Starting phenix.real_space_refine on Fri Dec 8 12:04:16 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7um5_26597/12_2023/7um5_26597_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7um5_26597/12_2023/7um5_26597.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7um5_26597/12_2023/7um5_26597_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7um5_26597/12_2023/7um5_26597_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7um5_26597/12_2023/7um5_26597_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7um5_26597/12_2023/7um5_26597.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7um5_26597/12_2023/7um5_26597.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7um5_26597/12_2023/7um5_26597_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7um5_26597/12_2023/7um5_26597_updated.pdb" } resolution = 2.73 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= 0.002 sd= 0.027 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 58 5.16 5 C 5287 2.51 5 N 1397 2.21 5 O 1535 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 8277 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2000 Classifications: {'peptide': 268} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 10, 'TRANS': 257} Chain breaks: 1 Unresolved non-hydrogen bonds: 148 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 100 Chain: "B" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1673 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 2497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2497 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'ARG:plan': 6, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 80 Chain: "D" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 372 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 49} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "E" Number of atoms: 1719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1719 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'8K3': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 5.20, per 1000 atoms: 0.63 Number of scatterers: 8277 At special positions: 0 Unit cell: (91.91, 123.76, 126.49, 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 58 16.00 O 1535 8.00 N 1397 7.00 C 5287 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 114 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.03 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: 2.98 Conformation dependent library (CDL) restraints added in 1.6 seconds 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2064 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 14 sheets defined 33.1% alpha, 22.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.65 Creating SS restraints... Processing helix chain 'A' and resid 42 through 67 removed outlier: 3.741A pdb=" N PHE A 55 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA A 56 " --> pdb=" O ALA A 52 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN A 58 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 59 " --> pdb=" O PHE A 55 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL A 61 " --> pdb=" O TRP A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 92 removed outlier: 3.568A pdb=" N ASN A 77 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU A 78 " --> pdb=" O PRO A 75 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER A 81 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER A 85 " --> pdb=" O MET A 82 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A 91 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU A 92 " --> pdb=" O VAL A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 102 removed outlier: 4.058A pdb=" N VAL A 99 " --> pdb=" O PRO A 95 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N HIS A 100 " --> pdb=" O LEU A 96 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLU A 101 " --> pdb=" O SER A 97 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LEU A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 144 removed outlier: 4.227A pdb=" N GLN A 115 " --> pdb=" O ARG A 111 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU A 116 " --> pdb=" O ARG A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 178 removed outlier: 3.531A pdb=" N VAL A 157 " --> pdb=" O THR A 153 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TRP A 166 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER A 169 " --> pdb=" O THR A 165 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE A 172 " --> pdb=" O LEU A 168 " (cutoff:3.500A) Proline residue: A 176 - end of helix Processing helix chain 'A' and resid 188 through 190 No H-bonds generated for 'chain 'A' and resid 188 through 190' Processing helix chain 'A' and resid 198 through 208 removed outlier: 3.562A pdb=" N THR A 205 " --> pdb=" O ALA A 201 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL A 206 " --> pdb=" O VAL A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 230 removed outlier: 3.638A pdb=" N CYS A 214 " --> pdb=" O