Starting phenix.real_space_refine on Fri Feb 14 10:06:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7srr_25402/02_2025/7srr_25402.cif Found real_map, /net/cci-nas-00/data/ceres_data/7srr_25402/02_2025/7srr_25402.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7srr_25402/02_2025/7srr_25402.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7srr_25402/02_2025/7srr_25402.map" model { file = "/net/cci-nas-00/data/ceres_data/7srr_25402/02_2025/7srr_25402.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7srr_25402/02_2025/7srr_25402.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1944 atoms to isotropic. 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 5395 2.51 5 N 1411 2.21 5 O 1534 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8394 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1713 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 6, 'TRANS': 218} Chain breaks: 2 Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 152 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 9, 'ARG:plan': 6, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 92 Chain: "C" Number of atoms: 2518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2518 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 3, 'ARG:plan': 6, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 73 Chain: "D" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 363 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "E" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1704 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 218} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 43 Chain: "R" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2072 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 12, 'TRANS': 261} Chain breaks: 1 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 61 Chain: "R" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'7LD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.20, per 1000 atoms: 0.74 Number of scatterers: 8394 At special positions: 0 Unit cell: (101.521, 117.139, 131.89, 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 1534 8.00 N 1411 7.00 C 5395 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 Simple disulfide: pdb=" SG CYS R 128 " - pdb=" SG CYS R 207 " distance=2.03 Simple disulfide: pdb=" SG CYS R 350 " - pdb=" SG CYS R 353 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 2.56 Conformation dependent library (CDL) restraints added in 1.1 seconds 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2096 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 13 sheets defined 36.8% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'B' and resid 6 through 30 Processing helix chain 'B' and resid 45 through 49 removed outlier: 3.626A pdb=" N ILE B 49 " --> pdb=" O LYS B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 130 Processing helix chain 'B' and resid 131 through 135 removed outlier: 3.506A pdb=" N LEU B 134 " --> pdb=" O ASN B 131 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ARG B 135 " --> pdb=" O ARG B 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 131 through 135' Processing helix chain 'B' and resid 145 through 156 Processing helix chain 'B' and resid 159 through 164 removed outlier: 4.255A pdb=" N TYR B 163 " --> pdb=" O LYS B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 168 Processing helix chain 'B' and resid 183 through 204 removed outlier: 4.379A pdb=" N SER B 204 " --> pdb=" O ILE B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 243 removed outlier: 3.703A pdb=" N ILE B 227 " --> pdb=" O ASN B 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 25 removed outlier: 3.579A pdb=" N CYS C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'C' and resid 128 through 132 removed outlier: 3.958A pdb=" N GLY C 131 " --> pdb=" O THR C 128 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASN C 132 " --> pdb=" O ARG C 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 128 through 132' Processing helix chain 'D' and resid 10 through 24 removed outlier: 3.814A pdb=" N LYS D 14 " --> pdb=" O ALA D 10 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.569A pdb=" N ALA D 33 " --> pdb=" O LYS D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 48 removed outlier: 3.517A pdb=" N ASP D 48 " --> pdb=" O ALA D 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 45 through 48' Processing helix chain 'D' and resid 55 through 59 