Starting phenix.real_space_refine on Fri Dec 8 11:37:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dpf_27633/12_2023/8dpf_27633_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dpf_27633/12_2023/8dpf_27633.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dpf_27633/12_2023/8dpf_27633_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dpf_27633/12_2023/8dpf_27633_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dpf_27633/12_2023/8dpf_27633_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dpf_27633/12_2023/8dpf_27633.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dpf_27633/12_2023/8dpf_27633.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dpf_27633/12_2023/8dpf_27633_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dpf_27633/12_2023/8dpf_27633_trim_updated.pdb" } resolution = 2.84 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= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 56 5.16 5 Cl 1 4.86 5 C 5236 2.51 5 N 1368 2.21 5 O 1499 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 157": "NH1" <-> "NH2" Residue "A GLU 161": "OE1" <-> "OE2" Residue "B GLU 8": "OE1" <-> "OE2" Residue "C PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 8160 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 1939 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 9, 'TRANS': 254} Chain breaks: 4 Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 205 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 80 Chain: "B" Number of atoms: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1683 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 6, 'TRANS': 214} Chain breaks: 2 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 101 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 5, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 88 Chain: "C" Number of atoms: 2479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2479 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 84 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 2, 'ARG:plan': 9, 'ASN:plan1': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 87 Chain: "D" Number of atoms: 284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 284 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 39} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1734 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 2 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'CLR': 1, 'T4U': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.92, per 1000 atoms: 0.60 Number of scatterers: 8160 At special positions: 0 Unit cell: (90.09, 120.12, 134.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 56 16.00 O 1499 8.00 N 1368 7.00 C 5236 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 127 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " 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: 3.10 Conformation dependent library (CDL) restraints added in 1.6 seconds 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2048 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 32 helices and 12 sheets defined 35.5% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'A' and resid 60 through 79 removed outlier: 3.588A pdb=" N MET A 66 " --> pdb=" O ILE A 63 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET A 76 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA A 77 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 105 removed outlier: 5.138A pdb=" N PHE A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N MET A 93 " --> pdb=" O ASN A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 116 removed outlier: 3.575A pdb=" N LEU A 111 " --> pdb=" O MET A 107 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 112 " --> pdb=" O PRO A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 157 removed outlier: 4.304A pdb=" N SER A 132 " --> pdb=" O PRO A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 165 Processing helix chain 'A' and resid 168 through 184 removed outlier: 3.902A pdb=" N MET A 173 " --> pdb=" O THR A 169 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLY A 184 " --> pdb=" O ALA A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 195 removed outlier: 3.925A pdb=" N VAL A 191 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG A 195 " --> pdb=" O VAL A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 199 No H-bonds generated for 'chain 'A' and resid 197 through 199' Processing helix chain 'A' and resid 212 through 222 removed outlier: 4.456A pdb=" N ILE A 217 " --> pdb=" O ASN A 213 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER A 219 " --> pdb=" O VAL A 215 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N PHE A 220 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL A 221 " --> pdb=" O ILE A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 246 removed outlier: 3.506A pdb=" N THR A 228 