Starting phenix.real_space_refine on Wed Feb 4 05:34:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kpt_62491/02_2026/9kpt_62491_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kpt_62491/02_2026/9kpt_62491.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kpt_62491/02_2026/9kpt_62491.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kpt_62491/02_2026/9kpt_62491.map" model { file = "/net/cci-nas-00/data/ceres_data/9kpt_62491/02_2026/9kpt_62491_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kpt_62491/02_2026/9kpt_62491_neut.cif" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.038 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: 6 Type Number sf(0) Gaussians Fe 9 7.16 5 P 3 5.49 5 S 66 5.16 5 C 5578 2.51 5 N 1509 2.21 5 O 1632 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8797 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4584 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 23, 'TRANS': 569} Chain: "B" Number of atoms: 1894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1894 Classifications: {'peptide': 237} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 222} Chain: "C" Number of atoms: 1163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1163 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 140} Chain: "D" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1015 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 9, 'TRANS': 121} Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 19 Unusual residues: {'F3S': 1, 'FES': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 69 Unusual residues: {'PEE': 1, 'UQ1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5112 SG CYS B 95 48.255 35.314 75.106 1.00 37.77 S ATOM 5194 SG CYS B 107 47.396 33.425 78.049 1.00 41.15 S ATOM 5058 SG CYS B 87 43.646 35.835 80.263 1.00 46.64 S ATOM 5096 SG CYS B 92 44.049 38.391 78.380 1.00 44.34 S ATOM 5833 SG CYS B 185 40.092 39.693 63.404 1.00 39.64 S ATOM 5794 SG CYS B 179 36.626 39.996 68.383 1.00 47.64 S ATOM 6334 SG CYS B 246 38.623 34.204 65.986 1.00 43.30 S ATOM 5816 SG CYS B 182 42.356 37.991 69.152 1.00 44.93 S ATOM 6256 SG CYS B 236 37.109 41.138 53.042 1.00 46.00 S ATOM 5858 SG CYS B 189 42.866 41.673 55.045 1.00 42.87 S ATOM 6303 SG CYS B 242 38.958 36.786 57.006 1.00 41.67 S Time building chain proxies: 1.75, per 1000 atoms: 0.20 Number of scatterers: 8797 At special positions: 0 Unit cell: (80.66, 84.36, 132.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 9 26.01 S 66 16.00 P 3 15.00 O 1632 8.00 N 1509 7.00 C 5578 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.37 Conformation dependent library (CDL) restraints added in 308.2 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S B 303 " pdb="FE3 F3S B 303 " - pdb=" SG CYS B 189 " pdb="FE4 F3S B 303 " - pdb=" SG CYS B 242 " pdb="FE1 F3S B 303 " - pdb=" SG CYS B 236 " pdb=" FES B 301 " pdb="FE2 FES B 301 " - pdb=" SG CYS B 92 " pdb="FE2 FES B 301 " - pdb=" SG CYS B 87 " pdb="FE1 FES B 301 " - pdb=" SG CYS B 107 " pdb="FE1 FES B 301 " - pdb=" SG CYS B 95 " pdb=" SF4 B 302 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 182 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 185 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 246 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 179 " Number of angles added : 27 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2028 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 8 sheets defined 39.3% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 70 through 75 removed outlier: 3.809A pdb=" N ALA A 74 " --> pdb=" O GLY A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 93 removed outlier: 3.809A pdb=" N SER A 89 " --> pdb=" O PRO A 86 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N HIS A 90 " --> pdb=" O THR A 87 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N THR A 91 " --> pdb=" O ARG A 88 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL A 92 " --> pdb=" O SER A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 120 removed outlier: 3.813A pdb=" N HIS A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR A 117 " --> pdb=" O HIS A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 136 removed outlier: 3.957A pdb=" N TYR A 132 " --> pdb=" O ASP A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 146 removed outlier: 3.657A pdb=" N SER A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE A 141 " --> pdb=" O ALA A 137 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE A 142 " --> pdb=" O PRO A 138 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU A 143 " --> pdb=" O LYS A 139 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 202 removed outlier: 3.732A pdb=" N THR A 194 " --> pdb=" O ALA A 190 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY A 197 " --> pdb=" O HIS A 193 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG A 201 " --> pdb=" O GLY A 197 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N HIS A 202 " --> pdb=" O GLN A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 273 Processing helix