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'R' and resid 57 through 82 removed outlier: 3.998A pdb=" N MET R 63 " --> pdb=" O LEU R 59 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N VAL R 64 " --> pdb=" O LEU R 60 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE R 65 " --> pdb=" O ILE R 61 " (cutoff:3.500A) Proline residue: R 67 - end of helix removed outlier: 3.552A pdb=" N ILE R 76 " --> pdb=" O ASN R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 107 removed outlier: 3.610A pdb=" N PHE R 92 " --> pdb=" O ALA R 88 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU R 93 " --> pdb=" O THR R 89 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N MET R 94 " --> pdb=" O ASN R 90 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER R 95 " --> pdb=" O TYR R 91 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU R 96 " --> pdb=" O PHE R 92 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL R 103 " --> pdb=" O ALA R 99 " (cutoff:3.500A) Processing helix chain 'R' and resid 107 through 117 removed outlier: 3.579A pdb=" N PHE R 117 " --> pdb=" O LEU R 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 159 removed outlier: 3.794A pdb=" N LEU R 132 " --> pdb=" O CYS R 128 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N PHE R 133 " --> pdb=" O PRO R 129 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER R 150 " --> pdb=" O LEU R 146 " (cutoff:3.500A) Processing helix chain 'R' and resid 159 through 164 Processing helix chain 'R' and resid 168 through 188 removed outlier: 3.737A pdb=" N ALA R 172 " --> pdb=" O SER R 168 " (cutoff:3.500A) Processing helix chain 'R' and resid 188 through 193 removed outlier: 3.999A pdb=" N ILE R 192 " --> pdb=" O ILE R 188 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS R 193 " --> pdb=" O PRO R 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 188 through 193' Processing helix chain 'R' and resid 216 through 221 removed outlier: 3.625A pdb=" N PHE R 220 " --> pdb=" O ASP R 216 " (cutoff:3.500A) Processing helix chain 'R' and resid 226 through 245 removed outlier: 3.509A pdb=" N ILE R 232 " --> pdb=" O THR R 228 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR R 237 " --> pdb=" O MET R 233 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N HIS R 242 " --> pdb=" O PHE R 238 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA R 243 " --> pdb=" O LEU R 239 " (cutoff:3.500A) Processing helix chain 'R' and resid 317 through 334 removed outlier: 3.760A pdb=" N ALA R 322 " --> pdb=" O ASN R 318 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER R 323 " --> pdb=" O GLU R 319 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLY R 327 " --> pdb=" O SER R 323 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL R 329 " --> pdb=" O VAL R 325 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N PHE R 330 " --> pdb=" O LEU R 326 " (cutoff:3.500A) Processing helix chain 'R' and resid 337 through 350 Processing helix chain 'R' and resid 354 through 362 removed outlier: 3.508A pdb=" N LEU R 358 " --> pdb=" O ASN R 354 " (cutoff:3.500A) Processing helix chain 'R' and resid 364 through 371 Processing helix chain 'R' and resid 372 through 374 No H-bonds generated for 'chain 'R' and resid 372 through 374' Processing helix chain 'R' and resid 375 through 380 Processing helix chain 'R' and resid 384 through 392 Processing helix chain 'R' and resid 393 through 395 No H-bonds generated for 'chain 'R' and resid 393 through 395' Processing sheet with id=AA1, first strand: chain 'B' and resid 69 through 76 removed outlier: 4.685A pdb=" N VAL B 86 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA B 105 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL B 109 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE B 106 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N PHE B 142 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N PHE B 108 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N ASN B 144 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL B 110 " --> pdb=" O ASN B 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.821A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 7.101A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 7.147A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151 removed outlier: 7.012A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 191 removed outlier: 3.693A pdb=" N PHE C 199 " --> pdb=" O TRP C 211 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 