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA A 245 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LEU A 246 " --> pdb=" O ARG A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 336 removed outlier: 4.329A pdb=" N GLU A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG A 307 " --> pdb=" O ILE A 303 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS A 308 " --> pdb=" O ASN A 304 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA A 309 " --> pdb=" O ASN A 305 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER A 310 " --> pdb=" O GLU A 306 " (cutoff:3.500A) Proline residue: A 326 - end of helix removed outlier: 3.851A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 361 removed outlier: 3.603A pdb=" N VAL A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N TRP A 355 " --> pdb=" O ASN A 351 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE A 356 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY A 357 " --> pdb=" O PHE A 353 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N SER A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 367 No H-bonds generated for 'chain 'A' and resid 364 through 367' Processing helix chain 'A' and resid 373 through 382 Processing helix chain 'B' and resid 7 through 32 removed outlier: 3.831A pdb=" N GLU B 28 " --> pdb=" O ARG B 24 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LYS B 29 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA B 30 " --> pdb=" O ASP B 26 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ARG B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 48 No H-bonds generated for 'chain 'B' and resid 46 through 48' Processing helix chain 'B' and resid 96 through 100 removed outlier: 3.595A pdb=" N CYS B 99 " --> pdb=" O TRP B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 129 removed outlier: 3.655A pdb=" N LEU B 118 " --> pdb=" O TYR B 115 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N GLN B 119 " --> pdb=" O ASN B 116 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU B 120 " --> pdb=" O ARG B 117 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TRP B 129 " --> pdb=" O LYS B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 134 No H-bonds generated for 'chain 'B' and resid 132 through 134' Processing helix chain 'B' and resid 146 through 155 Processing helix chain 'B' and resid 160 through 162 No H-bonds generated for 'chain 'B' and resid 160 through 162' Processing helix chain 'B' and resid 165 through 169 Processing helix chain 'B' and resid 186 through 203 removed outlier: 4.197A pdb=" N ILE B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER B 201 " --> pdb=" O PHE B 197 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA B 203 " --> pdb=" O ASP B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 242 Processing helix chain 'C' and resid 7 through 25 removed outlier: 4.126A pdb=" N CYS C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 36 removed outlier: 4.538A pdb=" N ASN C 35 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N ASN C 36 " --> pdb=" O GLN C 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 23 Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'D' and resid 45 through 47 No H-bonds generated for 'chain 'D' and resid 45 through 47' Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'B' and resid 211 through 215 removed outlier: 7.255A pdb=" N VAL B 139 " --> pdb=" O TYR B 212 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N HIS B 214 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU B 141 " --> pdb=" O HIS B 214 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ALA B 105 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ASN B 80 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N LEU B 36 " --> pdb=" O ASN B 80 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N HIS B 82 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LEU B 38 " --> pdb=" O HIS B 82 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N PHE B 84 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N GLY B 40 " --> pdb=" O PHE B 84 " (cutoff:3.500A) removed outlier: 8.915A pdb=" N VAL B 86 " --> pdb=" O GLY B 40 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE B 74 " --> pdb=" O PHE B 81 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.834A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 100 through 105 removed outlier: 7.002A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG C 137 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.769A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.664A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA C 203 " --> pdb=" O SER C 207 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N SER C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.734A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 273 through 278 removed outlier: 