Starting phenix.real_space_refine on Mon Mar 11 11:56:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7um7_26599/03_2024/7um7_26599_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7um7_26599/03_2024/7um7_26599.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7um7_26599/03_2024/7um7_26599.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7um7_26599/03_2024/7um7_26599.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7um7_26599/03_2024/7um7_26599_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7um7_26599/03_2024/7um7_26599_updated.pdb" } resolution = 2.75 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 54 5.16 5 C 5233 2.51 5 N 1367 2.21 5 O 1511 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8165 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1925 Classifications: {'peptide': 256} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 10, 'TRANS': 245} Chain breaks: 2 Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 91 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: 2477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2477 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 93 Chain: "D" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 353 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 46} 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: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1712 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 2 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'H8D': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.78, per 1000 atoms: 0.59 Number of scatterers: 8165 At special positions: 0 Unit cell: (101.01, 115.57, 130.13, 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 54 16.00 O 1511 8.00 N 1367 7.00 C 5233 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=2.04 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: 2.91 Conformation dependent library (CDL) restraints added in 1.5 seconds 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2038 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 14 sheets defined 31.6% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing helix chain 'A' and resid 41 through 67 removed outlier: 3.634A pdb=" N ARG A 67 " --> pdb=" O ALA A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 92 removed outlier: 4.401A pdb=" N LEU A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL A 79 " --> pdb=" O PRO A 75 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL A 89 " --> pdb=" O SER A 85 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA A 90 " --> pdb=" O ASP A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 103 removed outlier: 3.578A pdb=" N HIS A 100 " --> pdb=" O LEU A 96 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU A 101 " --> pdb=" O SER A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 144 Processing helix chain 'A' and resid 152 through 178 removed outlier: 3.573A pdb=" N TRP A 166 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER A 169 " --> pdb=" O THR A 165 " (cutoff:3.500A) Proline residue: A 176 - end of helix Processing helix chain 'A' and resid 200 through 206 removed outlier: 4.171A pdb=" N THR A 205 " --> pdb=" O ALA A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 229 removed outlier: 3.539A pdb=" N VAL A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 310 removed outlier: 3.554A pdb=" N PHE A 294 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TRP A 298 " --> pdb=" O PHE A 294 " (cutoff:3.500A) Proline residue: A 300 - end of helix removed outlier: 3.740A pdb=" N THR A 304 " --> pdb=" O PRO A 300 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU A 306 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER A 308 " --> pdb=" O THR A 304 " (cutoff:3.500A) Proline residue: A 309 - end of helix Processing helix chain 'A' and resid 317 through 338 removed outlier: 3.748A pdb=" N ILE A 322 " --> pdb=" O ILE A 318 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY A 327 " --> pdb=" O PHE A 323 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR A 328 " --> pdb=" O LEU A 324 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N SER A 331 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N PHE A 332 " --> pdb=" O TYR A 328 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE A 333 " --> pdb=" O SER A 329 " (cutoff:3.500A) Proline residue: A 335 - end of helix Processing helix chain 'A' and resid 345 through 348 No H-bonds generated for 'chain 'A' and resid 345 through 348' Processing helix chain 'B' and resid 4 through 28 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: 3.523A 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 151 removed outlier: 4.193A pdb=" N LYS B 151 " --> pdb=" O GLY