232 removed outlier: 6.947A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.800A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLY C 306 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 11 removed outlier: 6.003A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 11 removed outlier: 6.003A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 128 through 129 Processing sheet with id=AB4, first strand: chain 'E' and resid 134 through 136 removed outlier: 3.737A pdb=" N GLY E 213 " --> pdb=" O LEU E 233 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE E 177 " --> pdb=" O TRP E 164 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) 393 hydrogen bonds defined for protein. 1116 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: 2.54 Time building geometry restraints manager: 2.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2674 1.34 - 1.46: 1849 1.46 - 1.58: 3977 1.58 - 1.70: 0 1.70 - 1.82: 79 Bond restraints: 8579 Sorted by residual: bond pdb=" C14 7LD R 501 " pdb=" C16 7LD R 501 " ideal model delta sigma weight residual 1.525 1.403 0.122 2.00e-02 2.50e+03 3.71e+01 bond pdb=" C11 7LD R 501 " pdb=" C9 7LD R 501 " ideal model delta sigma weight residual 1.525 1.406 0.119 2.00e-02 2.50e+03 3.57e+01 bond pdb=" C10 7LD R 501 " pdb=" C14 7LD R 501 " ideal model delta sigma weight residual 1.501 1.398 0.103 2.00e-02 2.50e+03 2.67e+01 bond pdb=" C15 7LD R 501 " pdb=" C7 7LD R 501 " ideal model delta sigma weight residual 1.491 1.396 0.095 2.00e-02 2.50e+03 2.25e+01 bond pdb=" C3 7LD R 501 " pdb=" C7 7LD R 501 " ideal model delta sigma weight residual 1.414 1.322 0.092 2.00e-02 2.50e+03 2.13e+01 ... (remaining 8574 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 11357 1.72 - 3.44: 259 3.44 - 5.15: 57 5.15 - 6.87: 15 6.87 - 8.59: 6 Bond angle restraints: 11694 Sorted by residual: angle pdb=" N LYS R 247 " pdb=" CA LYS R 247 " pdb=" C LYS R 247 " ideal model delta sigma weight residual 112.57 104.65 7.92 1.13e+00 7.83e-01 4.91e+01 angle pdb=" N LEU R 244 " pdb=" CA LEU R 244 " pdb=" C LEU R 244 " ideal model delta sigma weight residual 113.23 105.54 7.69 1.24e+00 6.50e-01 3.85e+01 angle pdb=" N GLN R 320 " pdb=" CA GLN R 320 " pdb=" C GLN R 320 " ideal model delta sigma weight residual 113.88 106.26 7.62 1.23e+00 6.61e-01 3.84e+01 angle pdb=" C GLN R 320 " pdb=" CA GLN R 320 " pdb=" CB GLN R 320 " ideal model delta sigma weight residual 109.03 117.62 -8.59 1.62e+00 3.81e-01 2.81e+01 angle pdb=" N GLU R 319 " pdb=" CA GLU R 319 " pdb=" C GLU R 319 " ideal model delta sigma weight residual 113.17 106.59 6.58 1.26e+00 6.30e-01 2.73e+01 ... (remaining 11689 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.36: 4927 30.36 - 60.72: 100 60.72 - 91.07: 7 91.07 - 121.43: 0 121.43 - 151.79: 1 Dihedral angle restraints: 5035 sinusoidal: 1793 harmonic: 3242 Sorted by residual: dihedral pdb=" C16 7LD R 501 " pdb=" C17 7LD R 501 " pdb=" N3 7LD R 501 " pdb=" C18 7LD R 501 " ideal model delta sinusoidal sigma weight residual 91.75 -116.46 -151.79 1 3.00e+01 1.11e-03 2.01e+01 dihedral pdb=" CA GLU R 118 " pdb=" C GLU R 118 " pdb=" N ALA R 119 " pdb=" CA ALA R 119 " ideal model delta harmonic sigma weight residual -180.00 -160.48 -19.52 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA LYS B 73 " pdb=" C LYS B 73 " pdb=" N PHE B 74 " pdb=" CA PHE B 74 " ideal model delta harmonic sigma weight residual 180.00 161.36 18.64 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 5032 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1187 0.065 - 0.131: 172 0.131 - 0.196: 10 0.196 - 0.261: 3 0.261 - 0.326: 3 Chirality restraints: 1375 Sorted by residual: chirality pdb=" C14 7LD R 501 " pdb=" C10 7LD R 501 " pdb=" C13 7LD R 501 " pdb=" C16 7LD R 501 " both_signs ideal model delta sigma weight residual False 2.63 2.30 0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CB VAL R 325 " pdb=" CA VAL R 325 " pdb=" CG1 VAL R 325 " pdb=" CG2 VAL R 325 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" C11 7LD R 501 " pdb=" C15 7LD R 501 " pdb=" C9 7LD R 501 " pdb=" N2 7LD R 501 " both_signs ideal model delta sigma weight residual False 2.48 2.18 0.30 2.00e-01 2.50e+01 2.19e+00 ... (remaining 1372 not shown) Planarity restraints: 1469 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN R 86 " 0.014 2.00e-02 2.50e+03 2.89e-02 8.38e+00 pdb=" C GLN R 86 " -0.050 2.00e-02 2.50e+03 pdb=" O GLN R 86 " 0.019 2.00e-02 2.50e+03 pdb=" N TYR R 