ttm) cc_final: 0.6984 (tpt) REVERT: C 94 TRP cc_start: 0.7535 (t-100) cc_final: 0.6929 (m100) REVERT: C 237 THR cc_start: 0.7867 (t) cc_final: 0.7658 (t) REVERT: C 289 LYS cc_start: 0.8185 (mmmm) cc_final: 0.7906 (mmtp) REVERT: C 293 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7812 (mt0) REVERT: C 316 GLN cc_start: 0.8672 (tm-30) cc_final: 0.8440 (tm-30) REVERT: D 29 TYR cc_start: 0.7811 (m-80) cc_final: 0.7100 (t80) REVERT: D 58 GLN cc_start: 0.8528 (tt0) cc_final: 0.8048 (mt0) REVERT: D 61 MET cc_start: 0.8065 (ttm) cc_final: 0.7755 (ttm) REVERT: D 94 TRP cc_start: 0.7537 (t-100) cc_final: 0.6843 (m100) REVERT: D 293 GLN cc_start: 0.8288 (tt0) cc_final: 0.7795 (mt0) REVERT: E 54 LEU cc_start: 0.9460 (OUTLIER) cc_final: 0.9214 (mm) REVERT: E 61 MET cc_start: 0.8079 (ttm) cc_final: 0.7217 (tpt) REVERT: E 64 LYS cc_start: 0.9099 (mttt) cc_final: 0.8893 (mttm) REVERT: E 94 TRP cc_start: 0.7390 (t-100) cc_final: 0.6735 (m100) REVERT: E 154 MET cc_start: 0.8971 (mmp) cc_final: 0.8597 (mmp) REVERT: E 230 ILE cc_start: 0.7437 (mm) cc_final: 0.7020 (pt) REVERT: E 289 LYS cc_start: 0.8134 (mmmt) cc_final: 0.7780 (mmpt) REVERT: E 293 GLN cc_start: 0.8167 (tt0) cc_final: 0.7756 (mt0) REVERT: E 316 GLN cc_start: 0.8869 (tm-30) cc_final: 0.8559 (tm-30) outliers start: 44 outliers final: 8 residues processed: 184 average time/residue: 1.0932 time to fit residues: 221.3590 Evaluate side-chains 142 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 131 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain B residue 107 MET 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 293 GLN Chi-restraints excluded: chain C residue 294 LEU 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 134 optimal weight: 6.9990 chunk 102 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 15 optimal weight: 0.0270 chunk 65 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 144 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 overall best weight: 2.8046 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12997 Z= 0.208 Angle : 0.540 10.046 17665 Z= 0.271 Chirality : 0.042 0.137 1950 Planarity : 0.004 0.033 2194 Dihedral : 4.106 23.415 1700 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.30 % Allowed : 13.17 % Favored : 84.52 % 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: -1.47 (0.21), residues: 1510 helix: -0.32 (0.16), residues: 1090 sheet: None (None), residues: 0 loop : -2.52 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 229 HIS 0.002 0.000 HIS D 326 PHE 0.012 0.001 PHE B 272 TYR 0.030 0.001 TYR B 43 ARG 0.004 0.000 ARG C 223 *********************** 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 173 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 141 time to evaluate : 1.426 Fit side-chains REVERT: A 43 TYR cc_start: 0.8569 (t80) cc_final: 0.8237 (t80) REVERT: A 61 MET cc_start: 0.7934 (ttm) cc_final: 0.6918 (tpt) REVERT: A 92 ARG cc_start: 0.7731 (OUTLIER) cc_final: 0.7322 (tmt170) REVERT: A 94 TRP cc_start: 0.7580 (t-100) cc_final: 0.6874 (m100) REVERT: A 316 GLN cc_start: 0.8795 (tm130) cc_final: 0.8502 (tm-30) REVERT: B 61 MET cc_start: 0.7974 (ttm) cc_final: 0.7183 (tpt) REVERT: B 94 TRP cc_start: 