chain 'A' and resid 299 through 303 removed outlier: 3.684A pdb=" N ARG A 303 " --> pdb=" O GLU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 340 removed outlier: 3.709A pdb=" N ILE A 338 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR A 339 " --> pdb=" O SER A 335 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N MET A 340 " --> pdb=" O ARG A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 345 removed outlier: 3.620A pdb=" N GLU A 344 " --> pdb=" O MET A 340 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY A 345 " --> pdb=" O GLU A 341 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 340 through 345' Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 372 through 378 removed outlier: 3.753A pdb=" N GLU A 376 " --> pdb=" O PRO A 372 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR A 377 " --> pdb=" O GLY A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 456 removed outlier: 3.708A pdb=" N LEU A 453 " --> pdb=" O SER A 449 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL A 454 " --> pdb=" O LEU A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 466 removed outlier: 4.090A pdb=" N ALA A 461 " --> pdb=" O GLY A 457 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL A 464 " --> pdb=" O VAL A 460 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA A 465 " --> pdb=" O ALA A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 494 removed outlier: 3.800A pdb=" N LEU A 492 " --> pdb=" O ASN A 488 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASN A 494 " --> pdb=" O ASP A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 515 removed outlier: 3.508A pdb=" N GLN A 513 " --> pdb=" O LYS A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 537 removed outlier: 3.565A pdb=" N ARG A 530 " --> pdb=" O ASP A 526 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR A 533 " --> pdb=" O VAL A 529 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA A 534 " --> pdb=" O ARG A 530 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU A 536 " --> pdb=" O ILE A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 576 removed outlier: 3.677A pdb=" N LEU A 561 " --> pdb=" O GLU A 557 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN A 562 " --> pdb=" O THR A 558 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 564 " --> pdb=" O GLU A 560 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR A 566 " --> pdb=" O GLN A 562 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N CYS A 567 " --> pdb=" O ASN A 563 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN A 570 " --> pdb=" O THR A 566 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR A 571 " --> pdb=" O CYS A 567 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL A 573 " --> pdb=" O SER A 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 77 removed outlier: 3.713A pdb=" N LYS B 72 " --> pdb=" O ASP B 68 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE B 73 " --> pdb=" O ALA B 69 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP B 75 " --> pdb=" O LEU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 146 removed outlier: 3.503A pdb=" N LYS B 145 " --> pdb=" O TYR B 141 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER B 146 " --> pdb=" O GLN B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 174 removed outlier: 3.536A pdb=" N ASP B 174 " --> pdb=" O LYS B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 188 Processing helix chain 'B' and resid 189 through 195 removed outlier: 3.809A pdb=" N TRP B 194 " --> pdb=" O PRO B 190 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASN B 195 " --> pdb=" O SER B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 213 removed outlier: 3.673A pdb=" N GLN B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N TRP B 211 " --> pdb=" O GLN B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 226 removed outlier: 3.559A pdb=" N ALA B 225 " --> pdb=" O THR B 222 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N MET B 226 " --> pdb=" O ARG B 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 222 through 226' Processing helix chain 'B' and resid 240 through 245 removed outlier: 3.562A pdb=" N ARG B 244 " --> pdb=" O MET B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 265 removed outlier: 3.963A pdb=" N PHE B 265 " --> pdb=" O LYS B 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 73 removed outlier: 3.562A pdb=" N ALA C 63 " --> pdb=" O LYS C 59 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN C 66 " --> pdb=" O ILE C 62 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ILE C 67 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS C 70 " --> pdb=" O GLN C 66 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLN C 71 " --> pdb=" O ILE C 67 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA C 73 " --> pdb=" O ASN C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 113 removed outlier: 4.092A pdb=" N SER C 93 " --> pdb=" O THR C 89 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N HIS C 96 " --> pdb=" O LEU C 