87 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 325 " -0.012 2.00e-02 2.50e+03 2.44e-02 5.96e+00 pdb=" C VAL R 325 " 0.042 2.00e-02 2.50e+03 pdb=" O VAL R 325 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU R 326 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER R 323 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.20e+00 pdb=" C SER R 323 " -0.035 2.00e-02 2.50e+03 pdb=" O SER R 323 " 0.013 2.00e-02 2.50e+03 pdb=" N LYS R 324 " 0.012 2.00e-02 2.50e+03 ... (remaining 1466 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 479 2.74 - 3.28: 7850 3.28 - 3.82: 12976 3.82 - 4.36: 15424 4.36 - 4.90: 27767 Nonbonded interactions: 64496 Sorted by model distance: nonbonded pdb=" OG SER C 331 " pdb=" OD1 ASP C 333 " model vdw 2.196 3.040 nonbonded pdb=" O ILE R 205 " pdb=" OG1 THR R 206 " model vdw 2.303 3.040 nonbonded pdb=" NE2 GLN C 75 " pdb=" O SER C 98 " model vdw 2.362 3.120 nonbonded pdb=" O SER E 106 " pdb=" OG SER E 106 " model vdw 2.363 3.040 nonbonded pdb=" NH1 ARG E 190 " pdb=" OD2 ASP E 211 " model vdw 2.374 3.120 ... (remaining 64491 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 2.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.040 Find NCS groups from input model: 0.100 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:12.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 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 : 0.005 0.122 8579 Z= 0.319 Angle : 0.670 8.591 11694 Z= 0.403 Chirality : 0.048 0.326 1375 Planarity : 0.004 0.046 1469 Dihedral : 12.702 151.787 2927 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.12 % Allowed : 0.70 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 (0.26), residues: 1101 helix: 0.48 (0.29), residues: 377 sheet: 1.31 (0.33), residues: 275 loop : -0.96 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 121 HIS 0.012 0.002 HIS R 242 PHE 0.018 0.001 PHE R 133 TYR 0.023 0.001 TYR R 87 ARG 0.002 0.000 ARG R 213 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 163 time to evaluate : 0.876 Fit side-chains REVERT: B 199 ASP cc_start: 0.7358 (m-30) cc_final: 0.7092 (m-30) REVERT: C 188 MET cc_start: 0.8901 (mmm) cc_final: 0.8606 (mmm) REVERT: E 34 MET cc_start: 0.8697 (mmm) cc_final: 0.8419 (mmt) outliers start: 1 outliers final: 0 residues processed: 163 average time/residue: 1.1232 time to fit residues: 195.7209 Evaluate side-chains 148 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.2980 chunk 82 optimal weight: 0.3980 chunk 45 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 44 optimal weight: 0.2980 chunk 85 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 ASN C 293 ASN E 182 ASN R 318 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.127820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.107288 restraints weight = 12134.559| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.51 r_work: 0.3216 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.0939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8579 Z= 0.230 Angle : 0.556 7.091 11694 Z= 0.294 Chirality : 0.043 0.159 1375 Planarity : 0.004 0.047 1469 Dihedral : 6.921 143.291 1213 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.76 % Allowed : 8.43 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.41 (0.26), residues: 1101 helix: 0.79 (0.29), residues: 374 sheet: 1.30 (0.32), residues: 282 loop : -0.84 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 121 HIS 0.007 0.001 HIS B 209 PHE 0.017 0.001 PHE B 74 TYR 0.012 0.001 TYR E 178 ARG 0.005 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 148 time to evaluate : 0.876 Fit side-chains REVERT: B 199 ASP cc_start: 0.7943 (m-30) cc_final: 0.7573 (m-30) REVERT: C 188 MET cc_start: 0.9002 (mmm) cc_final: 0.8788 (mmm) REVERT: C 217 MET cc_start: 0.8455 (pmm) cc_final: 0.8016 (pmm) outliers start: 15 outliers final: 10 residues processed: 151 average time/residue: 1.0927 time to fit residues: 176.9788 Evaluate side-chains 158 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 148 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 114 THR Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 371 VAL Chi-restraints excluded: chain R residue 381 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 60 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 25 optimal weight: 0.1980 chunk 42 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 88 optimal weight: 0.0970 chunk 92 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 