Starting phenix.real_space_refine on Fri Mar 15 19:54:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n24_9322/03_2024/6n24_9322_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n24_9322/03_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_9322/03_2024/6n24_9322.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n24_9322/03_2024/6n24_9322.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n24_9322/03_2024/6n24_9322_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n24_9322/03_2024/6n24_9322_neut.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 6.61, per 1000 atoms: 0.52 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 - 3.50 Amino acid : False - 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: 4.82 Conformation dependent library (CDL) restraints added in 2.4 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: 1.18 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: 3.13 Time building geometry restraints manager: 5.27 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: 99.09 - 106.09: 262 106.09 - 113.09: 6869 113.09 - 120.09: 5259 120.09 - 127.09: 5095 127.09 - 134.09: 180 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 2.520 nonbonded pdb=" OD2 ASP C 104 " pdb=" NH2 ARG D 218 " model vdw 2.338 2.520 nonbonded pdb=" OE1 GLU B 63 " pdb=" OH TYR B 264 " model vdw 2.344 2.440 nonbonded pdb=" OE1 GLU D 63 " pdb=" OH TYR D 264 " model vdw 2.345 2.440 nonbonded pdb=" OE1 GLU A 63 " pdb=" OH TYR A 264 " model vdw 2.345 2.440 ... (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 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: 0.130 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: 1.440 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 34.760 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.470 ------------------------------------------------------------------------------- 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 : 1.401 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: 1.2645 time to fit residues: 436.2971 Evaluate side-chains 133 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 131 time to evaluate : 1.845 ------------------------------------------------------------------------------- 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: 5.9990 chunk 113 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 60 optimal weight: 20.0000 chunk 117 optimal weight: 9.9990 chunk 45 optimal weight: 8.9990 chunk 71 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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: 0.8175 moved from start: 0.2295 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= 0.201 Angle : 0.595 8.311 17665 Z= 0.312 Chirality : 0.043 0.160 1950 Planarity : 0.005 0.030 2194 Dihedral : 4.668 24.994 1704 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.59 % Allowed : 11.52 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.55 (0.18), residues: 1510 helix: -2.01 (0.13), residues: 1090 sheet: None (None), residues: 0 loop : -2.80 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 94 HIS 0.002 0.001 HIS D 326 PHE 0.022 0.001 PHE B 272 TYR 0.011 0.001 TYR B 43 ARG 0.006 0.001 ARG C 255 *********************** 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 201 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 165 time to evaluate : 1.475 Fit side-chains REVERT: A 29 TYR cc_start: 0.7820 (m-80) cc_final: 0.7256 (t80) REVERT: A 61 MET cc_start: 0.8043 (ttm) cc_final: 0.6947 (tpt) REVERT: A 94 TRP cc_start: 0.7450 (t-100) cc_final: 0.6843 (m100) REVERT: A 230 ILE cc_start: 0.6926 (mm) cc_final: 0.6579 (pt) REVERT: A 293 GLN cc_start: 0.8284 (tt0) cc_final: 0.7922 (tm-30) REVERT: A 316 GLN cc_start: 0.8785 (tm-30) cc_final: 0.8380 (tm-30) REVERT: B 29 TYR cc_start: 0.7762 (m-80) cc_final: 0.7056 (t80) REVERT: B 58 GLN cc_start: 0.8616 (tt0) cc_final: 0.8209 (mt0) REVERT: B 61 MET cc_start: 0.7954 (ttm) cc_final: 0.7110 (tpt) REVERT: B 94 TRP cc_start: 0.7304 (t-100) cc_final: 0.6741 (m100) REVERT: B 154 MET cc_start: 0.9137 (tpp) cc_final: 0.8863 (mmp) REVERT: B 289 LYS