0.7670 (t-100) cc_final: 0.6965 (m100) REVERT: B 230 ILE cc_start: 0.6941 (mm) cc_final: 0.6497 (pt) REVERT: B 293 GLN cc_start: 0.8259 (tt0) cc_final: 0.7904 (mt0) REVERT: B 316 GLN cc_start: 0.8847 (tm-30) cc_final: 0.8584 (tm-30) REVERT: C 29 TYR cc_start: 0.7779 (m-80) cc_final: 0.7234 (p90) REVERT: C 54 LEU cc_start: 0.9550 (OUTLIER) cc_final: 0.9337 (mm) REVERT: C 58 GLN cc_start: 0.8559 (mt0) cc_final: 0.8060 (mt0) REVERT: C 61 MET cc_start: 0.7879 (ttm) cc_final: 0.6935 (tpt) REVERT: C 94 TRP cc_start: 0.7506 (t-100) cc_final: 0.6876 (m100) REVERT: C 316 GLN cc_start: 0.8613 (tm-30) cc_final: 0.8397 (tm-30) REVERT: D 29 TYR cc_start: 0.7865 (m-80) cc_final: 0.7128 (t80) REVERT: D 30 LYS cc_start: 0.4291 (mptt) cc_final: 0.3520 (mptt) REVERT: D 58 GLN cc_start: 0.8564 (tt0) cc_final: 0.8049 (mt0) REVERT: D 61 MET cc_start: 0.8031 (ttm) cc_final: 0.7058 (tpt) REVERT: D 94 TRP cc_start: 0.7580 (t-100) cc_final: 0.6931 (m100) REVERT: D 223 ARG cc_start: 0.7843 (ttp-110) cc_final: 0.7628 (ttp-110) REVERT: D 256 GLN cc_start: 0.9020 (mm-40) cc_final: 0.8819 (mm-40) REVERT: D 293 GLN cc_start: 0.8259 (tt0) cc_final: 0.7859 (mt0) REVERT: E 54 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9210 (mm) REVERT: E 61 MET cc_start: 0.8106 (ttm) cc_final: 0.7235 (tpt) REVERT: E 64 LYS cc_start: 0.9117 (mttt) cc_final: 0.8905 (mttm) REVERT: E 94 TRP cc_start: 0.7481 (t-100) cc_final: 0.6881 (m100) REVERT: E 289 LYS cc_start: 0.8187 (mmmt) cc_final: 0.7850 (mmpt) REVERT: E 293 GLN cc_start: 0.8116 (tt0) cc_final: 0.7690 (mt0) REVERT: E 316 GLN cc_start: 0.8871 (tm-30) cc_final: 0.8573 (tm-30) outliers start: 32 outliers final: 11 residues processed: 166 average time/residue: 1.0732 time to fit residues: 196.2932 Evaluate side-chains 141 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 127 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain C residue 54 LEU 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 90 VAL 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 294 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 2.9990 chunk 82 optimal weight: 9.9990 chunk 2 optimal weight: 0.0570 chunk 107 optimal weight: 7.9990 chunk 59 optimal weight: 8.9990 chunk 123 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 74 optimal weight: 9.9990 chunk 130 optimal weight: 1.9990 chunk 36 optimal weight: 0.0470 overall best weight: 1.8202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS A 296 ASN B 238 GLN C 256 GLN C 267 HIS D 267 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12997 Z= 0.158 Angle : 0.515 10.712 17665 Z= 0.255 Chirality : 0.041 0.154 1950 Planarity : 0.003 0.035 2194 Dihedral : 3.928 21.500 1700 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.16 % Allowed : 13.25 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.93 (0.22), residues: 1510 helix: 0.05 (0.16), residues: 1115 sheet: None (None), residues: 0 loop : -2.36 (0.29), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 229 HIS 0.002 0.000 HIS A 267 PHE 0.012 0.001 PHE A 248 TYR 0.033 0.001 TYR C 43 ARG 0.004 0.000 ARG C 223 *********************** 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 169 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 