105 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 ASN C 293 ASN R 318 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.126568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.106173 restraints weight = 12321.018| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.61 r_work: 0.3177 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8579 Z= 0.260 Angle : 0.565 7.868 11694 Z= 0.298 Chirality : 0.044 0.155 1375 Planarity : 0.004 0.048 1469 Dihedral : 6.767 127.158 1213 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.22 % Allowed : 9.72 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.41 (0.26), residues: 1101 helix: 0.79 (0.29), residues: 379 sheet: 1.31 (0.32), residues: 282 loop : -0.86 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 121 HIS 0.007 0.001 HIS B 209 PHE 0.016 0.002 PHE R 227 TYR 0.012 0.001 TYR E 178 ARG 0.009 0.000 ARG C 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 0.965 Fit side-chains REVERT: B 73 LYS cc_start: 0.8308 (mmpt) cc_final: 0.7934 (mmpt) REVERT: B 126 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.7905 (tppp) REVERT: B 199 ASP cc_start: 0.7941 (m-30) cc_final: 0.7629 (m-30) REVERT: B 200 ILE cc_start: 0.7688 (tp) cc_final: 0.7440 (tt) REVERT: C 52 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.8305 (ptm160) REVERT: C 134 ARG cc_start: 0.8266 (mtm110) cc_final: 0.8009 (ptp-110) REVERT: C 217 MET cc_start: 0.8557 (OUTLIER) cc_final: 0.8123 (pmm) outliers start: 19 outliers final: 11 residues processed: 154 average time/residue: 1.1623 time to fit residues: 190.9844 Evaluate side-chains 162 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 148 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain R residue 114 THR Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 371 VAL Chi-restraints excluded: chain R residue 381 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 16 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 97 optimal weight: 0.0060 chunk 108 optimal weight: 0.0270 chunk 15 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 87 optimal weight: 0.3980 overall best weight: 0.6856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 ASN R 162 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.125916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.105409 restraints weight = 12191.605| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.64 r_work: 0.3161 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8579 Z= 0.283 Angle : 0.578 8.377 11694 Z= 0.304 Chirality : 0.045 0.133 1375 Planarity : 0.004 0.049 1469 Dihedral : 6.531 108.831 1213 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.16 % Allowed : 11.94 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.42 (0.26), residues: 1101 helix: 0.91 (0.29), residues: 373 sheet: 1.33 (0.32), residues: 282 loop : -0.94 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 121 HIS 0.007 0.001 HIS B 209 PHE 0.016 0.002 PHE R 227 TYR 0.012 0.001 TYR E 178 ARG 0.006 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 151 time to evaluate : 0.856 Fit side-chains REVERT: B 31 ARG cc_start: 0.7211 (ttp80) cc_final: 0.6952 (ttp-170) REVERT: B 126 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.7883 (ttmm) REVERT: B 199 ASP cc_start: 0.7924 (m-30) cc_final: 0.7632 (m-30) REVERT: C 52 ARG cc_start: 0.8804 (OUTLIER) cc_final: 0.8347 (ptm160) REVERT: C 217 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8197 (pmm) REVERT: R 90 ASN cc_start: 0.8313 (m-40) cc_final: 0.7983 (m-40) REVERT: R 158 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8123 (tmtm) outliers start: 27 outliers final: 14 residues processed: 163 average time/residue: 1.1182 time to fit residues: 195.1339 Evaluate side-chains 167 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 149 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 114 THR Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 158 LYS Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 381 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 45 optimal weight: 1.9990 chunk 6 optimal weight: 0.0980 chunk 78 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 66 optimal weight: 0.3980 chunk 60 optimal weight: 3.9990 chunk 99 optimal weight: 0.5980 chunk 18 optimal weight: 5.9990 chunk 25 optimal weight: 0.0670 chunk 29 optimal weight: 0.3980 overall best weight: 0.3118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 ASN B 116 ASN B 131 