cc_start: 0.8098 (mmmt) cc_final: 0.7499 (mmpt) REVERT: B 292 GLU cc_start: 0.7889 (pp20) cc_final: 0.7610 (pp20) REVERT: B 293 GLN cc_start: 0.8426 (tt0) cc_final: 0.7900 (mt0) REVERT: B 316 GLN cc_start: 0.8850 (tm-30) cc_final: 0.8477 (tm-30) REVERT: B 320 MET cc_start: 0.9117 (OUTLIER) cc_final: 0.8914 (ttm) REVERT: C 29 TYR cc_start: 0.7709 (m-80) cc_final: 0.7249 (p90) REVERT: C 30 LYS cc_start: 0.8267 (ttmt) cc_final: 0.8049 (mttt) REVERT: C 41 SER cc_start: 0.9623 (m) cc_final: 0.9414 (p) REVERT: C 61 MET cc_start: 0.7914 (ttm) cc_final: 0.6967 (tpt) REVERT: C 94 TRP cc_start: 0.7417 (t-100) cc_final: 0.6833 (m100) REVERT: C 316 GLN cc_start: 0.8663 (tm-30) cc_final: 0.8297 (tm-30) REVERT: D 29 TYR cc_start: 0.7738 (m-80) cc_final: 0.7153 (p90) REVERT: D 61 MET cc_start: 0.8013 (ttm) cc_final: 0.7677 (ttm) REVERT: D 94 TRP cc_start: 0.7407 (t-100) cc_final: 0.6792 (m100) REVERT: D 230 ILE cc_start: 0.6728 (mm) cc_final: 0.6458 (tp) REVERT: D 289 LYS cc_start: 0.7989 (mmmt) cc_final: 0.7630 (mptt) REVERT: D 293 GLN cc_start: 0.8382 (tt0) cc_final: 0.7891 (mt0) REVERT: E 61 MET cc_start: 0.8056 (ttm) cc_final: 0.7085 (tpt) REVERT: E 94 TRP cc_start: 0.7401 (t-100) cc_final: 0.6626 (m100) REVERT: E 289 LYS cc_start: 0.8064 (mmmt) cc_final: 0.7844 (mptt) REVERT: E 293 GLN cc_start: 0.8205 (tt0) cc_final: 0.7768 (mt0) REVERT: E 316 GLN cc_start: 0.8891 (tm-30) cc_final: 0.8562 (tm-30) outliers start: 36 outliers final: 8 residues processed: 196 average time/residue: 1.1590 time to fit residues: 249.5206 Evaluate side-chains 147 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 138 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain D residue 41 SER 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: 0.0270 chunk 42 optimal weight: 7.9990 chunk 113 optimal weight: 10.0000 chunk 92 optimal weight: 0.0270 chunk 37 optimal weight: 8.9990 chunk 136 optimal weight: 4.9990 chunk 147 optimal weight: 0.4980 chunk 121 optimal weight: 0.9990 chunk 135 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 109 optimal weight: 10.0000 overall best weight: 0.5100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12997 Z= 0.118 Angle : 0.507 10.325 17665 Z= 0.254 Chirality : 0.040 0.149 1950 Planarity : 0.003 0.029 2194 Dihedral : 4.145 23.597 1702 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.52 % Allowed : 12.46 % 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: -2.06 (0.20), residues: 1510 helix: -0.77 (0.15), residues: 1085 sheet: None (None), residues: 0 loop : -2.68 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 229 HIS 0.002 0.000 HIS C 326 PHE 0.013 0.001 PHE B 272 TYR 0.013 0.001 TYR C 97 ARG 0.005 0.000 ARG D 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 202 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 167 time to evaluate : 1.520 Fit side-chains revert: symmetry clash REVERT: A 43 TYR cc_start: 0.8520 (t80) cc_final: 0.8259 (t80) REVERT: A 61 MET cc_start: 0.7972 (ttm) cc_final: 0.6876 (tpt) REVERT: A 94 TRP cc_start: 0.7545 (t-100) cc_final: 0.6870 (m100) REVERT: A 230 ILE cc_start: 0.7014 (mm) cc_final: 0.6799 (pt) REVERT: A 316 GLN cc_start: 0.8837 (tm-30) cc_final: 0.8559 (tm-30) REVERT: B 29 TYR cc_start: 0.7738 (m-80) cc_final: 0.7063 (t80) REVERT: B 58 GLN cc_start: 0.8397 (tt0) cc_final: 0.8118 (mt0) REVERT: B 61 MET cc_start: 0.7938 (ttm) cc_final: 0.7146 (tpt) REVERT: B 94 TRP cc_start: 0.7418 (t-100) cc_final: 0.6705 (t60) REVERT: B 293 GLN cc_start: 0.8243 (tt0) cc_final: 0.7859 (mt0) REVERT: B 316 GLN cc_start: 0.8922 (tm-30) cc_final: 0.8614 (tm-30) REVERT: C 29 TYR cc_start: 0.7724 (m-80) cc_final: 0.7258 (p90) REVERT: C 41 SER cc_start: 0.9620 (m) cc_final: 0.9413 (p) REVERT: C 58 GLN cc_start: 0.8449 (tt0) cc_final: 0.8032 (mt0) REVERT: C 61 MET cc_start: 0.7827 (ttm) cc_final: 0.6960 (tpt) REVERT: C 94 TRP cc_start: 0.7355 (t-100) cc_final: 0.6726 (m100) REVERT: C 230 ILE cc_start: 0.6722 (mm) cc_final: 0.6513 (pt) REVERT: C 289 LYS cc_start: 0.8161 (mmmm) cc_final: 0.7825 (mmtp) REVERT: C 293 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7757 (mt0) REVERT: D 29 TYR cc_start: 0.7788 (m-80) cc_final: 0.7144 (t80) REVERT: D 58 GLN cc_start: 0.8481 (tt0) cc_final: 0.8019 (mt0) REVERT: D 61 MET cc_start: 0.7994 (ttm) cc_final: 0.7658 (ttm) REVERT: D 94 TRP cc_start: 0.7546 (t-100) cc_final: 0.6908 (m100) REVERT: D 180 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8398 (mttt) REVERT: E 54 LEU cc_start: 0.9442 (OUTLIER) cc_final: 0.9197 (mm) REVERT: E 61 MET cc_start: 0.8042 (ttm) cc_final: 0.7207 (tpt) REVERT: E 94 TRP cc_start: 0.7335 (t-100) cc_final: 0.6647 (m100) REVERT: E 262 LYS cc_start: 0.9465 (OUTLIER) cc_final: 0.9135 (mtmm) REVERT: E 289 LYS cc_start: 0.8115 (mmmt) cc_final: 0.7761 (mmpt) REVERT: E 293 GLN cc_start: 0.8126 (tt0) cc_final: 0.7718 (mt0) REVERT: E 316 GLN cc_start: 0.8872 (tm-30) cc_final: 0.8598 (tm-30) outliers start: 35 outliers final: 7 residues processed: 190 average time/residue: 1.0756 time to fit residues: 225.4618 Evaluate side-chains 148 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 137 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain B residue 294 LEU 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 180 LYS Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 262 LYS Chi-restraints excluded: chain E residue 294 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 10.0000 chunk 102 optimal weight: 9.9990 chunk 70 optimal weight: 6.9990 chunk 15 optimal weight: 0.2980 chunk 65 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 129 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- 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: 0.8164 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12997 Z= 0.213 Angle : 0.531 10.065 17665 Z= 0.263 Chirality : 0.042 0.165 1950 Planarity : 0.003 0.029 2194 Dihedral : 3.963 21.978 1700 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.81 % Allowed : 13.39 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.35 (0.21), residues: 1510 helix: -0.23 (0.16), residues: 1095 sheet: None (None), residues: 0 loop : -2.49 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 229 HIS 0.002 0.001 HIS B 178 PHE 0.012 0.001 PHE D 248 TYR 0.027 0.001 TYR B 43 ARG 0.003 0.000 ARG C 255 *********************** 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 182 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 143 time to evaluate : 1.594 Fit side-chains REVERT: A 61 MET cc_start: 0.7936 (ttm) cc_final: 0.6913 (tpt) REVERT: A 94 TRP cc_start: 0.7541 (t-100) cc_final: 0.6821 (m100) REVERT: A 316 GLN cc_start: 0.8833 (tm-30) cc_final: 0.8509 (tm-30) REVERT: B 29 TYR cc_start: 0.7820 (m-80) cc_final: 0.7057 (t80) REVERT: B 58 GLN cc_start: 0.8508 (tt0) cc_final: 0.8164 (mt0) REVERT: B 61 MET cc_start: 0.7961 (ttm) cc_final: 0.7170 (tpt) REVERT: B 94 TRP cc_start: 0.7606 (t-100) cc_final: 0.6702 (t60) REVERT: B 154 MET cc_start: 0.9110 (mmt) cc_final: 0.8892 (mmp) REVERT: B 293 GLN cc_start: 0.8277 (tt0) cc_final: 0.7944 (mt0) REVERT: C 30 LYS cc_start: 0.4516 (mptt) cc_final: 0.3123 (mmpt) REVERT: C 58 GLN cc_start: 0.8500 (tt0) cc_final: 0.8004 (mt0) REVERT: C 61 MET cc_start: 0.7872 (ttm) cc_final: 0.6925 (tpt) REVERT: C 94 TRP cc_start: 0.7384 (t-100) cc_final: 0.6735 (m100) REVERT: C 316 GLN cc_start: 0.8223 (tm-30) cc_final: 0.8012 (tm-30) REVERT: D 29 TYR cc_start: 0.7862 (m-80) cc_final: 0.7124 (t80) REVERT: D 58 GLN cc_start: 0.8572 (tt0) cc_final: 0.8068 (mt0) REVERT: D 61 MET cc_start: 0.8030 (ttm) cc_final: 0.7105 (tpt) REVERT: D 94 TRP cc_start: 0.7603 (t-100) cc_final: 0.6918 (m100) REVERT: D 293 GLN cc_start: 0.8291 (tt0) cc_final: 0.7769 (mt0) REVERT: E 58 GLN cc_start: 0.8537 (tt0) cc_final: 0.8149 (mt0) REVERT: E 61 MET cc_start: 0.8073 (ttm) cc_final: 0.7246 (tpt) REVERT: E 94 TRP cc_start: 0.7387 (t-100) cc_final: 0.6707 (m100) REVERT: E 262 LYS cc_start: 0.9474 (OUTLIER) cc_final: 0.9176 (mtmm) REVERT: E 289 LYS cc_start: 0.8141 (mmmt) cc_final: 0.7855 (mmpt) REVERT: E 293 GLN cc_start: 0.8118 (tt0) cc_final: 0.7712 (mt0) REVERT: E 316 GLN cc_start: 0.8895 (tm-30) cc_final: 0.8655 (tm-30) outliers start: 39 outliers final: 15 residues processed: 172 average time/residue: 1.0185 time to fit residues: 193.8759 Evaluate side-chains 143 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 127 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 262 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 2 optimal weight: 0.0070 chunk 107 optimal weight: 10.0000 chunk 59 optimal weight: 0.6980 chunk 123 optimal weight: 20.0000 chunk 100 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 overall best weight: 3.7404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN B 238 GLN D 267 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3268 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= 0.251 Angle : 0.536 10.182 17665 Z= 0.267 Chirality : 0.043 0.138 1950 Planarity : 0.003 0.026 2194 Dihedral : 3.975 21.707 1700 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.17 % Allowed : 13.10 % Favored : 83.73 % 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: -0.86 (0.22), residues: 1510 helix: 0.15 (0.16), residues: 1095 sheet: None (None), residues: 0 loop : -2.38 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 229 HIS 0.002 0.001 HIS A 267 PHE 0.014 0.001 PHE A 248 TYR 0.022 0.001 TYR D 43 ARG 0.003 0.000 ARG D 196 *********************** 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 181 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 137 time to evaluate : 1.459 Fit side-chains REVERT: A 61 MET cc_start: 0.7891 (ttm) cc_final: 0.6928 (tpt) REVERT: A 94 TRP cc_start: 0.7491 (t-100) cc_final: 0.6796 (m100) REVERT: A 180 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8593 (mttp) REVERT: B 29 TYR cc_start: 0.7903 (m-80) cc_final: 0.7124 (t80) REVERT: B 58 GLN cc_start: 0.8518 (tt0) cc_final: 0.8169 (mt0) REVERT: B 61 MET cc_start: 0.7973 (ttm) cc_final: 0.7212 (tpt) REVERT: B 94 TRP cc_start: 0.7561 (t-100) cc_final: 0.6716 (t60) REVERT: B 154 MET cc_start: 0.9142 (mmt) cc_final: 0.8894 (mmp) REVERT: B 293 GLN cc_start: 0.8213 (tt0) cc_final: 0.7891 (mt0) REVERT: C 29 TYR cc_start: 0.7850 (m-80) cc_final: 0.7118 (t80) REVERT: C 58 GLN cc_start: 0.8500 (tt0) cc_final: 0.7988 (mt0) REVERT: C 61 MET cc_start: 0.7868 (ttm) cc_final: 0.6953 (tpt) REVERT: C 94 TRP cc_start: 0.7383 (t-100) cc_final: 0.6748 (m100) REVERT: C 316 GLN cc_start: 0.8372 (tm-30) cc_final: 0.8061 (tm-30) REVERT: D 29 TYR cc_start: 0.7915 (m-80) cc_final: 0.7132 (t80) REVERT: D 30 LYS cc_start: 0.4132 (mptt) cc_final: 0.3530 (mptt) REVERT: D 58 GLN cc_start: 0.8549 (tt0) cc_final: 0.8079 (mt0) REVERT: D 61 MET cc_start: 0.8019 (ttm) cc_final: 0.7113 (tpt) REVERT: D 94 TRP cc_start: 0.7604 (t-100) cc_final: 0.6907 (m100) REVERT: E 58 GLN cc_start: 0.8597 (tt0) cc_final: 0.8135 (mt0) REVERT: E 61 MET cc_start: 0.8119 (ttm) cc_final: 0.7208 (tpt) REVERT: E 94 TRP cc_start: 0.7436 (t-100) cc_final: 0.6690 (m100) REVERT: E 262 LYS cc_start: 0.9486 (OUTLIER) cc_final: 0.9212 (mtmm) REVERT: E 289 LYS cc_start: 0.8170 (mmmt) cc_final: 0.7900 (mmpt) REVERT: E 293 GLN cc_start: 0.8138 (tt0) cc_final: 0.7746 (mt0) REVERT: E 316 GLN cc_start: 0.8821 (tm-30) cc_final: 0.8600 (tm-30) outliers start: 44 outliers final: 20 residues processed: 173 average time/residue: 0.9793 time to fit residues: 188.2664 Evaluate side-chains 150 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 128 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 180 LYS Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 88 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 C residue 336 LEU Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 262 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 6.9990 chunk 130 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 chunk 85 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 145 optimal weight: 8.9990 chunk 120 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 12 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS B 267 HIS C 267 HIS E 267 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12997 Z= 0.142 Angle : 0.514 11.174 17665 Z= 0.249 Chirality : 0.040 0.139 1950 Planarity : 0.003 0.022 2194 Dihedral : 3.837 20.393 1700 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.80 % Allowed : 15.41 % Favored : 82.79 % 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: -0.54 (0.22), residues: 1510 helix: 0.35 (0.16), residues: 1120 sheet: None (None), residues: 0 loop : -2.30 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 229 HIS 0.002 0.000 HIS D 326 PHE 0.011 0.001 PHE C 248 TYR 0.016 0.001 TYR E 29 ARG 0.003 0.000 ARG C 255 *********************** 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 171 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 146 time to evaluate : 1.411 Fit side-chains revert: symmetry clash REVERT: A 61 MET cc_start: 0.7827 (ttm) cc_final: 0.6871 (tpt) REVERT: A 94 TRP cc_start: 0.7499 (t-100) cc_final: 0.6804 (m100) REVERT: A 316 GLN cc_start: 0.8509 (tm-30) cc_final: 0.8248 (tm-30) REVERT: B 29 TYR cc_start: 0.7945 (m-80) cc_final: 0.7126 (t80) REVERT: B 58 GLN cc_start: 0.8505 (tt0) cc_final: 0.8181 (mt0) REVERT: B 61 MET cc_start: 0.7975 (ttm) cc_final: 0.7203 (tpt) REVERT: B 94 TRP cc_start: 0.7618 (t-100) cc_final: 0.6754 (t60) REVERT: B 293 GLN cc_start: 0.8195 (tt0) cc_final: 0.7873 (mt0) REVERT: C 29 TYR cc_start: 0.7880 (m-80) cc_final: 0.7140 (t80) REVERT: C 58 GLN cc_start: 0.8507 (tt0) cc_final: 0.8001 (mt0) REVERT: C 61 MET cc_start: 0.7783 (ttm) cc_final: 0.6868 (tpt) REVERT: C 94 TRP cc_start: 0.7429 (t-100) cc_final: 0.6784 (m100) REVERT: D 29 TYR cc_start: 0.7984 (m-80) cc_final: 0.7156 (t80) REVERT: D 58 GLN cc_start: 0.8565 (tt0) cc_final: 0.8053 (mt0) REVERT: D 61 MET cc_start: 0.7991 (ttm) cc_final: 0.7085 (tpt) REVERT: D 94 TRP cc_start: 0.7589 (t-100) cc_final: 0.6914 (m100) REVERT: E 58 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.8089 (mt0) REVERT: E 61 MET cc_start: 0.8068 (ttm) cc_final: 0.7231 (tpt) REVERT: E 94 TRP cc_start: 0.7439 (t-100) cc_final: 0.6678 (m100) REVERT: E 289 LYS cc_start: 0.8148 (mmmt) cc_final: 0.7896 (mmpt) REVERT: E 293 GLN cc_start: 0.8127 (tt0) cc_final: 0.7735 (mt0) REVERT: E 316 GLN cc_start: 0.8803 (tm-30) cc_final: 0.8600 (tm-30) outliers start: 25 outliers final: 12 residues processed: 164 average time/residue: 1.0160 time to fit residues: 184.7983 Evaluate side-chains 141 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 128 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain C residue 88 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 41 SER Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain E residue 58 GLN Chi-restraints excluded: chain E residue 107 MET Chi-restraints excluded: chain E residue 219 SER 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: 8.9990 chunk 82 optimal weight: 10.0000 chunk 105 optimal weight: 0.8980 chunk 122 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 144 optimal weight: 8.9990 chunk 90 optimal weight: 20.0000 chunk 88 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 89 optimal weight: 0.0470 chunk 57 optimal weight: 6.9990 overall best weight: 2.3682 ------------------------------------------------------------------------------- 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: 0.8166 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12997 Z= 0.185 Angle : 0.528 11.446 17665 Z= 0.256 Chirality : 0.041 0.132 1950 Planarity : 0.003 0.023 2194 Dihedral : 3.790 19.016 1700 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.09 % Allowed : 16.27 % Favored : 81.64 % 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: -0.30 (0.22), residues: 1510 helix: 0.58 (0.16), residues: 1110 sheet: None (None), residues: 0 loop : -2.31 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 229 HIS 0.002 0.000 HIS E 326 PHE 0.012 0.001 PHE A 248 TYR 0.019 0.001 TYR A 43 ARG 0.002 0.000 ARG D 196 *********************** 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 163 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 134 time to evaluate : 1.300 Fit side-chains revert: symmetry clash REVERT: A 61 MET cc_start: 0.7826 (ttm) cc_final: 0.6874 (tpt) REVERT: A 94 TRP cc_start: 0.7507 (t-100) cc_final: 0.6824 (m100) REVERT: A 316 GLN cc_start: 0.8413 (tm-30) cc_final: 0.8145 (tm-30) REVERT: B 29 TYR cc_start: 0.8005 (m-80) cc_final: 0.7156 (t80) REVERT: B 58 GLN cc_start: 0.8554 (tt0) cc_final: 0.8176 (mt0) REVERT: B 61 MET cc_start: 0.8019 (ttm) cc_final: 0.7217 (tpt) REVERT: B 94 TRP cc_start: 0.7614 (t-100) cc_final: 0.6752 (t60) REVERT: B 293 GLN cc_start: 0.8210 (tt0) cc_final: 0.7903 (mt0) REVERT: C 29 TYR cc_start: 0.7962 (m-80) cc_final: 0.7128 (t80) REVERT: C 58 GLN cc_start: 0.8495 (tt0) cc_final: 0.7986 (mt0) REVERT: C 61 MET cc_start: 0.7793 (ttm) cc_final: 0.6872 (tpt) REVERT: C 94 TRP cc_start: 0.7417 (t-100) cc_final: 0.6773 (m100) REVERT: C 289 LYS cc_start: 0.8071 (mmtp) cc_final: 0.7855 (mmpt) REVERT: C 316 GLN cc_start: 0.8226 (tm-30) cc_final: 0.7983 (tm-30) REVERT: D 29 TYR cc_start: 0.8040 (m-80) cc_final: 0.7184 (t80) REVERT: D 58 GLN cc_start: 0.8564 (tt0) cc_final: 0.8055 (mt0) REVERT: D 61 MET cc_start: 0.8000 (ttm) cc_final: 0.7100 (tpt) REVERT: D 94 TRP cc_start: 0.7625 (t-100) cc_final: 0.6915 (m100) REVERT: E 58 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.8089 (mt0) REVERT: E 61 MET cc_start: 0.8052 (ttm) cc_final: 0.7236 (tpt) REVERT: E 94 TRP cc_start: 0.7552 (t-100) cc_final: 0.6933 (m100) REVERT: E 289 LYS cc_start: 0.8147 (mmmt) cc_final: 0.7903 (mmpt) REVERT: E 293 GLN cc_start: 0.8130 (tt0) cc_final: 0.7740 (mt0) outliers start: 29 outliers final: 14 residues processed: 155 average time/residue: 1.0979 time to fit residues: 187.6289 Evaluate side-chains 145 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 130 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain C residue 88 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 41 SER Chi-restraints excluded: chain D residue 219 SER Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 293 GLN Chi-restraints excluded: chain E residue 58 GLN Chi-restraints excluded: chain E residue 107 MET Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 249 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 2.9990 chunk 43 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 13 optimal weight: 9.9990 chunk 113 optimal weight: 6.9990 chunk 131 optimal weight: 0.9990 chunk 138 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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: 0.8164 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12997 Z= 0.186 Angle : 0.536 11.739 17665 Z= 0.259 Chirality : 0.041 0.154 1950 Planarity : 0.003 0.024 2194 Dihedral : 3.750 18.163 1700 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.80 % Allowed : 16.92 % Favored : 81.28 % 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: -0.12 (0.22), residues: 1510 helix: 0.71 (0.16), residues: 1110 sheet: None (None), residues: 0 loop : -2.27 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 229 HIS 0.002 0.000 HIS E 326 PHE 0.012 0.001 PHE A 248 TYR 0.012 0.001 TYR A 43 ARG 0.002 0.000 ARG B 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 160 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 135 time to evaluate : 1.364 Fit side-chains revert: symmetry clash REVERT: A 61 MET cc_start: 0.7828 (ttm) cc_final: 0.6883 (tpt) REVERT: A 94 TRP cc_start: 0.7512 (t-100) cc_final: 0.6846 (m100) REVERT: A 100 ILE cc_start: 0.8617 (mm) cc_final: 0.8095 (pt) REVERT: B 29 TYR cc_start: 0.8075 (m-80) cc_final: 0.7160 (t80) REVERT: B 58 GLN cc_start: 0.8543 (tt0) cc_final: 0.8176 (mt0) REVERT: B 61 MET cc_start: 0.8017 (ttm) cc_final: 0.7217 (tpt) REVERT: B 94 TRP cc_start: 0.7555 (t-100) cc_final: 0.6683 (t60) REVERT: B 293 GLN cc_start: 0.8205 (tt0) cc_final: 0.7904 (mt0) REVERT: C 29 TYR cc_start: 0.7994 (m-80) cc_final: 0.7097 (t80) REVERT: C 58 GLN cc_start: 0.8483 (tt0) cc_final: 0.7971 (mt0) REVERT: C 61 MET cc_start: 0.7789 (ttm) cc_final: 0.6873 (tpt) REVERT: C 94 TRP cc_start: 0.7361 (t-100) cc_final: 0.6700 (m100) REVERT: C 316 GLN cc_start: 0.8289 (tm-30) cc_final: 0.8078 (tm-30) REVERT: D 29 TYR cc_start: 0.7973 (m-80) cc_final: 0.7160 (t80) REVERT: D 58 