139 time to evaluate : 1.607 Fit side-chains REVERT: A 61 MET cc_start: 0.7866 (ttm) cc_final: 0.6858 (tpt) REVERT: A 94 TRP cc_start: 0.7519 (t-100) cc_final: 0.6858 (m100) REVERT: A 180 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8524 (mttp) REVERT: A 316 GLN cc_start: 0.8714 (tm130) cc_final: 0.8454 (tm-30) REVERT: B 61 MET cc_start: 0.7982 (ttm) cc_final: 0.7215 (tpt) REVERT: B 94 TRP cc_start: 0.7632 (t-100) cc_final: 0.6939 (m100) REVERT: B 230 ILE cc_start: 0.7025 (mm) cc_final: 0.6747 (pt) REVERT: B 293 GLN cc_start: 0.8253 (tt0) cc_final: 0.7893 (mt0) REVERT: B 316 GLN cc_start: 0.8830 (tm-30) cc_final: 0.8585 (tm-30) REVERT: C 58 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.8036 (mt0) REVERT: C 61 MET cc_start: 0.7829 (ttm) cc_final: 0.6905 (tpt) REVERT: C 94 TRP cc_start: 0.7471 (t-100) cc_final: 0.6860 (m100) REVERT: C 316 GLN cc_start: 0.8475 (tm-30) cc_final: 0.8268 (tm-30) REVERT: D 29 TYR cc_start: 0.7918 (m-80) cc_final: 0.7156 (t80) REVERT: D 30 LYS cc_start: 0.4196 (mptt) cc_final: 0.3585 (mptt) REVERT: D 58 GLN cc_start: 0.8528 (tt0) cc_final: 0.7987 (mt0) REVERT: D 61 MET cc_start: 0.7992 (ttm) cc_final: 0.7081 (tpt) REVERT: D 94 TRP cc_start: 0.7466 (t-100) cc_final: 0.6827 (m100) REVERT: D 293 GLN cc_start: 0.8269 (tt0) cc_final: 0.7830 (mt0) REVERT: E 54 LEU cc_start: 0.9494 (OUTLIER) cc_final: 0.9272 (mm) REVERT: E 58 GLN cc_start: 0.8549 (tt0) cc_final: 0.8140 (mt0) REVERT: E 61 MET cc_start: 0.8043 (ttm) cc_final: 0.7179 (tpt) REVERT: E 64 LYS cc_start: 0.9103 (mttt) cc_final: 0.8888 (mttm) REVERT: E 92 ARG cc_start: 0.7714 (OUTLIER) cc_final: 0.7019 (tmt170) REVERT: E 94 TRP cc_start: 0.7429 (t-100) cc_final: 0.6703 (m100) REVERT: E 289 LYS cc_start: 0.8206 (mmmt) cc_final: 0.7937 (mmpt) REVERT: E 293 GLN cc_start: 0.8138 (tt0) cc_final: 0.7737 (mt0) REVERT: E 316 GLN cc_start: 0.8774 (tm-30) cc_final: 0.8540 (tm-30) outliers start: 30 outliers final: 10 residues processed: 163 average time/residue: 1.1854 time to fit residues: 211.4796 Evaluate side-chains 142 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 128 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 LYS Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain C residue 58 GLN 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 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 294 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 145 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 139 optimal weight: 6.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12997 Z= 0.228 Angle : 0.537 10.320 17665 Z= 0.266 Chirality : 0.042 0.147 1950 Planarity : 0.004 0.036 2194 Dihedral : 3.929 20.513 1700 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.66 % Allowed : 14.83 % Favored : 83.51 % 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: -0.59 (0.22), residues: 1510 helix: 0.31 (0.16), residues: 1115 sheet: None (None), residues: 0 loop : -2.27 (0.29), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 229 HIS 0.002 0.000 HIS C 326 PHE 0.013 0.001 PHE A 248 TYR 0.020 0.001 TYR A 43 ARG 0.003 0.000 ARG C 223 *********************** 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 