ASN C 16 ASN C 88 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.124233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.103793 restraints weight = 12176.820| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.60 r_work: 0.3206 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8579 Z= 0.163 Angle : 0.521 6.507 11694 Z= 0.277 Chirality : 0.042 0.166 1375 Planarity : 0.004 0.046 1469 Dihedral : 5.966 91.276 1213 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.58 % Allowed : 13.23 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.26), residues: 1101 helix: 1.18 (0.29), residues: 376 sheet: 1.36 (0.32), residues: 282 loop : -0.88 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 121 HIS 0.004 0.001 HIS B 209 PHE 0.013 0.001 PHE B 74 TYR 0.013 0.001 TYR E 178 ARG 0.009 0.000 ARG C 134 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 0.873 Fit side-chains REVERT: B 126 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.7776 (tppp) REVERT: B 199 ASP cc_start: 0.7870 (m-30) cc_final: 0.7564 (m-30) REVERT: C 52 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.8324 (ptm160) REVERT: C 217 MET cc_start: 0.8589 (pmm) cc_final: 0.8127 (pmm) REVERT: R 90 ASN cc_start: 0.8272 (m-40) cc_final: 0.7956 (m-40) REVERT: R 158 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8039 (tmtm) outliers start: 22 outliers final: 14 residues processed: 155 average time/residue: 1.1364 time to fit residues: 188.0012 Evaluate side-chains 159 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 114 THR Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 158 LYS Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 381 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 16 optimal weight: 0.5980 chunk 89 optimal weight: 0.8980 chunk 67 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 25 optimal weight: 0.4980 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 HIS B 101 ASN B 116 ASN B 131 ASN R 162 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.122750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.102253 restraints weight = 12115.104| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.57 r_work: 0.3178 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8579 Z= 0.249 Angle : 0.569 8.184 11694 Z= 0.298 Chirality : 0.043 0.142 1375 Planarity : 0.004 0.047 1469 Dihedral : 5.831 72.056 1213 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.58 % Allowed : 14.17 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.49 (0.26), residues: 1101 helix: 1.04 (0.29), residues: 379 sheet: 1.23 (0.32), residues: 276 loop : -0.88 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 121 HIS 0.006 0.001 HIS B 209 PHE 0.016 0.002 PHE R 227 TYR 0.011 0.001 TYR E 178 ARG 0.010 0.000 ARG C 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 0.918 Fit side-chains REVERT: B 31 ARG cc_start: 0.7217 (ttp80) cc_final: 0.6983 (ttp-170) REVERT: B 126 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7960 (ttmm) REVERT: B 199 ASP cc_start: 0.7839 (m-30) cc_final: 0.7485 (m-30) REVERT: C 52 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.8355 (ptm160) REVERT: C 217 MET cc_start: 0.8588 (OUTLIER) cc_final: 0.8186 (pmm) REVERT: R 90 ASN cc_start: 0.8292 (m-40) cc_final: 0.7967 (m-40) REVERT: R 158 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8104 (tmtm) outliers start: 22 outliers final: 14 residues processed: 161 average time/residue: 1.1334 time to fit residues: 195.6218 Evaluate side-chains 168 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 114 THR Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 158 LYS Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 381 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 103 optimal weight: 0.4980 chunk 97 optimal weight: 0.9990 chunk 102 optimal weight: 0.3980 chunk 55 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 HIS B 101 ASN B 116 ASN B 131 ASN C 16 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.125261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.104557 restraints weight = 12341.323| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.63 r_work: 0.3151 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 8579 Z= 0.305 Angle : 0.617 13.576 11694 Z= 0.319 Chirality : 0.045 0.226 1375 Planarity : 0.004 0.047 1469 Dihedral : 5.800 58.577 1213 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.81 % Allowed : 15.22 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.44 (0.26), residues: 1101 helix: 0.96 (0.29), residues: 379 sheet: 1.23 (0.32), residues: 280 loop : -0.89 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP R 121 HIS 0.008 0.002 HIS B 209 PHE 0.017 0.002 PHE R 227 TYR 0.011 0.001 TYR E 178 ARG 0.012 0.001 ARG C 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 152 time to evaluate : 0.933 Fit side-chains REVERT: B 31 ARG cc_start: 0.7315 (ttp80) cc_final: 0.7066 (ttp80) REVERT: B 199 ASP cc_start: 0.7806 (m-30) cc_final: 0.7501 (m-30) REVERT: C 52 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.8321 (ptm160) REVERT: C 217 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.8215 (pmm) REVERT: R 90 ASN cc_start: 0.8307 (m-40) cc_final: 0.7990 (m-40) REVERT: R 158 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8150 (tmtm) outliers start: 24 outliers final: 18 residues processed: 164 average time/residue: 1.1389 time to fit residues: 199.5147 Evaluate side-chains 170 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 114 THR Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 158 LYS Chi-restraints excluded: chain R residue 205 ILE Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 352 SER Chi-restraints excluded: chain R residue 381 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 7 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 83 optimal weight: 0.0270 chunk 89 optimal weight: 0.5980 chunk 71 optimal weight: 0.0970 chunk 59 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 HIS B 101 ASN B 116 ASN B 131 ASN C 16 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.126798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.106152 restraints weight = 12268.038| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.64 r_work: 0.3169 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8579 Z= 0.209 Angle : 0.566 11.130 11694 Z= 0.293 Chirality : 0.043 0.140 1375 Planarity : 0.004 0.052 1469 Dihedral : 5.499 56.148 1213 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.81 % Allowed : 15.81 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.62 (0.26), residues: 1101 helix: 1.12 (0.29), residues: 379 sheet: 1.32 (0.31), residues: 286 loop : -0.83 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 121 HIS 0.006 0.001 HIS B 209 PHE 0.014 0.001 PHE B 74 TYR 0.011 0.001 TYR E 178 ARG 0.013 0.001 ARG C 134 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 148 time to evaluate : 1.229 Fit side-chains REVERT: B 31 ARG cc_start: 0.7274 (ttp80) cc_final: 0.7059 (ttp80) REVERT: B 126 LYS cc_start: 0.8375 (tppp) cc_final: 0.7990 (ttmm) REVERT: B 199 ASP cc_start: 0.7908 (m-30) cc_final: 0.7576 (m-30) REVERT: C 217 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.8240 (pmm) REVERT: C 237 ASN cc_start: 0.8184 (t0) cc_final: 0.7934 (t0) REVERT: R 90 ASN cc_start: 0.8285 (m-40) cc_final: 0.7938 (m-40) REVERT: R 158 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8094 (tmtm) outliers start: 24 outliers final: 17 residues processed: 161 average time/residue: 1.1365 time to fit residues: 195.3284 Evaluate side-chains 166 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 147 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 114 THR Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 158 LYS Chi-restraints excluded: chain R residue 205 ILE Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 381 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 91 optimal weight: 0.3980 chunk 23 optimal weight: 0.9980 chunk 8 optimal weight: 0.0070 chunk 0 optimal weight: 3.9990 chunk 98 optimal weight: 0.5980 chunk 108 optimal weight: 0.2980 chunk 51 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 95 optimal weight: 0.0020 overall best weight: 0.2606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 HIS B 101 ASN B 131 ASN C 16 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.128402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.107622 restraints weight = 12358.967| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.54 r_work: 0.3210 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8579 Z= 0.148 Angle : 0.536 10.462 11694 Z= 0.278 Chirality : 0.042 0.211 1375 Planarity : 0.004 0.055 1469 Dihedral : 5.120 52.605 1213 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.46 % Allowed : 16.86 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1101 helix: 1.35 (0.29), residues: 382 sheet: 1.29 (0.32), residues: 281 loop : -0.76 