GLN cc_start: 0.8573 (tt0) cc_final: 0.8077 (mt0) REVERT: D 61 MET cc_start: 0.8000 (ttm) cc_final: 0.7101 (tpt) REVERT: D 94 TRP cc_start: 0.7660 (t-100) cc_final: 0.6910 (m100) REVERT: E 58 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.8082 (mt0) REVERT: E 61 MET cc_start: 0.8058 (ttm) cc_final: 0.7210 (tpt) REVERT: E 94 TRP cc_start: 0.7547 (t-100) cc_final: 0.6907 (m100) REVERT: E 107 MET cc_start: 0.8294 (OUTLIER) cc_final: 0.8002 (ptp) REVERT: E 289 LYS cc_start: 0.8170 (mmmt) cc_final: 0.7922 (mmpt) REVERT: E 293 GLN cc_start: 0.8136 (tt0) cc_final: 0.7750 (mt0) outliers start: 25 outliers final: 12 residues processed: 152 average time/residue: 1.1321 time to fit residues: 189.0368 Evaluate side-chains 142 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 128 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 336 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 41 SER Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain E residue 58 GLN Chi-restraints excluded: chain E residue 107 MET Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 249 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 0.5980 chunk 138 optimal weight: 0.8980 chunk 81 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 chunk 105 optimal weight: 0.4980 chunk 41 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 88 optimal weight: 8.9990 chunk 142 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8123 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12997 Z= 0.123 Angle : 0.524 12.127 17665 Z= 0.251 Chirality : 0.039 0.146 1950 Planarity : 0.003 0.025 2194 Dihedral : 3.584 17.004 1700 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.94 % Allowed : 17.71 % Favored : 81.35 % 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: 0.22 (0.22), residues: 1510 helix: 0.95 (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 0.024 0.001 TRP B 229 HIS 0.002 0.000 HIS A 326 PHE 0.010 0.001 PHE E 248 TYR 0.012 0.001 TYR E 29 ARG 0.002 0.000 ARG C 255 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 150 time to evaluate : 1.313 Fit side-chains REVERT: A 61 MET cc_start: 0.7792 (ttm) cc_final: 0.6851 (tpt) REVERT: A 94 TRP cc_start: 0.7417 (t-100) cc_final: 0.6794 (m100) REVERT: A 100 ILE cc_start: 0.8570 (mm) cc_final: 0.8046 (pt) REVERT: B 58 GLN cc_start: 0.8498 (tt0) cc_final: 0.8123 (mt0) REVERT: B 61 MET cc_start: 0.8028 (ttm) cc_final: 0.7227 (tpt) REVERT: B 94 TRP cc_start: 0.7540 (t-100) cc_final: 0.6649 (t60) REVERT: C 58 GLN cc_start: 0.8399 (tt0) cc_final: 0.7944 (mt0) REVERT: C 61 MET cc_start: 0.7837 (ttm) cc_final: 0.6894 (tpt) REVERT: C 94 TRP cc_start: 0.7357 (t-100) cc_final: 0.6732 (m100) REVERT: C 229 TRP cc_start: 0.7724 (p-90) cc_final: 0.7454 (p-90) REVERT: C 316 GLN cc_start: 0.8337 (tm-30) cc_final: 0.8114 (tm-30) REVERT: D 29 TYR cc_start: 0.8026 (m-80) cc_final: 0.7125 (t80) REVERT: D 30 LYS cc_start: 0.4289 (mptt) cc_final: 0.3684 (mptt) REVERT: D 58 GLN cc_start: 0.8529 (tt0) cc_final: 0.8011 (mt0) REVERT: D 61 MET cc_start: 0.7977 (ttm) cc_final: 0.7083 (tpt) REVERT: D 94 TRP cc_start: 0.7565 (t-100) cc_final: 0.6839 (m100) REVERT: E 58 GLN cc_start: 0.8515 (tt0) cc_final: 0.8088 (mt0) REVERT: E 61 MET cc_start: 0.8030 (ttm) cc_final: 0.7187 (tpt) REVERT: E 94 TRP cc_start: 0.7504 (t-100) cc_final: 0.6904 (m100) REVERT: E 289 LYS cc_start: 0.8119 (mmmt) cc_final: 0.7877 (mmpt) REVERT: E 293 GLN cc_start: 0.8155 (tt0) cc_final: 0.7757 (mt0) outliers start: 13 outliers final: 6 residues processed: 157 average time/residue: 0.9918 time to fit residues: 173.1018 Evaluate side-chains 137 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 131 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 D residue 293 GLN Chi-restraints excluded: chain E residue 107 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 0.7980 chunk 99 optimal weight: 8.9990 chunk 149 optimal weight: 6.9990 chunk 137 optimal weight: 8.9990 chunk 118 optimal weight: 8.9990 chunk 12 optimal weight: 7.9990 chunk 91 optimal weight: 0.9990 chunk 72 optimal weight: 8.9990 chunk 94 optimal weight: 3.9990 chunk 126 optimal weight: 20.0000 chunk 36 optimal weight: 5.