6.365A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N PHE C 278 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N LEU C 284 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.714A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.817A pdb=" N SER E 21 " --> pdb=" O SER E 7 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.655A pdb=" N ALA E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ALA E 40 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N LEU E 45 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.975A pdb=" N LYS E 232 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY E 213 " --> pdb=" O LEU E 233 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE E 177 " --> pdb=" O TRP E 164 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 143 through 148 357 hydrogen bonds defined for protein. 897 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: 2.42 Time building geometry restraints manager: 3.30 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: 2618 1.34 - 1.46: 1981 1.46 - 1.58: 3645 1.58 - 1.70: 0 1.70 - 1.82: 84 Bond restraints: 8328 Sorted by residual: bond pdb=" N ILE A 156 " pdb=" CA ILE A 156 " ideal model delta sigma weight residual 1.460 1.507 -0.047 1.32e-02 5.74e+03 1.26e+01 bond pdb=" C ASN A 158 " pdb=" N PRO A 159 " ideal model delta sigma weight residual 1.335 1.369 -0.034 1.36e-02 5.41e+03 6.29e+00 bond pdb=" C GLU E 222 " pdb=" N TYR E 223 " ideal model delta sigma weight residual 1.331 1.290 0.041 2.07e-02 2.33e+03 3.85e+00 bond pdb=" N ASN A 158 " pdb=" CA ASN A 158 " ideal model delta sigma weight residual 1.461 1.479 -0.018 1.07e-02 8.73e+03 2.81e+00 bond pdb=" N ARG A 157 " pdb=" CA ARG A 157 " ideal model delta sigma weight residual 1.459 1.479 -0.021 1.28e-02 6.10e+03 2.58e+00 ... (remaining 8323 not shown) Histogram of bond angle deviations from ideal: 99.46 - 106.38: 194 106.38 - 113.29: 4525 113.29 - 120.21: 3007 120.21 - 127.12: 3538 127.12 - 134.04: 87 Bond angle restraints: 11351 Sorted by residual: angle pdb=" CA ASN A 158 " pdb=" C ASN A 158 " pdb=" N PRO A 159 " ideal model delta sigma weight residual 117.73 123.68 -5.95 1.04e+00 9.25e-01 3.28e+01 angle pdb=" O ALA A 155 " pdb=" C ALA A 155 " pdb=" N ILE A 156 " ideal model delta sigma weight residual 122.22 117.21 5.01 1.17e+00 7.31e-01 1.83e+01 angle pdb=" C07 T4U A 501 " pdb=" C08 T4U A 501 " pdb=" C11 T4U A 501 " ideal model delta sigma weight residual 111.03 123.85 -12.82 3.00e+00 1.11e-01 1.83e+01 angle pdb=" C08 T4U A 501 " pdb=" C11 T4U A 501 " pdb=" C09 T4U A 501 " ideal model delta sigma weight residual 111.00 122.66 -11.66 3.00e+00 1.11e-01 1.51e+01 angle pdb=" CA ASN A 158 " pdb=" C ASN A 158 " pdb=" O ASN A 158 " ideal model delta sigma weight residual 120.80 115.72 5.08 1.32e+00 5.74e-01 1.48e+01 ... (remaining 11346 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.94: 4872 34.94 - 69.89: 33 69.89 - 104.83: 8 104.83 - 139.78: 0 139.78 - 174.72: 1 Dihedral angle restraints: 4914 sinusoidal: 1750 harmonic: 3164 Sorted by residual: dihedral pdb=" CA ALA E 131 " pdb=" C ALA E 131 " pdb=" N THR E 132 " pdb=" CA THR E 132 " ideal model delta harmonic sigma weight residual 180.00 135.65 44.35 0 5.00e+00 4.00e-02 7.87e+01 dihedral pdb=" C09 T4U A 501 " pdb=" C04 T4U A 501 " pdb=" C05 T4U A 501 " pdb=" N13 T4U A 501 " ideal model delta sinusoidal sigma weight residual 93.19 -81.53 174.72 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CA PHE A 223 " pdb=" C PHE A 223 " pdb=" N PHE A 224 " pdb=" CA PHE A 224 " ideal model delta harmonic sigma weight residual -180.00 -158.42 -21.58 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 4911 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.372: 1345 0.372 - 0.745: 0 0.745 - 1.117: 0 1.117 - 1.489: 0 1.489 - 1.862: 1 Chirality restraints: 1346 Sorted by residual: chirality pdb=" C08 T4U A 501 " pdb=" C01 T4U A 501 " pdb=" C07 T4U A 501 " pdb=" C11 T4U A 501 " both_signs ideal model delta sigma weight residual False -2.75 -0.89 -1.86 2.00e-01 2.50e+01 8.67e+01 chirality pdb=" CB ILE A 156 " pdb=" CA ILE A 156 " pdb=" CG1 ILE A 156 " pdb=" CG2 ILE A 156 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.77e-01 chirality pdb=" CA PRO C 236 " pdb=" N PRO C 236 " pdb=" C PRO C 236 " pdb=" CB PRO C 236 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.25e-01 ... (remaining 1343 not shown) Planarity restraints: 1424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 155 " 0.012 2.00e-02 2.50e+03 2.33e-02 5.42e+00 pdb=" C ALA A 155 " -0.040 2.00e-02 2.50e+03 pdb=" O ALA A 155 " 0.014 2.00e-02 2.50e+03 pdb=" N ILE A 156 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 151 " 0.014 2.00e-02 2.50e+03 1.19e-02 2.47e+00 pdb=" CG PHE C 151 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE C 151 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE C 151 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE C 151 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE C 151 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE C 151 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 193 " -0.026 5.00e-02 4.00e+02 3.90e-02 2.44e+00 pdb=" N PRO C 194 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO C 194 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 194 " -0.022 5.00e-02 4.00e+02 ... (remaining 1421 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 50 2.65 - 3.22: 7174 3.22 - 3.78: 11462 3.78 - 4.34: 16050 4.34 - 4.90: 27154 Nonbonded interactions: 61890 Sorted by model distance: nonbonded pdb=" OD2 ASP A 151 " pdb=" OH TYR B 243 " model vdw 2.093 2.440 nonbonded pdb=" OG SER C 245 " pdb=" OD1 ASP C 247 " model vdw 2.274 2.440 nonbonded pdb=" OG SER E 134 " pdb=" OE1 GLU E 234 " model vdw 2.328 2.440 nonbonded pdb=" NH2 ARG E 98 " pdb=" OD2 ASP E 109 " model vdw 2.346 2.520 nonbonded pdb=" OE1 GLN C 176 " pdb=" OG1 THR C 179 " model vdw 2.367 2.440 ... (remaining 61885 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.320 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: 5.170 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 25.570 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 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 : 0.004 0.047 8328 Z= 0.291 Angle : 0.767 12.823 11351 Z= 0.414 Chirality : 0.069 1.862 1346 Planarity : 0.005 0.039 1424 Dihedral : 11.099 174.719 2860 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.12 % Allowed : 0.37 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 1.40 (0.25), residues: 1065 helix: 1.51 (0.29), residues: 326 sheet: 1.31 (0.30), residues: 271 loop : 0.40 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP C 63 HIS 0.008 0.002 HIS E 220 PHE 0.027 0.003 PHE C 151 TYR 0.017 0.002 TYR A 375 ARG 0.007 0.001 ARG B 132 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 194 time to evaluate : 0.962 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 194 average time/residue: 0.9325 time to fit residues: 194.5343 Evaluate side-chains 172 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 0.814 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.5980 chunk 81 optimal weight: 10.0000 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN B 223 ASN B 244 ASN C 75 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8328 Z= 0.254 Angle : 0.635 10.921 11351 Z= 0.341 Chirality : 0.045 0.190 1346 Planarity : 0.005 0.048 1424 Dihedral : 8.206 170.244 1231 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.32 % Allowed : 7.07 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.19 (0.25), residues: 1065 helix: 1.45 (0.29), residues: 337 sheet: 1.17 (0.31), residues: 272 loop : 0.14 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 130 HIS 0.011 0.002 HIS B 209 PHE 0.018 0.002 PHE C 199 TYR 0.010 0.002 TYR A 375 ARG 0.005 0.001 ARG B 185 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 176 time to evaluate : 0.914 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 8 residues processed: 184 average time/residue: 0.9602 time to fit residues: 189.7805 Evaluate side-chains 178 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 170 time to evaluate : 0.884 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 3 residues processed: 5 average time/residue: 0.7341 time to fit residues: 5.2106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 98 optimal weight: 0.7980 chunk 106 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 33 optimal weight: 0.0050 chunk 78 optimal weight: 2.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN B 244 ASN C 239 ASN C 295 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8328 Z= 0.199 Angle : 0.566 10.671 11351 Z= 0.303 Chirality : 0.044 0.171 1346 Planarity : 0.005 0.051 1424 Dihedral : 7.904 171.040 1231 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.68 % Allowed : 9.27 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.04 (0.26), residues: 1065 helix: 1.34 (0.29), residues: 348 sheet: 1.10 (0.32), residues: 275 loop : -0.01 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 130 HIS 0.009 0.001 HIS B 209 PHE 0.016 0.002 PHE C 199 TYR 0.007 0.001 TYR A 375 ARG 0.005 0.000 ARG B 185 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 172 time to evaluate : 0.967 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 12 residues processed: 181 average time/residue: 0.9973 time to fit residues: 193.5564 Evaluate side-chains 179 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 167 time to evaluate : 0.906 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 6 residues processed: 6 average time/residue: 0.7556 time to fit residues: 6.1678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 50 optimal weight: 0.3980 chunk 10 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 98 optimal weight: 0.3980 