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 121 HIS 0.004 0.001 HIS B 209 PHE 0.014 0.001 PHE B 74 TYR 0.011 0.001 TYR E 178 ARG 0.014 0.000 ARG C 134 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 150 time to evaluate : 0.952 Fit side-chains REVERT: B 31 ARG cc_start: 0.7181 (ttp80) cc_final: 0.6967 (ttp-170) REVERT: B 199 ASP cc_start: 0.7875 (m-30) cc_final: 0.7554 (m-30) REVERT: C 217 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.8169 (pmm) REVERT: R 90 ASN cc_start: 0.8267 (m-40) cc_final: 0.7921 (m-40) REVERT: R 158 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.7993 (tmtm) outliers start: 21 outliers final: 14 residues processed: 159 average time/residue: 1.1388 time to fit residues: 193.8265 Evaluate side-chains 164 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 114 THR Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 158 LYS Chi-restraints excluded: chain R residue 205 ILE Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 381 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 37 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 chunk 99 optimal weight: 0.0010 chunk 48 optimal weight: 0.7980 chunk 94 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 47 optimal weight: 0.4980 chunk 40 optimal weight: 0.9990 chunk 36 optimal weight: 0.0870 chunk 108 optimal weight: 0.9990 overall best weight: 0.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 HIS B 116 ASN B 131 ASN C 293 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.127884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.107203 restraints weight = 12194.368| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.62 r_work: 0.3193 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8579 Z= 0.177 Angle : 0.556 9.868 11694 Z= 0.287 Chirality : 0.042 0.141 1375 Planarity : 0.004 0.059 1469 Dihedral : 5.129 53.158 1213 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.34 % Allowed : 17.80 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1101 helix: 1.38 (0.29), residues: 382 sheet: 1.19 (0.32), residues: 284 loop : -0.71 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 121 HIS 0.005 0.001 HIS B 209 PHE 0.014 0.001 PHE B 74 TYR 0.011 0.001 TYR E 178 ARG 0.014 0.001 ARG C 134 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 1.054 Fit side-chains REVERT: B 31 ARG cc_start: 0.7209 (ttp80) cc_final: 0.6966 (ttp80) REVERT: B 199 ASP cc_start: 0.7808 (m-30) cc_final: 0.7514 (m-30) REVERT: C 217 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.8187 (pmm) REVERT: R 90 ASN cc_start: 0.8276 (m-40) cc_final: 0.7930 (m-40) REVERT: R 125 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8277 (mm) REVERT: R 158 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8046 (tmtm) REVERT: R 318 ASN cc_start: 0.8335 (m-40) cc_final: 0.8015 (m-40) outliers start: 20 outliers final: 15 residues processed: 161 average time/residue: 1.1557 time to fit residues: 198.9980 Evaluate side-chains 167 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 149 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 114 THR Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 158 LYS Chi-restraints excluded: chain R residue 205 ILE Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 381 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 30 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 90 optimal weight: 0.0980 chunk 10 optimal weight: 1.9990 chunk 95 optimal weight: 0.0870 chunk 46 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 HIS B 101 ASN B 131 ASN C 293 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.126826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.106179 restraints weight = 12280.467| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.59 r_work: 0.3180 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8579 Z= 0.219 Angle : 0.575 9.579 11694 Z= 0.297 Chirality : 0.044 0.233 1375 Planarity : 0.004 0.059 1469 Dihedral : 5.281 54.950 1213 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.22 % Allowed : 18.15 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1101 helix: 1.32 (0.29), residues: 379 sheet: 1.29 (0.31), residues: 286 loop : -0.75 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 121 HIS 0.006 0.001 HIS B 209 PHE 0.014 0.001 PHE R 227 TYR 0.010 0.001 TYR E 178 ARG 0.014 0.001 ARG C 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7025.14 seconds wall clock time: 124 minutes 22.65 seconds (7462.65 seconds total)