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 HIS ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12997 Z= 0.261 Angle : 0.575 12.321 17665 Z= 0.278 Chirality : 0.043 0.177 1950 Planarity : 0.003 0.036 2194 Dihedral : 3.679 16.888 1700 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.15 % Allowed : 18.57 % Favored : 80.27 % 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: 0.19 (0.22), residues: 1510 helix: 0.87 (0.16), residues: 1125 sheet: None (None), residues: 0 loop : -2.02 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 229 HIS 0.002 0.001 HIS B 178 PHE 0.013 0.001 PHE A 248 TYR 0.011 0.001 TYR B 29 ARG 0.003 0.000 ARG D 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 147 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 131 time to evaluate : 1.557 Fit side-chains REVERT: A 58 GLN cc_start: 0.8610 (mt0) cc_final: 0.7973 (mt0) REVERT: A 61 MET cc_start: 0.7830 (ttm) cc_final: 0.6886 (tpt) REVERT: A 94 TRP cc_start: 0.7543 (t-100) cc_final: 0.6874 (m100) REVERT: A 100 ILE cc_start: 0.8664 (mm) cc_final: 0.8188 (pt) REVERT: B 58 GLN cc_start: 0.8561 (tt0) cc_final: 0.8202 (mt0) REVERT: B 61 MET cc_start: 0.8027 (ttm) cc_final: 0.7228 (tpt) REVERT: B 94 TRP cc_start: 0.7526 (t-100) cc_final: 0.6640 (t60) REVERT: B 293 GLN cc_start: 0.8140 (tt0) cc_final: 0.7873 (tm-30) REVERT: C 58 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.7972 (mt0) REVERT: C 61 MET cc_start: 0.7799 (ttm) cc_final: 0.6883 (tpt) REVERT: C 94 TRP cc_start: 0.7336 (t-100) cc_final: 0.6674 (m100) REVERT: C 229 TRP cc_start: 0.7797 (p-90) cc_final: 0.7527 (p-90) REVERT: D 29 TYR cc_start: 0.8025 (m-80) cc_final: 0.7131 (t80) REVERT: D 30 LYS cc_start: 0.4427 (mptt) cc_final: 0.3751 (mptt) REVERT: D 58 GLN cc_start: 0.8506 (tt0) cc_final: 0.8034 (mt0) REVERT: D 61 MET cc_start: 0.8015 (ttm) cc_final: 0.7123 (tpt) REVERT: D 94 TRP cc_start: 0.7556 (t-100) cc_final: 0.6835 (m100) REVERT: E 58 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.8113 (mt0) REVERT: E 61 MET cc_start: 0.8069 (ttm) cc_final: 0.7223 (tpt) REVERT: E 94 TRP cc_start: 0.7573 (t-100) cc_final: 0.6939 (m100) REVERT: E 107 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.8071 (ptp) REVERT: E 289 LYS cc_start: 0.8163 (mmmt) cc_final: 0.7917 (mmpt) REVERT: E 293 GLN cc_start: 0.8157 (tt0) cc_final: 0.7762 (mt0) outliers start: 16 outliers final: 8 residues processed: 139 average time/residue: 1.0879 time to fit residues: 166.9105 Evaluate side-chains 138 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 127 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU 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 294 LEU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 293 GLN Chi-restraints excluded: chain E residue 58 GLN Chi-restraints excluded: chain E residue 107 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 chunk 33 optimal weight: 20.0000 chunk 119 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 104 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 86 optimal weight: 9.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.093932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.068659 restraints weight = 24946.296| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 3.47 r_work: 0.2781 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12997 Z= 0.162 Angle : 0.547 11.974 17665 Z= 0.264 Chirality : 0.041 0.178 1950 Planarity : 0.003 0.037 2194 Dihedral : 3.624 16.811 1700 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.08 % Allowed : 18.50 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.36 (0.22), residues: 1510 helix: 1.00 (0.16), residues: 1120 sheet: None (None), residues: 0 loop : -1.96 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 229 HIS 0.002 0.000 HIS D 326 PHE 0.011 0.001 PHE A 248 TYR 0.012 0.001 TYR B 29 ARG 0.002 0.000 ARG B 196 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3888.50 seconds wall clock time: 69 minutes 35.26 seconds (4175.26 seconds total)