TYR A 210 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 307 removed outlier: 3.503A pdb=" N VAL A 287 " --> pdb=" O ALA A 283 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TRP A 298 " --> pdb=" O PHE A 294 " (cutoff:3.500A) Proline residue: A 300 - end of helix removed outlier: 3.934A pdb=" N THR A 304 " --> pdb=" O PRO A 300 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU A 306 " --> pdb=" O PHE A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 333 removed outlier: 3.500A pdb=" N SER A 321 " --> pdb=" O ALA A 317 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU A 324 " --> pdb=" O LYS A 320 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 326 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLY A 327 " --> pdb=" O PHE A 323 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N SER A 331 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N PHE A 332 " --> pdb=" O TYR A 328 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE A 333 " --> pdb=" O SER A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 338 No H-bonds generated for 'chain 'A' and resid 335 through 338' Processing helix chain 'A' and resid 343 through 351 removed outlier: 3.638A pdb=" N SER A 347 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA A 348 " --> pdb=" O ASN A 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 28 removed outlier: 3.572A pdb=" N GLU B 11 " --> pdb=" O LYS B 7 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG B 12 " --> pdb=" O ALA B 8 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER B 26 " --> pdb=" O GLU B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 92 No H-bonds generated for 'chain 'B' and resid 90 through 92' Processing helix chain 'B' and resid 94 through 97 removed outlier: 3.531A pdb=" N PHE B 97 " --> pdb=" O ILE B 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 94 through 97' Processing helix chain 'B' and resid 118 through 126 Processing helix chain 'B' and resid 129 through 131 No H-bonds generated for 'chain 'B' and resid 129 through 131' Processing helix chain 'B' and resid 143 through 148 removed outlier: 3.577A pdb=" N GLU B 148 " --> pdb=" O ASP B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 182 removed outlier: 4.274A pdb=" N LYS B 182 " --> pdb=" O GLN B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 222 Processing helix chain 'C' and resid 4 through 25 removed outlier: 3.678A pdb=" N GLU C 12 " --> pdb=" O ARG C 8 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN C 17 " --> pdb=" O GLN C 13 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 35 Processing helix chain 'C' and resid 129 through 131 No H-bonds generated for 'chain 'C' and resid 129 through 131' Processing helix chain 'D' and resid 9 through 22 removed outlier: 3.693A pdb=" N GLU D 17 " --> pdb=" O ARG D 13 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN D 18 " --> pdb=" O LYS D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 42 removed outlier: 3.597A pdb=" N TYR D 40 " --> pdb=" O ASP D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 47 No H-bonds generated for 'chain 'D' and resid 45 through 47' Processing helix chain 'D' and resid 56 through 58 No H-bonds generated for 'chain 'D' and resid 56 through 58' 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 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 190 through 194 removed outlier: 6.883A pdb=" N ILE B 136 " --> pdb=" O TYR B 191 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N HIS B 193 " --> pdb=" O ILE B 136 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU B 138 " --> pdb=" O HIS B 193 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ALA B 102 " --> pdb=" O LYS B 32 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.939A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU C 70 " --> pdb=" O TRP C 82 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.182A 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: 6.870A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG C 137 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.200A 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: 6.885A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.091A 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: 6.825A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.399A 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: 6.599A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 5.890A 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: 6.494A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N PHE C 278 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU C 284 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 46 through 51 removed outlier: 6.674A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N CYS C 317 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.552A pdb=" N ALA E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 96 through 98 removed outlier: 4.335A pdb=" N CYS E 96 " --> pdb=" O GLY E 112 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.575A pdb=" N LYS E 232 " --> pdb=" O VAL E 135 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'E' and resid 143 through 148 Processing sheet with id= N, first strand: chain 'E' and resid 214 through 218 removed outlier: 3.511A pdb=" N ILE E 177 " --> pdb=" O TRP E 164 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) 342 hydrogen bonds defined for protein. 