B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 182 removed outlier: 4.468A 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 6 through 24 removed outlier: 3.752A pdb=" N GLU C 10 " --> pdb=" O GLN C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 33 No H-bonds generated for 'chain 'C' and resid 30 through 33' 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 12 through 22 Processing helix chain 'D' and resid 30 through 43 removed outlier: 3.682A pdb=" N TYR D 40 " --> pdb=" O ASP D 36 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N CYS D 41 " --> pdb=" O LEU D 37 " (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 '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: 6.699A pdb=" N ILE B 136 " --> pdb=" O TYR B 191 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N HIS B 193 " --> pdb=" O ILE B 136 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU B 138 " --> pdb=" O HIS B 193 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA B 102 " --> pdb=" O LYS B 32 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL B 67 " --> pdb=" O ASP B 82 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 58 through 63 removed outlier: 7.142A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU C 70 " --> pdb=" O TRP C 82 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.181A 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: 6.908A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG C 137 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.291A 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: 6.845A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.194A 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: 6.731A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE C 199 " --> pdb=" O TRP C 211 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.533A 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: 6.744A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER C 245 " --> pdb=" O THR C 249 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N THR C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.213A 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: 6.573A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.313A 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: 4.823A pdb=" N PHE C 278 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N LEU C 284 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY C 306 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 327 through 330 removed outlier: 3.825A pdb=" N LEU C 336 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG C 49 " --> pdb=" O ILE C 338 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ASN C 340 " --> pdb=" O THR C 47 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N THR C 47 " --> pdb=" O ASN C 340 " (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: 3.628A pdb=" N GLY E 10 " --> pdb=" O THR E 116 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ALA E 40 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LEU E 45 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 96 through 98 removed outlier: 4.225A pdb=" N CYS E 96 " --> pdb=" O GLY E 112 " (cutoff:3.500A) removed outlier: 4.552A 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: 6.705A 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 219 removed outlier: 3.683A pdb=" N ILE E 177 " --> pdb=" O TRP E 164 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) 341 hydrogen bonds defined for protein. 978 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: 2.34 Time building geometry restraints manager: 3.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2614 1.34 - 1.46: 2091 1.46 - 1.58: 3566 1.58 - 1.70: 0 1.70 - 1.82: 74 Bond restraints: 8345 Sorted by residual: bond pdb=" CA SER A 331 " pdb=" CB SER A 331 " ideal model delta sigma weight residual 1.531 1.478 0.053 1.72e-02 3.38e+03 9.39e+00 bond pdb=" N SER A 331 " pdb=" CA SER A 331 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.32e-02 5.74e+03 7.12e+00 bond pdb=" CA SER A 128 " pdb=" CB SER A 128 " ideal model delta sigma weight residual 1.529 1.492 0.037 1.55e-02 4.16e+03 5.70e+00 bond pdb=" N ASP A 86 " pdb=" CA ASP A 86 " ideal model delta sigma weight residual 1.458 1.486 -0.029 1.28e-02 6.10e+03 5.12e+00 bond pdb=" N SER A 128 " pdb=" CA SER A 128 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.19e-02 7.06e+03 4.81e+00 ... (remaining 8340 not shown) Histogram of bond angle deviations from ideal: 100.45 - 107.48: 267 107.48 - 114.51: 4880 114.51 - 121.54: 4126 121.54 - 128.57: 2025 128.57 - 135.60: 75 Bond angle restraints: 11373 Sorted by residual: angle pdb=" C GLY E 197 " pdb=" N THR E 198 " pdb=" CA THR E 198 " ideal model delta sigma weight