chunk 104 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 28 optimal weight: 0.0070 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN B 244 ASN C 239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8328 Z= 0.186 Angle : 0.540 10.725 11351 Z= 0.287 Chirality : 0.043 0.171 1346 Planarity : 0.004 0.053 1424 Dihedral : 7.716 172.793 1231 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.20 % Allowed : 11.59 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.09 (0.26), residues: 1065 helix: 1.38 (0.29), residues: 350 sheet: 1.33 (0.31), residues: 285 loop : -0.20 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 130 HIS 0.007 0.001 HIS B 209 PHE 0.014 0.002 PHE C 151 TYR 0.007 0.001 TYR E 216 ARG 0.006 0.000 ARG B 185 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 174 time to evaluate : 0.938 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 7 residues processed: 182 average time/residue: 1.0086 time to fit residues: 196.5377 Evaluate side-chains 173 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 166 time to evaluate : 0.884 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 3 average time/residue: 1.0676 time to fit residues: 4.6302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.7980 chunk 59 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 43 optimal weight: 0.0670 chunk 89 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 0 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN B 223 ASN B 244 ASN C 239 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8328 Z= 0.199 Angle : 0.546 10.715 11351 Z= 0.288 Chirality : 0.043 0.177 1346 Planarity : 0.004 0.053 1424 Dihedral : 7.679 173.884 1231 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.20 % Allowed : 13.05 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.05 (0.26), residues: 1065 helix: 1.40 (0.29), residues: 350 sheet: 1.36 (0.32), residues: 279 loop : -0.28 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 130 HIS 0.008 0.001 HIS B 209 PHE 0.016 0.002 PHE C 151 TYR 0.008 0.001 TYR A 153 ARG 0.006 0.000 ARG B 185 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 170 time to evaluate : 0.997 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 10 residues processed: 178 average time/residue: 1.0866 time to fit residues: 206.5018 Evaluate side-chains 180 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 170 time to evaluate : 0.930 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 4 residues processed: 6 average time/residue: 0.4640 time to fit residues: 4.4404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 20 optimal weight: 0.0980 chunk 61 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 chunk 8 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN B 223 ASN B 244 ASN C 239 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8328 Z= 0.256 Angle : 0.596 10.725 11351 Z= 0.312 Chirality : 0.044 0.188 1346 Planarity : 0.005 0.061 1424 Dihedral : 7.760 175.101 1231 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.59 % Allowed : 13.41 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.85 (0.26), residues: 1065 helix: 1.18 (0.29), residues: 355 sheet: 1.26 (0.32), residues: 275 loop : -0.35 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 130 HIS 0.009 0.001 HIS B 209 PHE 0.019 0.002 PHE C 151 TYR 0.009 0.001 TYR A 375 ARG 0.006 0.000 ARG B 185 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 174 time to evaluate : 0.884 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 180 average time/residue: 1.1035 time to fit residues: 211.5653 Evaluate side-chains 176 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 169 time to evaluate : 0.802 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 3 residues processed: 4 average time/residue: 0.8536 time to fit residues: 4.8324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 48 optimal weight: 9.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN B 223 ASN C 75 GLN C 239 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8328 Z= 0.254 Angle : 0.592 10.710 11351 Z= 0.309 Chirality : 0.044 0.191 1346 Planarity : 0.005 0.054 1424 Dihedral : 7.779 175.606 1231 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.71 % Allowed : 14.27 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.78 (0.26), residues: 1065 helix: 1.10 (0.29), residues: 358 sheet: 1.22 (0.32), residues: 270 loop : -0.37 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 130 HIS 0.009 0.002 HIS B 209 PHE 0.019 0.002 PHE C 151 TYR 0.010 0.001 TYR E 59 ARG 0.004 0.000 ARG B 185 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 171 time to evaluate : 0.804 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 178 average time/residue: 1.1031 time to fit residues: 210.6594 Evaluate side-chains 176 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 170 time to evaluate : 0.904 