936 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: 3.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1337 1.31 - 1.43: 2362 1.43 - 1.56: 4678 1.56 - 1.69: 0 1.69 - 1.81: 80 Bond restraints: 8457 Sorted by residual: bond pdb=" CA SER A 128 " pdb=" CB SER A 128 " ideal model delta sigma weight residual 1.528 1.468 0.061 1.59e-02 3.96e+03 1.46e+01 bond pdb=" C PRO A 335 " pdb=" O PRO A 335 " ideal model delta sigma weight residual 1.238 1.194 0.044 1.37e-02 5.33e+03 1.01e+01 bond pdb=" C ASN A 334 " pdb=" N PRO A 335 " ideal model delta sigma weight residual 1.337 1.369 -0.033 1.11e-02 8.12e+03 8.78e+00 bond pdb=" N ASN A 334 " pdb=" CA ASN A 334 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.41e-02 5.03e+03 5.31e+00 bond pdb=" N SER A 331 " pdb=" CA SER A 331 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.35e-02 5.49e+03 5.11e+00 ... (remaining 8452 not shown) Histogram of bond angle deviations from ideal: 100.18 - 106.98: 199 106.98 - 113.77: 4724 113.77 - 120.57: 3290 120.57 - 127.37: 3209 127.37 - 134.16: 99 Bond angle restraints: 11521 Sorted by residual: angle pdb=" C03 8K3 A 401 " pdb=" C04 8K3 A 401 " pdb=" C05 8K3 A 401 " ideal model delta sigma weight residual 112.74 126.32 -13.58 3.00e+00 1.11e-01 2.05e+01 angle pdb=" C03 8K3 A 401 " pdb=" C04 8K3 A 401 " pdb=" C08 8K3 A 401 " ideal model delta sigma weight residual 139.25 125.75 13.50 3.00e+00 1.11e-01 2.03e+01 angle pdb=" C PHE A 179 " pdb=" CA PHE A 179 " pdb=" CB PHE A 179 " ideal model delta sigma weight residual 110.42 118.15 -7.73 1.99e+00 2.53e-01 1.51e+01 angle pdb=" CA ASN A 334 " pdb=" C ASN A 334 " pdb=" N PRO A 335 " ideal model delta sigma weight residual 118.44 123.88 -5.44 1.59e+00 3.96e-01 1.17e+01 angle pdb=" CA PRO A 75 " pdb=" N PRO A 75 " pdb=" CD PRO A 75 " ideal model delta sigma weight residual 112.00 107.39 4.61 1.40e+00 5.10e-01 1.08e+01 ... (remaining 11516 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 4596 17.33 - 34.66: 272 34.66 - 52.00: 56 52.00 - 69.33: 5 69.33 - 86.66: 5 Dihedral angle restraints: 4934 sinusoidal: 1737 harmonic: 3197 Sorted by residual: dihedral pdb=" CB CYS E 147 " pdb=" SG CYS E 147 " pdb=" SG CYS E 217 " pdb=" CB CYS E 217 " ideal model delta sinusoidal sigma weight residual 93.00 157.54 -64.54 1 1.00e+01 1.00e-02 5.47e+01 dihedral pdb=" CA LEU A 178 " pdb=" C LEU A 178 " pdb=" N PHE A 179 " pdb=" CA PHE A 179 " ideal model delta harmonic sigma weight residual 180.00 159.55 20.45 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA HIS B 116 " pdb=" C HIS B 116 " pdb=" N GLU B 117 " pdb=" CA GLU B 117 " ideal model delta harmonic sigma weight residual 180.00 163.37 16.63 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 4931 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 906 0.036 - 0.073: 313 0.073 - 0.109: 84 0.109 - 0.145: 34 0.145 - 0.182: 3 Chirality restraints: 1340 Sorted by residual: chirality pdb=" CA LEU A 177 " pdb=" N LEU A 177 " pdb=" C LEU A 177 " pdb=" CB LEU A 177 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.24e-01 chirality pdb=" CA LEU A 336 " pdb=" N LEU A 336 " pdb=" C LEU A 336 " pdb=" CB LEU A 336 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.97e-01 chirality pdb=" CA TRP A 57 " pdb=" N TRP A 57 " pdb=" C TRP A 57 " pdb=" CB TRP A 57 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.81e-01 ... (remaining 1337 not shown) Planarity restraints: 1454 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 74 " 0.044 5.00e-02 4.00e+02 6.54e-02 6.85e+00 pdb=" N PRO A 75 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 75 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 75 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER A 329 " 0.012 2.00e-02 2.50e+03 2.36e-02 5.58e+00 pdb=" C SER A 329 " -0.041 2.00e-02 2.50e+03 pdb=" O SER A 329 " 0.015 2.00e-02 2.50e+03 pdb=" N ASN A 330 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 333 " 0.010 2.00e-02 2.50e+03 1.95e-02 3.82e+00 pdb=" C PHE A 333 " -0.034 2.00e-02 2.50e+03 pdb=" O PHE A 333 " 0.013 2.00e-02 2.50e+03 pdb=" N ASN A 334 " 0.012 2.00e-02 2.50e+03 ... (remaining 1451 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2164 2.80 - 3.33: 7020 3.33 - 3.85: 12351 3.85 - 4.38: 14562 4.38 - 4.90: 26167 Nonbonded interactions: 62264 Sorted by model distance: nonbonded pdb=" O LEU A 42 " pdb=" OG1 THR A 45 " model vdw 2.281 2.440 nonbonded pdb=" NH1 ARG E 190 " pdb=" OD2 ASP E 211 " model vdw 2.285 2.520 nonbonded pdb=" O THR B 134 " pdb=" NZ LYS B 188 " model vdw 2.314 2.520 nonbonded pdb=" OD1 ASP C 254 " pdb=" N LEU C 255 " model vdw 2.331 2.520 nonbonded pdb=" OD1 ASP A 138 " pdb=" OH TYR A 149 " model vdw 2.354 2.440 ... (remaining 62259 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: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 3.920 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 26.740 Find NCS groups from input model: 0.250 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:13.