Starting phenix.real_space_refine (version: 1.21rc1) on Sat Aug 12 20:59:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n24_9322/08_2023/6n24_9322_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n24_9322/08_2023/6n24_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_9322/08_2023/6n24_9322.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n24_9322/08_2023/6n24_9322.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n24_9322/08_2023/6n24_9322_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n24_9322/08_2023/6n24_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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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: 6.62, 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: 4.86 Conformation dependent library (CDL) restraints added in 1.8 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: 1.32 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: 3.22 Time building geometry restraints manager: 5.28 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: 0.120 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: 2.050 Check model and map are aligned: 0.190 Set scattering table: 0.130 Process input model: 34.010 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.930 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 1.627 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 318 average time/residue: 1.2469 time to fit residues: 430.3069 Evaluate side-chains 124 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 122 time to evaluate : 1.603 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 2 average time/residue: 0.1547 time to fit residues: 2.6380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 3.9990 chunk 113 optimal weight: 7.9990 chunk 63 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 60 optimal weight: 20.0000 chunk 117 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 B 133 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 12997 Z= 0.192 Angle : 0.594 8.383 17665 Z= 0.310 Chirality : 0.042 0.151 1950 Planarity : 0.005 0.031 2194 Dihedral : 4.635 25.335 1700 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer Outliers : 3.24 % 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: -3.69 (0.17), residues: 1510 helix: -2.10 (0.12), residues: 1095 sheet: None (None), residues: 0 loop : -2.89 (0.26), residues: 415 *********************** 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 219 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 174 time to evaluate : 1.504 Fit side-chains outliers start: 45 outliers final: 13 residues processed: 210 average time/residue: 1.1105 time to fit residues: 256.5924 Evaluate side-chains 147 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 134 time to evaluate : 1.609 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 12 residues processed: 1 average time/residue: 0.3255 time to fit residues: 2.5486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 113 optimal weight: 9.9990 chunk 92 optimal weight: 10.0000 chunk 37 optimal weight: 0.0370 chunk 136 optimal weight: 0.9980 chunk 147 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 overall best weight: 0.8060 ------------------------------------------------------------------------------- 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 B 133 ASN B 220 GLN B 256 GLN C 133 ASN E 133 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 12997 Z= 0.138 Angle : 0.524 10.318 17665 Z= 0.265 Chirality : 0.040 0.157 1950 Planarity : 0.003 0.026 2194 Dihedral : 4.234 24.088 1700 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer Outliers : 2.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.20), residues: 1510 helix: -0.88 (0.15), residues: 1085 sheet: None (None), residues: 0 loop : -2.74 (0.27), residues: 425 *********************** 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 196 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 156 time to evaluate : 1.632 Fit side-chains outliers start: 40 outliers final: 13 residues processed: 183 average time/residue: 1.0536 time to fit residues: 213.3637 Evaluate side-chains 139 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 126 time to evaluate : 1.521 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 13 residues processed: 0 time to fit residues: 2.0057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 136 optimal weight: 2.9990 chunk 144 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 129 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN C 133 ASN E 133 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 12997 Z= 0.217 Angle : 0.539 9.749 17665 Z= 0.270 Chirality : 0.042 0.132 1950 Planarity : 0.003 0.026 2194 Dihedral : 4.113 23.757 1700 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer Outliers : 3.24 % 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: -1.39 (0.21), residues: 1510 helix: -0.22 (0.16), residues: 1085 sheet: None (None), residues: 0 loop : -2.59 (0.28), residues: 425 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 128 time to evaluate : 1.545 Fit side-chains outliers start: 45 outliers final: 17 residues processed: 163 average time/residue: 1.0859 time to fit residues: 196.0882 Evaluate side-chains 132 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 115 time to evaluate : 1.461 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 17 residues processed: 0 time to fit residues: 1.9682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 9.9990 chunk 82 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 107 optimal weight: 8.9990 chunk 59 optimal weight: 0.7980 chunk 123 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 74 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 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 296 ASN B 238 GLN B 267 HIS C 256 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 12997 Z= 0.258 Angle : 0.552 10.177 17665 Z= 0.275 Chirality : 0.043 0.144 1950 Planarity : 0.003 0.027 2194 Dihedral : 4.074 21.951 1700 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer Outliers : 2.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.22), residues: 1510 helix: 0.16 (0.16), residues: 1085 sheet: None (None), residues: 0 loop : -2.45 (0.29), residues: 425 *********************** 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 163 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 123 time to evaluate : 1.491 Fit side-chains outliers start: 40 outliers final: 19 residues processed: 155 average time/residue: 1.0018 time to fit residues: 173.2921 Evaluate side-chains 132 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 113 time to evaluate : 1.587 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 18 residues processed: 1 average time/residue: 0.3108 time to fit residues: 2.6841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 7.9990 chunk 130 optimal weight: 3.9990 chunk 28 optimal weight: 0.0060 chunk 85 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 145 optimal weight: 8.9990 chunk 120 optimal weight: 10.0000 chunk 67 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 overall best weight: 2.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN C 267 HIS D 267 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 12997 Z= 0.196 Angle : 0.532 10.781 17665 Z= 0.262 Chirality : 0.041 0.145 1950 Planarity : 0.003 0.020 2194 Dihedral : 3.974 21.264 1700 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer Outliers : 2.