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 3 residues processed: 3 average time/residue: 1.1626 time to fit residues: 4.9481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 9 optimal weight: 0.3980 chunk 81 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN B 223 ASN C 75 GLN C 239 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8328 Z= 0.279 Angle : 0.623 10.715 11351 Z= 0.323 Chirality : 0.045 0.193 1346 Planarity : 0.005 0.061 1424 Dihedral : 7.822 175.592 1231 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.59 % Allowed : 14.51 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.67 (0.26), residues: 1065 helix: 1.04 (0.29), residues: 358 sheet: 1.19 (0.32), residues: 270 loop : -0.48 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 130 HIS 0.010 0.002 HIS B 209 PHE 0.020 0.002 PHE C 151 TYR 0.010 0.002 TYR C 289 ARG 0.004 0.000 ARG B 185 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 174 time to evaluate : 0.889 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 179 average time/residue: 1.1295 time to fit residues: 215.4468 Evaluate side-chains 177 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 169 time to evaluate : 0.934 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 4 residues processed: 4 average time/residue: 1.3178 time to fit residues: 6.7826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN B 223 ASN C 75 GLN C 239 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8328 Z= 0.251 Angle : 0.605 10.708 11351 Z= 0.314 Chirality : 0.044 0.190 1346 Planarity : 0.005 0.054 1424 Dihedral : 7.793 175.766 1231 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.98 % Allowed : 15.98 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.68 (0.26), residues: 1065 helix: 1.05 (0.29), residues: 357 sheet: 1.25 (0.32), residues: 268 loop : -0.50 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 130 HIS 0.008 0.001 HIS B 209 PHE 0.018 0.002 PHE C 151 TYR 0.010 0.001 TYR E 59 ARG 0.004 0.000 ARG B 185 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 173 time to evaluate : 1.023 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 178 average time/residue: 1.1415 time to fit residues: 216.1505 Evaluate side-chains 178 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 172 time to evaluate : 0.867 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 0.2166 time to fit residues: 1.4930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 71 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 52 optimal weight: 0.0270 chunk 68 optimal weight: 0.6980 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN B 223 ASN C 75 GLN C 239 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8328 Z= 0.250 Angle : 0.606 11.192 11351 Z= 0.314 Chirality : 0.044 0.191 1346 Planarity : 0.005 0.055 1424 Dihedral : 7.837 176.084 1231 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.10 % Allowed : 15.85 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.65 (0.26), residues: 1065 helix: 1.04 (0.29), residues: 357 sheet: 1.30 (0.32), residues: 268 loop : -0.58 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 130 HIS 0.009 0.002 HIS B 209 PHE 0.019 0.002 PHE C 151 TYR 0.009 0.001 TYR E 59 ARG 0.004 0.000 ARG B 185 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 179 time to evaluate : 0.945 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 8 residues processed: 184 average time/residue: 1.1480 time to fit residues: 224.4401 Evaluate side-chains 185 residues out of total 943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 177 time to evaluate : 0.850 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 4 residues processed: 4 average time/residue: 1.0271 time to fit residues: 5.6145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 85 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 88 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN B 223 ASN C 75 GLN C 239 ASN C 340 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.124070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.110005 restraints weight = 12200.501| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.79 r_work: 0.3345 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8328 Z= 0.253 Angle : 0.611 11.844 11351 Z= 0.315 Chirality : 0.044 0.193 1346 Planarity : 0.005 0.054 1424 Dihedral : 7.819 176.274 1231 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.22 % Allowed : 16.34 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.63 (0.26), residues: 1065 helix: 1.05 (0.29), residues: 357 sheet: 1.24 (0.32), residues: 269 loop : -0.60 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 130 HIS 0.009 0.002 HIS B 209 PHE 0.019 0.002 PHE C 151 TYR 0.009 0.001 TYR E 59 ARG 0.004 0.000 ARG B 185 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3718.87 seconds wall clock time: 66 minutes 26.40 seconds (3986.40 seconds total)