159 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 136 time to evaluate : 1.520 Fit side-chains revert: symmetry clash REVERT: A 43 TYR cc_start: 0.8687 (t80) cc_final: 0.8467 (t80) REVERT: A 61 MET cc_start: 0.7876 (ttm) cc_final: 0.6917 (tpt) REVERT: A 94 TRP cc_start: 0.7519 (t-100) cc_final: 0.6849 (m100) REVERT: A 180 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8518 (mttp) REVERT: B 61 MET cc_start: 0.7974 (ttm) cc_final: 0.7254 (tpt) REVERT: B 94 TRP cc_start: 0.7547 (t-100) cc_final: 0.6819 (m100) REVERT: B 230 ILE cc_start: 0.7015 (mm) cc_final: 0.6775 (pt) REVERT: B 293 GLN cc_start: 0.8214 (tt0) cc_final: 0.7872 (mt0) REVERT: B 316 GLN cc_start: 0.8847 (tm-30) cc_final: 0.8611 (tm-30) REVERT: C 58 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.8037 (mt0) REVERT: C 61 MET cc_start: 0.7807 (ttm) cc_final: 0.6874 (tpt) REVERT: C 94 TRP cc_start: 0.7483 (t-100) cc_final: 0.6823 (m100) REVERT: C 316 GLN cc_start: 0.8456 (tm-30) cc_final: 0.8247 (tm-30) REVERT: D 29 TYR cc_start: 0.8004 (m-80) cc_final: 0.7167 (t80) REVERT: D 58 GLN cc_start: 0.8582 (tt0) cc_final: 0.8065 (mt0) REVERT: D 61 MET cc_start: 0.8007 (ttm) cc_final: 0.7106 (tpt) REVERT: D 94 TRP cc_start: 0.7477 (t-100) cc_final: 0.6806 (m100) REVERT: D 293 GLN cc_start: 0.8261 (tt0) cc_final: 0.7862 (mt0) REVERT: E 54 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.9251 (mm) REVERT: E 58 GLN cc_start: 0.8581 (tt0) cc_final: 0.8188 (mt0) REVERT: E 61 MET cc_start: 0.8051 (ttm) cc_final: 0.7223 (tpt) REVERT: E 94 TRP cc_start: 0.7440 (t-100) cc_final: 0.6703 (m100) REVERT: E 289 LYS cc_start: 0.8172 (mmmt) cc_final: 0.7914 (mmpt) REVERT: E 293 GLN cc_start: 0.8138 (tt0) cc_final: 0.7758 (mt0) REVERT: E 316 GLN cc_start: 0.8764 (tm-30) cc_final: 0.8529 (tm-30) outliers start: 23 outliers final: 12 residues processed: 153 average time/residue: 1.1396 time to fit residues: 191.6121 Evaluate side-chains 141 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 126 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 180 LYS Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 58 GLN 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 249 LEU Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 294 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 122 optimal weight: 10.0000 chunk 81 optimal weight: 8.9990 chunk 144 optimal weight: 0.8980 chunk 90 optimal weight: 10.0000 chunk 88 optimal weight: 7.9990 chunk 66 optimal weight: 20.0000 chunk 89 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12997 Z= 0.215 Angle : 0.543 10.762 17665 Z= 0.268 Chirality : 0.042 0.146 1950 Planarity : 0.003 0.038 2194 Dihedral : 3.894 20.055 1700 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.87 % Allowed : 15.05 % Favored : 83.08 % 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: -0.34 (0.22), residues: 1510 helix: 0.50 (0.16), residues: 1115 sheet: None (None), residues: 0 loop : -2.20 (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 0.013 0.001 PHE A 248 TYR 0.016 0.001 TYR A 43 ARG 0.004 0.000 ARG E 92 *********************** 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 159 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 