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.22), residues: 1510 helix: 0.40 (0.16), residues: 1085 sheet: None (None), residues: 0 loop : -2.31 (0.29), residues: 425 *********************** 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 158 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 127 time to evaluate : 1.630 Fit side-chains outliers start: 31 outliers final: 18 residues processed: 153 average time/residue: 1.0568 time to fit residues: 179.6545 Evaluate side-chains 131 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 113 time to evaluate : 1.552 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 17 residues processed: 1 average time/residue: 1.2329 time to fit residues: 3.4955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 105 optimal weight: 0.7980 chunk 122 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 144 optimal weight: 1.9990 chunk 90 optimal weight: 20.0000 chunk 88 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 12997 Z= 0.248 Angle : 0.562 10.931 17665 Z= 0.275 Chirality : 0.043 0.135 1950 Planarity : 0.003 0.023 2194 Dihedral : 3.989 20.167 1700 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer Outliers : 2.38 % 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: -0.45 (0.22), residues: 1510 helix: 0.39 (0.16), residues: 1125 sheet: None (None), residues: 0 loop : -2.23 (0.29), residues: 385 *********************** 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 156 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 123 time to evaluate : 1.666 Fit side-chains outliers start: 33 outliers final: 20 residues processed: 150 average time/residue: 1.0848 time to fit residues: 180.1129 Evaluate side-chains 131 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 111 time to evaluate : 1.473 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 18 residues processed: 2 average time/residue: 0.6913 time to fit residues: 3.5952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 9.9990 chunk 43 optimal weight: 0.0980 chunk 28 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 113 optimal weight: 3.9990 chunk 131 optimal weight: 0.8980 chunk 138 optimal weight: 3.9990 chunk 126 optimal weight: 9.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN ** A 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 GLN ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 12997 Z= 0.158 Angle : 0.546 11.801 17665 Z= 0.265 Chirality : 0.040 0.138 1950 Planarity : 0.003 0.023 2194 Dihedral : 3.883 19.473 1700 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer Outliers : 2.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.22), residues: 1510 helix: 0.67 (0.16), residues: 1110 sheet: None (None), residues: 0 loop : -2.20 (0.29), residues: 400 *********************** 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 167 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 133 time to evaluate : 1.606 Fit side-chains outliers start: 34 outliers final: 22 residues processed: 159 average time/residue: 1.0391 time to fit residues: 184.1704 Evaluate side-chains 139 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 117 time to evaluate : 1.694 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 19 residues processed: 3 average time/residue: 0.5464 time to fit residues: 4.2214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 0.0000 chunk 138 optimal weight: 7.9990 chunk 81 optimal weight: 9.9990 chunk 58 optimal weight: 9.9990 chunk 105 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 142 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 overall best weight: 1.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN ** A 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN D 178 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 12997 Z= 0.178 Angle : 0.541 11.874 17665 Z= 0.264 Chirality : 0.041 0.163 1950 Planarity : 0.003 0.029 2194 Dihedral : 3.798 18.927 1700 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer Outliers : 2.16 % 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: 0.06 (0.22), residues: 1510 helix: 0.77 (0.16), residues: 1120 sheet: None (None), residues: 0 loop : -2.02 (0.29), residues: 390 *********************** 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 155 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 125 time to evaluate : 1.531 Fit side-chains outliers start: 30 outliers final: 21 residues processed: 149 average time/residue: 0.9621 time to fit residues: 160.8917 Evaluate side-chains 139 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 118 time to evaluate : 1.562 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 20 residues processed: 1 average time/residue: 1.1604 time to fit residues: 3.3164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 20.0000 chunk 99 optimal weight: 9.9990 chunk 149 optimal weight: 0.0870 chunk 137 optimal weight: 10.0000 chunk 118 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 72 optimal weight: 6.9990 chunk 94 optimal weight: 7.9990 chunk 126 optimal weight: 6.9990 chunk 36 optimal weight: 8.9990 overall best weight: 3.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 178 HIS C 96 GLN D 96 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.4123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 12997 Z= 0.225 Angle : 0.581 12.119 17665 Z= 0.278 Chirality : 0.042 0.128 1950 Planarity : 0.003 0.039 2194 Dihedral : 3.821 18.227 1700 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer Outliers : 1.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.22), residues: 1510 helix: 0.81 (0.16), residues: 1120 sheet: None (None), residues: 0 loop : -2.05 (0.29), residues: 390 ********************** 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 148 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 121 time to evaluate : 1.514 Fit side-chains outliers start: 27 outliers final: 22 residues processed: 144 average time/residue: 1.0041 time to fit residues: 161.4583 Evaluate side-chains 140 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 118 time to evaluate : 1.627 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 19 residues processed: 3 average time/residue: 0.5463 time to fit residues: 4.2746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 119 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 122 optimal weight: 0.0070 chunk 15 optimal weight: 9.9990 chunk 21 optimal weight: 0.9980 chunk 104 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 chunk 86 optimal weight: 9.9990 overall best weight: 3.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 GLN ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.089269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.064160 restraints weight = 25224.994| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 3.58 r_work: 0.2577 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 12997 Z= 0.220 Angle : 0.571 11.786 17665 Z= 0.276 Chirality : 0.042 0.176 1950 Planarity : 0.003 0.043 2194 Dihedral : 3.843 17.941 1700 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer Outliers : 1.80 % 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: 0.21 (0.22), residues: 1510 helix: 0.76 (0.16), residues: 1145 sheet: None (None), residues: 0 loop : -1.70 (0.30), residues: 365 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3755.49 seconds wall clock time: 67 minutes 42.30 seconds (4062.30 seconds total)