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 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 : 0.003 0.061 8457 Z= 0.203 Angle : 0.565 13.585 11521 Z= 0.299 Chirality : 0.042 0.182 1340 Planarity : 0.004 0.065 1454 Dihedral : 11.843 86.660 2864 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.74 (0.24), residues: 1086 helix: -0.26 (0.27), residues: 359 sheet: 0.98 (0.33), residues: 263 loop : -1.54 (0.25), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 63 HIS 0.004 0.001 HIS A 100 PHE 0.015 0.001 PHE A 333 TYR 0.010 0.001 TYR E 178 ARG 0.007 0.000 ARG A 196 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 0.926 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.8524 time to fit residues: 173.8479 Evaluate side-chains 178 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 0.931 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1177 ------------------------------------------------------------------------------- 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: 0.0770 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 84 optimal weight: 0.0030 chunk 32 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 98 optimal weight: 0.0470 overall best weight: 0.3646 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 ASN C 293 ASN C 340 ASN D 59 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8457 Z= 0.156 Angle : 0.526 7.471 11521 Z= 0.277 Chirality : 0.042 0.140 1340 Planarity : 0.004 0.035 1454 Dihedral : 4.160 49.892 1177 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.77 % Allowed : 8.38 % Favored : 89.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.02 (0.25), residues: 1086 helix: 0.91 (0.29), residues: 349 sheet: 1.02 (0.32), residues: 283 loop : -1.45 (0.25), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 297 HIS 0.003 0.001 HIS E 35 PHE 0.010 0.001 PHE C 234 TYR 0.010 0.001 TYR A 220 ARG 0.006 0.000 ARG A 196 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 189 time to evaluate : 0.830 Fit side-chains outliers start: 15 outliers final: 4 residues processed: 194 average time/residue: 0.8899 time to fit residues: 187.0154 Evaluate side-chains 185 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 181 time to evaluate : 0.911 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.2708 time to fit residues: 1.5707 ------------------------------------------------------------------------------- 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: 2.9990 chunk 30 optimal weight: 0.7980 chunk 81 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 98 optimal weight: 0.0170 chunk 106 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8457 Z= 0.173 Angle : 0.513 8.832 11521 Z= 0.267 Chirality : 0.042 0.200 1340 Planarity : 0.003 0.034 1454 Dihedral : 4.129 45.316 1177 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.13 % Allowed : 12.04 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.25), residues: 1086 helix: 1.10 (0.29), residues: 356 sheet: 1.03 (0.32), residues: 283 loop : -1.37 (0.26), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 117 HIS 0.003 0.001 HIS E 35 PHE 0.013 0.001 PHE A 203 TYR 0.010 0.001 TYR E 178 ARG 0.005 0.000 ARG A 196 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 182 time to evaluate : 0.962 Fit side-chains outliers start: 18 outliers final: 9 residues processed: 189 average time/residue: 0.8568 time to fit residues: 176.0926 Evaluate side-chains 187 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 178 time to evaluate : 0.915 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 3 residues processed: 6 average time/residue: 0.1040 time to fit residues: 2.2802 ------------------------------------------------------------------------------- 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: 5.9990 chunk 73 optimal weight: 0.0770 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 98 optimal weight: 0.9990 chunk 104 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 93 optimal weight: 0.0020 chunk 28 optimal weight: 0.8980 overall best weight: 0.4946 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 293 ASN ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8457 Z= 0.157 Angle : 0.509 9.055 11521 Z= 0.262 Chirality : 0.042 0.228 1340 Planarity : 0.003 0.035 1454 Dihedral : 4.033 39.914 1177 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.01 % Allowed : 13.70 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.25), residues: 1086 helix: 1.31 (0.29), residues: 356 