residual 121.54 128.02 -6.48 1.91e+00 2.74e-01 1.15e+01 angle pdb=" C ARG A 73 " pdb=" N VAL A 74 " pdb=" CA VAL A 74 " ideal model delta sigma weight residual 120.33 122.97 -2.64 8.00e-01 1.56e+00 1.09e+01 angle pdb=" N SER A 331 " pdb=" CA SER A 331 " pdb=" C SER A 331 " ideal model delta sigma weight residual 113.20 109.29 3.91 1.21e+00 6.83e-01 1.05e+01 angle pdb=" C LEU B 224 " pdb=" N TYR B 225 " pdb=" CA TYR B 225 " ideal model delta sigma weight residual 121.70 116.24 5.46 1.80e+00 3.09e-01 9.20e+00 angle pdb=" N SER A 128 " pdb=" CA SER A 128 " pdb=" CB SER A 128 " ideal model delta sigma weight residual 110.01 114.21 -4.20 1.45e+00 4.76e-01 8.38e+00 ... (remaining 11368 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.38: 4809 34.38 - 68.75: 67 68.75 - 103.13: 6 103.13 - 137.51: 0 137.51 - 171.88: 1 Dihedral angle restraints: 4883 sinusoidal: 1728 harmonic: 3155 Sorted by residual: dihedral pdb=" C21 H8D A 401 " pdb=" C19 H8D A 401 " pdb=" C20 H8D A 401 " pdb=" N3 H8D A 401 " ideal model delta sinusoidal sigma weight residual 62.30 -109.58 171.88 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" CB CYS A 114 " pdb=" SG CYS A 114 " pdb=" SG CYS A 192 " pdb=" CB CYS A 192 " ideal model delta sinusoidal sigma weight residual 93.00 127.57 -34.57 1 1.00e+01 1.00e-02 1.70e+01 dihedral pdb=" CA TYR B 168 " pdb=" C TYR B 168 " pdb=" N GLU B 169 " pdb=" CA GLU B 169 " ideal model delta harmonic sigma weight residual -180.00 -160.33 -19.67 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 4880 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 792 0.027 - 0.054: 324 0.054 - 0.082: 118 0.082 - 0.109: 66 0.109 - 0.136: 30 Chirality restraints: 1330 Sorted by residual: chirality pdb=" CA SER A 331 " pdb=" N SER A 331 " pdb=" C SER A 331 " pdb=" CB SER A 331 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.62e-01 chirality pdb=" CA ILE E 177 " pdb=" N ILE E 177 " pdb=" C ILE E 177 " pdb=" CB ILE E 177 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.20e-01 chirality pdb=" CA ILE B 137 " pdb=" N ILE B 137 " pdb=" C ILE B 137 " pdb=" CB ILE B 137 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.17e-01 ... (remaining 1327 not shown) Planarity restraints: 1429 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C14 H8D A 401 " -0.179 2.00e-02 2.50e+03 2.76e-01 9.51e+02 pdb=" C16 H8D A 401 " 0.084 2.00e-02 2.50e+03 pdb=" C19 H8D A 401 " -0.325 2.00e-02 2.50e+03 pdb=" N3 H8D A 401 " 0.482 2.00e-02 2.50e+03 pdb=" O1 H8D A 401 " -0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 198 " 0.010 2.00e-02 2.50e+03 2.01e-02 4.03e+00 pdb=" C THR E 198 " -0.035 2.00e-02 2.50e+03 pdb=" O THR E 198 " 0.013 2.00e-02 2.50e+03 pdb=" N ALA E 199 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 330 " -0.009 2.00e-02 2.50e+03 1.85e-02 3.42e+00 pdb=" C ASN A 330 " 0.032 2.00e-02 2.50e+03 pdb=" O ASN A 330 " -0.012 2.00e-02 2.50e+03 pdb=" N SER A 331 " -0.011 2.00e-02 2.50e+03 ... (remaining 1426 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1023 2.76 - 3.29: 7198 3.29 - 3.83: 12250 3.83 - 4.36: 14665 4.36 - 4.90: 26314 Nonbonded interactions: 61450 Sorted by model distance: nonbonded pdb=" O PRO A 335 " pdb=" OG1 THR A 339 " model vdw 2.220 2.440 nonbonded pdb=" NH2 ARG A 230 " pdb=" OD1 ASP B 212 " model vdw 2.334 2.520 nonbonded pdb=" OG SER E 149 " pdb=" O LYS E 151 " model vdw 2.378 2.440 nonbonded pdb=" OD1 ASP A 138 " pdb=" OH TYR A 149 " model vdw 2.379 2.440 nonbonded pdb=" O SER E 85 " pdb=" OG SER E 85 " model vdw 2.398 2.440 ... (remaining 61445 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: 1.060 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: 3.810 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 25.070 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 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 : 0.002 0.053 8345 Z= 0.129 Angle : 0.476 7.409 11373 Z= 0.259 Chirality : 0.040 0.136 1330 Planarity : 0.008 0.276 1429 Dihedral : 13.052 171.882 2839 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % 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: -0.25 (0.25), residues: 1069 helix: 0.51 (0.28), residues: 329 sheet: 1.06 (0.31), residues: 274 loop : -1.45 (0.26), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 63 HIS 0.002 0.000 HIS E 35 PHE 0.008 0.001 PHE C 199 TYR 0.009 0.001 TYR E 178 ARG 0.007 0.000 ARG E 168 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 0.806 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 1.0070 time to fit residues: 193.7998 Evaluate side-chains 174 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.0050 chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 97 optimal weight: 0.2980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 