133 time to evaluate : 1.700 Fit side-chains revert: symmetry clash REVERT: A 61 MET cc_start: 0.7869 (ttm) cc_final: 0.6919 (tpt) REVERT: A 92 ARG cc_start: 0.7641 (OUTLIER) cc_final: 0.7367 (tmt170) REVERT: A 94 TRP cc_start: 0.7554 (t-100) cc_final: 0.6865 (m100) REVERT: A 316 GLN cc_start: 0.8442 (tm-30) cc_final: 0.8217 (tm130) REVERT: B 61 MET cc_start: 0.7964 (ttm) cc_final: 0.7254 (tpt) REVERT: B 94 TRP cc_start: 0.7548 (t-100) cc_final: 0.6798 (m100) REVERT: B 230 ILE cc_start: 0.6933 (mm) cc_final: 0.6714 (pt) REVERT: B 293 GLN cc_start: 0.8215 (tt0) cc_final: 0.7877 (mt0) REVERT: B 316 GLN cc_start: 0.8844 (tm-30) cc_final: 0.8640 (tm-30) REVERT: C 58 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8040 (mt0) REVERT: C 61 MET cc_start: 0.7802 (ttm) cc_final: 0.6883 (tpt) REVERT: C 94 TRP cc_start: 0.7496 (t-100) cc_final: 0.6838 (m100) REVERT: C 107 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.8289 (ttt) REVERT: C 316 GLN cc_start: 0.8452 (tm-30) cc_final: 0.8239 (tm-30) REVERT: D 29 TYR cc_start: 0.7987 (m-80) cc_final: 0.7187 (t80) REVERT: D 58 GLN cc_start: 0.8592 (tt0) cc_final: 0.8048 (mt0) REVERT: D 61 MET cc_start: 0.8004 (ttm) cc_final: 0.7106 (tpt) REVERT: D 94 TRP cc_start: 0.7612 (t-100) cc_final: 0.6950 (m100) REVERT: D 293 GLN cc_start: 0.8252 (tt0) cc_final: 0.7858 (mt0) REVERT: E 54 LEU cc_start: 0.9501 (OUTLIER) cc_final: 0.9261 (mm) REVERT: E 58 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.8146 (mt0) REVERT: E 61 MET cc_start: 0.8052 (ttm) cc_final: 0.7222 (tpt) REVERT: E 94 TRP cc_start: 0.7517 (t-100) cc_final: 0.6896 (m100) REVERT: E 289 LYS cc_start: 0.8170 (mmmt) cc_final: 0.7914 (mmpt) REVERT: E 293 GLN cc_start: 0.8140 (tt0) cc_final: 0.7759 (mt0) REVERT: E 316 GLN cc_start: 0.8760 (tm-30) cc_final: 0.8512 (tm-30) outliers start: 26 outliers final: 12 residues processed: 152 average time/residue: 1.1803 time to fit residues: 198.8075 Evaluate side-chains 142 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 125 time to evaluate : 1.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 58 GLN Chi-restraints excluded: chain C residue 107 MET 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 275 VAL Chi-restraints excluded: chain C residue 294 LEU 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 249 LEU Chi-restraints excluded: chain E residue 294 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 8.9990 chunk 43 optimal weight: 0.7980 chunk 28 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 98 optimal weight: 0.2980 chunk 71 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 131 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 178 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12997 Z= 0.145 Angle : 0.520 11.409 17665 Z= 0.254 Chirality : 0.040 0.172 1950 Planarity : 0.003 0.025 2194 Dihedral : 3.758 18.892 1700 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.37 % Allowed : 15.69 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.03 (0.22), residues: 1510 helix: 0.74 (0.16), residues: 1110 sheet: None (None), residues: 0 loop : -2.12 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 229 HIS 0.002 0.000 HIS C 326 PHE 0.011 