sheet: 1.15 (0.32), residues: 278 loop : -1.36 (0.26), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 117 HIS 0.003 0.001 HIS E 35 PHE 0.011 0.001 PHE E 80 TYR 0.010 0.001 TYR E 178 ARG 0.004 0.000 ARG A 196 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 176 time to evaluate : 0.913 Fit side-chains outliers start: 17 outliers final: 9 residues processed: 183 average time/residue: 0.8561 time to fit residues: 170.3048 Evaluate side-chains 181 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 172 time to evaluate : 0.866 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 6 residues processed: 3 average time/residue: 0.0891 time to fit residues: 1.7232 ------------------------------------------------------------------------------- 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: 4.9990 chunk 59 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 72 optimal weight: 0.0980 chunk 0 optimal weight: 0.9990 chunk 53 optimal weight: 0.2980 chunk 93 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 ASN ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8457 Z= 0.190 Angle : 0.525 8.703 11521 Z= 0.272 Chirality : 0.043 0.249 1340 Planarity : 0.003 0.033 1454 Dihedral : 4.095 38.303 1177 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.36 % Allowed : 13.58 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.25), residues: 1086 helix: 1.36 (0.29), residues: 356 sheet: 1.14 (0.32), residues: 277 loop : -1.35 (0.26), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 211 HIS 0.004 0.001 HIS E 35 PHE 0.014 0.001 PHE A 203 TYR 0.010 0.001 TYR E 178 ARG 0.003 0.000 ARG A 196 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 173 time to evaluate : 0.933 Fit side-chains outliers start: 20 outliers final: 11 residues processed: 182 average time/residue: 0.8983 time to fit residues: 177.4014 Evaluate side-chains 181 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 170 time to evaluate : 0.930 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 6 residues processed: 5 average time/residue: 0.1294 time to fit residues: 2.2141 ------------------------------------------------------------------------------- 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: 0.7980 chunk 94 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 34 optimal weight: 0.0470 chunk 54 optimal weight: 2.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 293 ASN ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN E 113 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8457 Z= 0.178 Angle : 0.515 7.213 11521 Z= 0.267 Chirality : 0.043 0.271 1340 Planarity : 0.003 0.033 1454 Dihedral : 4.073 37.103 1177 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.48 % Allowed : 14.52 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.38 (0.25), residues: 1086 helix: 1.46 (0.29), residues: 356 sheet: 1.16 (0.32), residues: 277 loop : -1.37 (0.26), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 211 HIS 0.003 0.001 HIS E 35 PHE 0.014 0.001 PHE E 80 TYR 0.010 0.001 TYR E 178 ARG 0.003 0.000 ARG A 196 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 172 time to evaluate : 0.907 Fit side-chains outliers start: 21 outliers final: 10 residues processed: 186 average time/residue: 0.8712 time to fit residues: 176.1076 Evaluate side-chains 178 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 168 time to evaluate : 0.906 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 6 residues processed: 4 average time/residue: 0.1274 time to fit residues: 2.0002 ------------------------------------------------------------------------------- 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: 0.8980 chunk 11 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 chunk 76 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 65 optimal weight: 0.3980 chunk 63 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8457 Z= 0.193 Angle : 0.536 8.442 11521 Z= 0.275 Chirality : 0.043 0.287 1340 Planarity : 0.003 0.032 1454 Dihedral : 4.103 35.777 1177 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.89 % Allowed : 15.23 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.38 (0.25), residues: 1086 helix: 1.47 (0.29), residues: 355 sheet: 1.16 (0.32), residues: 277 loop : -1.37 (0.26), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 211 HIS 0.004 0.001 HIS E 35 PHE 0.015 0.001 PHE E 80 TYR 0.010 0.001 TYR A 220 ARG 0.003 0.000 ARG C 68 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 175 time to evaluate : 0.921 Fit side-chains outliers start: 16 outliers final: 10 residues processed: 184 average time/residue: 0.9224 time to fit residues: 184.0204 Evaluate side-chains 181 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 171 time to evaluate : 0.847 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 6 residues processed: 4 average time/residue: 0.1157 time to fit residues: 1.9671 ------------------------------------------------------------------------------- 