ASN B 183 ASN C 293 ASN E 167 GLN E 174 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8345 Z= 0.190 Angle : 0.532 7.493 11373 Z= 0.280 Chirality : 0.042 0.138 1330 Planarity : 0.003 0.029 1429 Dihedral : 5.611 86.836 1183 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.92 % Allowed : 7.93 % Favored : 90.14 % 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: 0.54 (0.25), residues: 1069 helix: 2.09 (0.29), residues: 329 sheet: 1.07 (0.30), residues: 288 loop : -1.53 (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 0.010 0.001 PHE C 199 TYR 0.011 0.001 TYR A 220 ARG 0.005 0.000 ARG E 168 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 161 time to evaluate : 0.924 Fit side-chains REVERT: C 189 SER cc_start: 0.8160 (t) cc_final: 0.7924 (p) outliers start: 16 outliers final: 6 residues processed: 167 average time/residue: 1.0132 time to fit residues: 181.3236 Evaluate side-chains 163 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 157 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain C residue 161 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 80 optimal weight: 0.0060 chunk 66 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 97 optimal weight: 0.0050 chunk 105 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 78 optimal weight: 0.0470 overall best weight: 0.3508 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 ASN E 174 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8345 Z= 0.129 Angle : 0.467 8.987 11373 Z= 0.243 Chirality : 0.040 0.130 1330 Planarity : 0.003 0.026 1429 Dihedral : 5.295 73.356 1183 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.28 % Allowed : 9.86 % Favored : 87.86 % 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: 0.87 (0.26), residues: 1069 helix: 2.60 (0.30), residues: 329 sheet: 1.11 (0.30), residues: 286 loop : -1.40 (0.26), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 117 HIS 0.002 0.000 HIS C 54 PHE 0.010 0.001 PHE C 199 TYR 0.009 0.001 TYR E 178 ARG 0.002 0.000 ARG E 168 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 159 time to evaluate : 0.872 Fit side-chains REVERT: C 189 SER cc_start: 0.8151 (t) cc_final: 0.7924 (p) outliers start: 19 outliers final: 8 residues processed: 165 average time/residue: 0.9793 time to fit residues: 173.3142 Evaluate side-chains 158 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 150 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain E residue 63 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 0.0870 chunk 73 optimal weight: 0.3980 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 46 optimal weight: 8.9990 chunk 65 optimal weight: 0.0670 chunk 97 optimal weight: 0.0030 chunk 103 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 27 optimal weight: 0.1980 overall best weight: 0.1506 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 174 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8345 Z= 0.103 Angle : 0.442 8.697 11373 Z= 0.227 Chirality : 0.040 0.146 1330 Planarity : 0.003 0.028 1429 Dihedral : 5.031 73.691 1183 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.04 % Allowed : 12.26 % Favored : 85.70 % 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: 1.03 (0.26), residues: 1069 helix: 2.78 (0.30), residues: 329 sheet: 1.25 (0.30), residues: 280 loop : -1.36 (0.26), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 117 HIS 0.001 0.000 HIS E 35 PHE 0.017 0.001 PHE A 55 TYR 0.009 0.001 TYR E 178 ARG 0.002 0.000 ARG E 168 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 156 time to evaluate : 0.906 Fit side-chains REVERT: C 189 SER cc_start: 0.8164 (t) cc_final: 0.7931 (p) REVERT: C 256 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.6756 (mtp180) outliers start: 17 outliers final: 8 residues processed: 161 average time/residue: 1.0092 time to fit residues: 174.0928 Evaluate side-chains 167 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 158 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain B residue 19 ASN Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain C residue 256 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 0.0030 chunk 58 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 ASN C 293 ASN E 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 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 0.029 8345 Z= 0.188 Angle : 0.516 9.672 11373 Z= 0.265 Chirality : 0.041 0.143 1330 Planarity : 0.003 0.028 1429 Dihedral : 5.227 71.552 1183 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.28 % Allowed : 13.82 % Favored : 83.89 % 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: 0.90 (0.26), residues: 1069 helix: 2.72 (0.30), residues: 329 sheet: 1.14 (0.30), residues: 277 loop : -1.43 (0.26), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 93 HIS 0.005 0.001 HIS E 35 PHE 0.020 0.001 PHE A 301 TYR 0.012 0.001 TYR A 220 ARG 0.002 0.000 ARG E 168 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 157 time to evaluate : 0.963 Fit side-chains REVERT: C 189 SER cc_start: 0.8197 (t) cc_final: 0.7969 (p) REVERT: C 256 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.6891 (mtp180) outliers start: 19 outliers final: 13 residues processed: 164 average time/residue: 0.9651 time to fit residues: 169.9686 Evaluate side-chains 167 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 153 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 154 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 85 optimal weight: 0.3980 chunk 47 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 99 optimal weight: 0.4980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 HIS B 128 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8345 Z= 0.190 Angle : 0.503 9.169 11373 Z= 0.262 Chirality : 0.041 0.132 1330 Planarity : 0.003 0.030 1429 Dihedral : 5.198 63.043 1183 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.00 % Allowed : 13.94 % Favored : 83.05 % 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: 0.85 (0.26), residues: 1069 helix: 2.66 (0.29), residues: 329 sheet: 1.11 (0.30), residues: 280 loop : -1.46 (0.26), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 93 HIS 0.004 0.001 HIS E 35 PHE 0.013 0.001 PHE A 301 TYR 0.011 0.001 TYR A 220 ARG 0.004 0.000 ARG B 184 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 157 time to evaluate : 1.076 Fit side-chains REVERT: A 82 MET cc_start: 0.7684 (ttp) cc_final: 0.7418 (ttm) REVERT: A 101 GLU cc_start: 0.5427 (OUTLIER) cc_final: 0.5187 (pm20) REVERT: C 234 PHE cc_start: 0.8832 (OUTLIER) cc_final: 0.8500 (m-80) REVERT: C 256 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.6891 (mtp180) REVERT: E 83 MET cc_start: 0.8546 (mtm) cc_final: 0.8243 (ptp) REVERT: E 183 LEU cc_start: 0.8555 (tt) cc_final: 0.8332 (tt) outliers start: 25 outliers final: 13 residues processed: 167 average time/residue: 1.0566 time to fit residues: 188.7304 Evaluate side-chains 172 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 156 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 154 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 64 optimal weight: 0.4980 chunk 62 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8345 Z= 0.189 Angle : 0.510 9.691 11373 Z= 0.264 Chirality : 0.041 0.137 1330 Planarity : 0.003 0.030 1429 Dihedral : 4.951 47.306 1183 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.76 % Allowed : 14.78 % Favored : 82.45 % 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: 0.87 (0.26), residues: 1069 helix: 2.66 (0.29), residues: 329 sheet: 1.11 (0.30), residues: 291 loop : -1.50 (0.26), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 93 HIS 0.004 0.001 HIS E 35 PHE 0.013 0.001 PHE A 301 TYR 0.011 0.001 TYR A 220 ARG 0.004 0.000 ARG B 184 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 160 time to evaluate : 0.870 Fit side-chains REVERT: A 82 MET cc_start: 0.7667 (ttp) cc_final: 0.7376 (ttm) REVERT: A 101 GLU cc_start: 0.5420 (OUTLIER) cc_final: 0.5181 (pm20) REVERT: C 234 PHE cc_start: 0.8829 (OUTLIER) cc_final: 0.8495 (m-80) REVERT: C 256 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.6892 (mtp180) REVERT: E 19 LYS cc_start: 0.8698 (ttmm) cc_final: 0.8492 (ttmm) REVERT: E 83 MET cc_start: 0.8522 (mtm) cc_final: 0.8238 (ptp) outliers start: 23 outliers final: 15 residues processed: 171 average time/residue: 0.9718 time to fit residues: 178.4590 Evaluate side-chains 175 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 157 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 154 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8345 Z= 0.223 Angle : 0.530 10.830 11373 Z= 0.276 Chirality : 0.042 0.143 1330 Planarity : 0.003 0.032 1429 Dihedral : 4.804 34.435 1183 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.00 % Allowed : 14.78 % Favored : 82.21 % 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: 0.79 (0.26), residues: 1069 helix: 2.58 (0.29), residues: 329 sheet: 1.09 (0.30), residues: 291 loop : -1.55 (0.26), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 63 HIS 0.005 0.001 HIS E 35 PHE 0.014 0.001 PHE C 234 TYR 0.012 0.001 TYR A 220 ARG 0.004 0.000 ARG B 184 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 157 time to evaluate : 0.887 Fit side-chains REVERT: A 82 MET cc_start: 0.7694 (ttp) cc_final: 0.7405 (ttm) REVERT: A 101 GLU cc_start: 0.5425 (OUTLIER) cc_final: 0.5186 (pm20) REVERT: C 234 PHE cc_start: 0.8844 (OUTLIER) cc_final: 0.8509 (m-80) REVERT: C 256 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.6908 (mtp180) REVERT: E 83 MET cc_start: 0.8528 (mtm) cc_final: 0.8253 (ptp) REVERT: E 87 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.7278 (mtt180) REVERT: E 183 LEU cc_start: 0.8519 (tp) cc_final: 0.8302 (tt) outliers start: 25 outliers final: 15 residues processed: 168 average time/residue: 0.9756 time to fit residues: 175.9570 Evaluate side-chains 176 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 157 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 154 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8345 Z= 0.219 Angle : 0.528 11.069 11373 Z= 0.275 Chirality : 0.042 0.150 1330 Planarity : 0.003 0.032 1429 Dihedral : 4.774 34.558 1183 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.76 % Allowed : 15.14 % Favored : 82.09 % 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: 0.77 (0.26), residues: 1069 helix: 2.56 (0.29), residues: 329 sheet: 1.05 (0.29), residues: 297 loop : -1.56 (0.26), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 63 HIS 0.004 0.001 HIS E 35 PHE 0.014 0.001 PHE A 301 TYR 0.011 0.001 TYR A 220 ARG 0.003 0.000 ARG B 184 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 154 time to evaluate : 0.873 Fit side-chains REVERT: A 82 MET cc_start: 0.7696 (ttp) cc_final: 0.7406 (ttm) REVERT: A 101 GLU cc_start: 0.5424 (OUTLIER) cc_final: 0.5184 (pm20) REVERT: C 234 PHE cc_start: 0.8838 (OUTLIER) cc_final: 0.8495 (m-80) REVERT: C 256 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.6894 (mtp180) REVERT: E 83 MET cc_start: 0.8538 (mtm) cc_final: 0.8241 (ptp) REVERT: E 87 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.7288 (mtt180) REVERT: E 183 LEU cc_start: 0.8505 (tp) cc_final: 0.8301 (tt) outliers start: 23 outliers final: 16 residues processed: 164 average time/residue: 1.0536 time to fit residues: 185.4554 Evaluate side-chains 174 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 154 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 154 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 70 optimal weight: 0.5980 chunk 106 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 chunk 90 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: B 128 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8345 Z= 0.200 Angle : 0.516 10.981 11373 Z= 0.269 Chirality : 0.042 0.140 1330 Planarity : 0.003 0.031 1429 Dihedral : 4.752 35.306 1183 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.40 % Allowed : 15.38 % Favored : 82.21 % 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: 0.80 (0.26), residues: 1069 helix: 2.60 (0.29), residues: 329 sheet: 1.03 (0.29), residues: 297 loop : -1.54 (0.26), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 63 HIS 0.004 0.001 HIS E 35 PHE 0.012 0.001 PHE A 301 TYR 0.011 0.001 TYR E 95 ARG 0.003 0.000 ARG B 184 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 151 time to evaluate : 0.903 Fit side-chains REVERT: A 82 MET cc_start: 0.7679 (ttp) cc_final: 0.7396 (ttm) REVERT: A 101 GLU cc_start: 0.5422 (OUTLIER) cc_final: 0.5180 (pm20) REVERT: C 234 PHE cc_start: 0.8827 (OUTLIER) cc_final: 0.8483 (m-80) REVERT: C 256 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.6891 (mtp180) REVERT: E 19 LYS cc_start: 0.8743 (ttmm) cc_final: 0.8441 (ttmt) REVERT: E 83 MET cc_start: 0.8530 (mtm) cc_final: 0.8243 (ptp) REVERT: E 87 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.7286 (mtt180) REVERT: E 183 LEU cc_start: 0.8505 (tp) cc_final: 0.8292 (tt) outliers start: 20 outliers final: 16 residues processed: 160 average time/residue: 0.9944 time to fit residues: 170.5035 Evaluate side-chains 171 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 151 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 154 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 0.6980 chunk 78 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.114741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.099521 restraints weight = 11451.691| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.70 r_work: 0.3169 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8345 Z= 0.308 Angle : 0.586 10.584 11373 Z= 0.305 Chirality : 0.044 0.152 1330 Planarity : 0.004 0.036 1429 Dihedral : 4.964 32.446 1183 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.88 % Allowed : 15.26 % Favored : 81.85 % 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: 0.57 (0.25), residues: 1069 helix: 2.31 (0.29), residues: 330 sheet: 0.96 (0.29), residues: 296 loop : -1.65 (0.26), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 63 HIS 0.006 0.001 HIS E 35 PHE 0.018 0.002 PHE A 301 TYR 0.014 0.002 TYR A 220 ARG 0.004 0.000 ARG B 184 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3640.50 seconds wall clock time: 65 minutes 9.16 seconds (3909.16 seconds total)