0.001 PHE A 248 TYR 0.010 0.001 TYR A 43 ARG 0.002 0.000 ARG C 196 *********************** 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 166 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 147 time to evaluate : 1.555 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.7815 (ttm) cc_final: 0.6873 (tpt) REVERT: A 92 ARG cc_start: 0.7575 (OUTLIER) cc_final: 0.7324 (tmt170) REVERT: A 94 TRP cc_start: 0.7529 (t-100) cc_final: 0.6885 (m100) REVERT: A 316 GLN cc_start: 0.8393 (tm-30) cc_final: 0.8051 (tm-30) REVERT: B 61 MET cc_start: 0.7979 (ttm) cc_final: 0.7234 (tpt) REVERT: B 94 TRP cc_start: 0.7571 (t-100) cc_final: 0.6819 (m100) REVERT: B 230 ILE cc_start: 0.6832 (mm) cc_final: 0.6606 (pt) REVERT: B 293 GLN cc_start: 0.8209 (tt0) cc_final: 0.7886 (mt0) REVERT: B 316 GLN cc_start: 0.8781 (tm-30) cc_final: 0.8535 (tm-30) REVERT: C 58 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.8020 (mt0) REVERT: C 61 MET cc_start: 0.7842 (ttm) cc_final: 0.6884 (tpt) REVERT: C 94 TRP cc_start: 0.7441 (t-100) cc_final: 0.6792 (m100) REVERT: D 29 TYR cc_start: 0.8002 (m-80) cc_final: 0.7192 (t80) REVERT: D 58 GLN cc_start: 0.8570 (tt0) cc_final: 0.8058 (mt0) REVERT: D 61 MET cc_start: 0.8000 (ttm) cc_final: 0.7107 (tpt) REVERT: D 94 TRP cc_start: 0.7568 (t-100) cc_final: 0.6911 (m100) REVERT: D 293 GLN cc_start: 0.8249 (tt0) cc_final: 0.7854 (mt0) REVERT: E 54 LEU cc_start: 0.9490 (OUTLIER) cc_final: 0.9242 (mm) REVERT: E 58 GLN cc_start: 0.8576 (tt0) cc_final: 0.8107 (mt0) REVERT: E 61 MET cc_start: 0.7982 (ttm) cc_final: 0.7131 (tpt) REVERT: E 94 TRP cc_start: 0.7441 (t-100) cc_final: 0.6800 (m100) REVERT: E 289 LYS cc_start: 0.8188 (mmmt) cc_final: 0.7936 (mmpt) REVERT: E 293 GLN cc_start: 0.8130 (tt0) cc_final: 0.7782 (mt0) REVERT: E 316 GLN cc_start: 0.8759 (tm-30) cc_final: 0.8510 (tm-30) outliers start: 19 outliers final: 10 residues processed: 161 average time/residue: 1.0251 time to fit residues: 183.2063 Evaluate side-chains 144 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 131 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain C residue 58 GLN 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 275 VAL 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 294 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 121 optimal weight: 0.9980 chunk 127 optimal weight: 7.9990 chunk 88 optimal weight: 6.9990 chunk 142 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12997 Z= 0.183 Angle : 0.536 10.932 17665 Z= 0.262 Chirality : 0.041 0.159 1950 Planarity : 0.003 0.032 2194 Dihedral : 3.743 18.027 1700 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.73 % Allowed : 16.05 % 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: 0.10 (0.22), residues: 1510 helix: 0.84 (0.16), residues: 1110 sheet: None (None), residues: 0 loop : -2.10 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 229 HIS 0.002 0.000 HIS C 326 PHE 0.011 0.001 PHE A 248 TYR 0.021 0.001 TYR C 43 ARG 0.003 0.000 ARG B 126 *********************** 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 161 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 137 time to evaluate : 1.542 Fit side-chains revert: symmetry clash REVERT: A 61 