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: 0.5980 chunk 62 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 94 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 237 ASN C 293 ASN ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8457 Z= 0.211 Angle : 0.549 8.389 11521 Z= 0.283 Chirality : 0.044 0.306 1340 Planarity : 0.003 0.034 1454 Dihedral : 4.168 34.339 1177 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.30 % Allowed : 16.17 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.25), residues: 1086 helix: 1.44 (0.29), residues: 355 sheet: 1.13 (0.31), residues: 282 loop : -1.43 (0.26), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 211 HIS 0.004 0.001 HIS E 35 PHE 0.017 0.002 PHE E 80 TYR 0.011 0.001 TYR E 178 ARG 0.003 0.000 ARG C 68 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 172 time to evaluate : 0.888 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 180 average time/residue: 0.9122 time to fit residues: 177.6907 Evaluate side-chains 180 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 172 time to evaluate : 0.905 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 6 residues processed: 2 average time/residue: 0.1035 time to fit residues: 1.6324 ------------------------------------------------------------------------------- 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: 2.9990 chunk 97 optimal weight: 4.9990 chunk 99 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 237 ASN ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8457 Z= 0.252 Angle : 0.580 9.043 11521 Z= 0.300 Chirality : 0.045 0.324 1340 Planarity : 0.004 0.034 1454 Dihedral : 4.259 32.949 1177 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.18 % Allowed : 16.77 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.27 (0.25), residues: 1086 helix: 1.35 (0.28), residues: 355 sheet: 1.09 (0.31), residues: 285 loop : -1.46 (0.26), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 211 HIS 0.004 0.001 HIS E 35 PHE 0.018 0.002 PHE E 80 TYR 0.020 0.002 TYR C 105 ARG 0.003 0.000 ARG C 68 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 173 time to evaluate : 0.979 Fit side-chains outliers start: 10 outliers final: 9 residues processed: 181 average time/residue: 0.8836 time to fit residues: 173.9970 Evaluate side-chains 180 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 171 time to evaluate : 0.946 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 7 residues processed: 2 average time/residue: 0.1267 time to fit residues: 1.6641 ------------------------------------------------------------------------------- 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: 0.9980 chunk 62 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 ASN C 237 ASN C 293 ASN ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8457 Z= 0.227 Angle : 0.576 9.201 11521 Z= 0.296 Chirality : 0.044 0.325 1340 Planarity : 0.004 0.034 1454 Dihedral : 4.242 32.043 1177 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.06 % Allowed : 17.71 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.27 (0.25), residues: 1086 helix: 1.45 (0.29), residues: 350 sheet: 1.05 (0.31), residues: 283 loop : -1.46 (0.25), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 211 HIS 0.004 0.001 HIS E 35 PHE 0.017 0.002 PHE E 80 TYR 0.016 0.001 TYR C 105 ARG 0.003 0.000 ARG C 68 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 167 time to evaluate : 1.075 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 175 average time/residue: 0.9131 time to fit residues: 172.9631 Evaluate side-chains 175 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 167 time to evaluate : 0.954 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 7 residues processed: 1 average time/residue: 0.1267 time to fit residues: 1.4899 ------------------------------------------------------------------------------- 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: 0.7980 chunk 26 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 237 ASN ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.107978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.093397 restraints weight = 12094.270| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.65 r_work: 0.3093 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8457 Z= 0.215 Angle : 0.570 9.253 11521 Z= 0.293 Chirality : 0.044 0.323 1340 Planarity : 0.004 0.034 1454 Dihedral : 4.209 31.086 1177 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.30 % Allowed : 17.36 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.25), residues: 1086 helix: 1.50 (0.29), residues: 350 sheet: 1.04 (0.31), residues: 283 loop : -1.46 (0.25), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 211 HIS 0.004 0.001 HIS A 100 PHE 0.016 0.002 PHE E 80 TYR 0.016 0.001 TYR C 105 ARG 0.003 0.000 ARG C 68 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3491.72 seconds wall clock time: 62 minutes 26.83 seconds (3746.83 seconds total)