MET cc_start: 0.7820 (ttm) cc_final: 0.6881 (tpt) REVERT: A 92 ARG cc_start: 0.7581 (OUTLIER) cc_final: 0.7335 (tmt170) REVERT: A 94 TRP cc_start: 0.7556 (t-100) cc_final: 0.6892 (m100) REVERT: A 316 GLN cc_start: 0.8361 (tm-30) cc_final: 0.8059 (tm-30) REVERT: B 61 MET cc_start: 0.8003 (ttm) cc_final: 0.7215 (tpt) REVERT: B 94 TRP cc_start: 0.7587 (t-100) cc_final: 0.6793 (m100) REVERT: B 293 GLN cc_start: 0.8205 (tt0) cc_final: 0.7888 (mt0) REVERT: B 316 GLN cc_start: 0.8778 (tm-30) cc_final: 0.8556 (tm-30) REVERT: C 58 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.8019 (mt0) REVERT: C 61 MET cc_start: 0.7780 (ttm) cc_final: 0.6869 (tpt) REVERT: C 94 TRP cc_start: 0.7439 (t-100) cc_final: 0.6799 (m100) REVERT: D 29 TYR cc_start: 0.8046 (m-80) cc_final: 0.7200 (t80) REVERT: D 30 LYS cc_start: 0.4344 (mptt) cc_final: 0.3716 (mptt) REVERT: D 43 TYR cc_start: 0.8750 (t80) cc_final: 0.8510 (t80) REVERT: D 58 GLN cc_start: 0.8522 (tt0) cc_final: 0.8017 (mt0) REVERT: D 61 MET cc_start: 0.8008 (ttm) cc_final: 0.7120 (tpt) REVERT: D 94 TRP cc_start: 0.7564 (t-100) cc_final: 0.6908 (m100) REVERT: D 293 GLN cc_start: 0.8251 (tt0) cc_final: 0.7867 (mt0) REVERT: E 54 LEU cc_start: 0.9496 (OUTLIER) cc_final: 0.9234 (mm) REVERT: E 58 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.8112 (mt0) REVERT: E 61 MET cc_start: 0.8005 (ttm) cc_final: 0.7199 (tpt) REVERT: E 94 TRP cc_start: 0.7422 (t-100) cc_final: 0.6784 (m100) REVERT: E 289 LYS cc_start: 0.8152 (mmmt) cc_final: 0.7908 (mmpt) REVERT: E 293 GLN cc_start: 0.8143 (tt0) cc_final: 0.7804 (mt0) REVERT: E 316 GLN cc_start: 0.8735 (tm-30) cc_final: 0.8499 (tm-30) outliers start: 24 outliers final: 10 residues processed: 151 average time/residue: 1.0688 time to fit residues: 178.5663 Evaluate side-chains 147 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 133 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain C residue 58 GLN 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 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 249 LEU Chi-restraints excluded: chain E residue 294 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 chunk 137 optimal weight: 7.9990 chunk 118 optimal weight: 4.9990 chunk 12 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 chunk 94 optimal weight: 0.7980 chunk 126 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12997 Z= 0.207 Angle : 0.543 11.325 17665 Z= 0.267 Chirality : 0.042 0.177 1950 Planarity : 0.003 0.034 2194 Dihedral : 3.772 17.669 1700 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.44 % Allowed : 16.41 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.17 (0.22), residues: 1510 helix: 0.90 (0.16), residues: 1110 sheet: None (None), residues: 0 loop : -2.08 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP E 229 HIS 0.002 0.000 HIS D 326 PHE 0.012 0.001 PHE A 248 TYR 0.010 0.001 TYR A 43 ARG 0.003 0.000 ARG C 196 ********************** 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 154 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 134 time to evaluate : 1.431 Fit side-chains revert: symmetry clash REVERT: A 61 MET cc_start: 0.7820 (ttm) cc_final: 0.6882 (tpt) REVERT: A 92 ARG cc_start: 0.7553 (OUTLIER) cc_final: 0.7309 (tmt170) REVERT: A 94 TRP cc_start: 0.7572 (t-100) cc_final: 0.6876 (m100) REVERT: A 100 ILE cc_start: 0.8633 (mm) cc_final: 0.8104 (pt) REVERT: A 249 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8998 (tm) REVERT: A 316 GLN cc_start: 0.8367 (tm-30) cc_final: 0.8067 (tm-30) REVERT: B 61 MET cc_start: 0.8007 (ttm) cc_final: 0.7223 (tpt) REVERT: B 94 TRP cc_start: 0.7610 (t-100) cc_final: 0.6816 (m100) REVERT: B 293 GLN cc_start: 0.8236 (tt0) cc_final: 0.7923 (mt0) REVERT: B 316 GLN cc_start: 0.8756 (tm-30) cc_final: 0.8546 (tm-30) REVERT: C 58 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.7999 (mt0) REVERT: C 61 MET cc_start: 0.7786 (ttm) cc_final: 0.6877 (tpt) REVERT: C 94 TRP cc_start: 0.7451 (t-100) cc_final: 0.6562 (t60) REVERT: D 29 TYR cc_start: 0.8039 (m-80) cc_final: 0.7186 (t80) REVERT: D 30 LYS cc_start: 0.4371 (mptt) cc_final: 0.3718 (mptt) REVERT: D 58 GLN cc_start: 0.8504 (tt0) cc_final: 0.8010 (mt0) REVERT: D 61 MET cc_start: 0.7999 (ttm) cc_final: 0.7102 (tpt) REVERT: D 94 TRP cc_start: 0.7609 (t-100) cc_final: 0.6933 (m100) REVERT: D 293 GLN cc_start: 0.8265 (tt0) cc_final: 0.7880 (mt0) REVERT: E 54 LEU cc_start: 0.9508 (OUTLIER) cc_final: 0.9246 (mm) REVERT: E 58 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.8118 (mt0) REVERT: E 61 MET cc_start: 0.8013 (ttm) cc_final: 0.7206 (tpt) REVERT: E 94 TRP cc_start: 0.7464 (t-100) cc_final: 0.6813 (m100) REVERT: E 289 LYS cc_start: 0.8163 (mmmt) cc_final: 0.7915 (mmpt) REVERT: E 293 GLN cc_start: 0.8161 (tt0) cc_final: 0.7809 (mt0) REVERT: E 316 GLN cc_start: 0.8738 (tm-30) cc_final: 0.8498 (tm-30) outliers start: 20 outliers final: 10 residues processed: 145 average time/residue: 1.1208 time to fit residues: 179.4073 Evaluate side-chains 145 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 130 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain C residue 58 GLN Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 275 VAL 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 249 LEU Chi-restraints excluded: chain E residue 294 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 chunk 119 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 86 optimal weight: 7.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.098684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.073028 restraints weight = 24664.080| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 3.47 r_work: 0.2798 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12997 Z= 0.138 Angle : 0.543 12.474 17665 Z= 0.261 Chirality : 0.040 0.173 1950 Planarity : 0.003 0.025 2194 Dihedral : 3.674 17.144 1700 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.08 % Allowed : 16.92 % Favored : 82.00 % 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: 0.33 (0.23), residues: 1510 helix: 0.96 (0.16), residues: 1120 sheet: None (None), residues: 0 loop : -1.89 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP B 229 HIS 0.002 0.000 HIS C 326 PHE 0.010 0.001 PHE E 248 TYR 0.019 0.001 TYR C 43 ARG 0.004 0.000 ARG D 218 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3945.62 seconds wall clock time: 71 minutes 18.32 seconds (4278.32 seconds total)