92 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ARG C 97 " --> pdb=" O SER C 93 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU C 100 " --> pdb=" O HIS C 96 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY C 106 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR C 111 " --> pdb=" O PHE C 107 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 120 removed outlier: 3.588A pdb=" N LEU C 119 " --> pdb=" O GLY C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 135 removed outlier: 4.035A pdb=" N TRP C 132 " --> pdb=" O LYS C 128 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN C 135 " --> pdb=" O ASN C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 166 removed outlier: 3.700A pdb=" N TRP C 143 " --> pdb=" O LYS C 139 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA C 150 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR C 151 " --> pdb=" O GLY C 147 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N HIS C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE C 161 " --> pdb=" O TYR C 157 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU C 164 " --> pdb=" O ALA C 160 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE C 165 " --> pdb=" O ILE C 161 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TRP C 166 " --> pdb=" O ARG C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 198 removed outlier: 3.816A pdb=" N TYR C 178 " --> pdb=" O LEU C 174 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR C 180 " --> pdb=" O GLY C 176 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR C 182 " --> pdb=" O TYR C 178 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU C 184 " --> pdb=" O THR C 180 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N PHE C 187 " --> pdb=" O ALA C 183 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR C 193 " --> pdb=" O ALA C 189 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU C 196 " --> pdb=" O GLY C 192 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU C 198 " --> pdb=" O TYR C 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 76 removed outlier: 3.628A pdb=" N TYR D 70 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N MET D 71 " --> pdb=" O TYR D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.678A pdb=" N ALA D 86 " --> pdb=" O ALA D 83 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N MET D 87 " --> pdb=" O THR D 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 83 through 87' Processing helix chain 'D' and resid 95 through 121 removed outlier: 3.829A pdb=" N PHE D 100 " --> pdb=" O ALA D 96 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHE D 101 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU D 106 " --> pdb=" O SER D 102 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU D 112 " --> pdb=" O TYR D 108 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE D 113 " --> pdb=" O CYS D 109 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR D 118 " --> pdb=" O ASN D 114 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR D 120 " --> pdb=" O CYS D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 135 removed outlier: 3.589A pdb=" N ALA D 133 " --> pdb=" O TRP D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 144 Processing helix chain 'D' and resid 145 through 153 removed outlier: 3.512A pdb=" N TYR D 149 " --> pdb=" O LEU D 145 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU D 151 " --> pdb=" O GLY D 147 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR D 153 " --> pdb=" O TYR D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 163 Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 52 removed outlier: 6.590A pdb=" N ILE A 49 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N ARG A 239 " --> pdb=" O ILE A 49 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N HIS A 51 " --> pdb=" O ARG A 239 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLY A 224 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP A 214 " --> pdb=" O ILE A 226 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TYR A 228 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N ALA A 212 " --> pdb=" O TYR A 228 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 205 through 207 removed outlier: 6.926A pdb=" N THR A 78 " --> pdb=" O HIS A 205 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N PHE A 207 " --> pdb=" O THR A 78 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N CYS A 80 " --> pdb=" O PHE A 207 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE A 425 " --> pdb=" O ALA A 412 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ALA A 412 " --> pdb=" O ILE A 425 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 278 through 279 removed outlier: 3.534A pdb=" N THR A 614 " --> pdb=" O TRP A 605 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 284 through 287 removed outlier: 6.555A pdb=" N GLN A 285 " --> pdb=" O HIS A 398 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR A 396 " --> pdb=" O HIS A 287 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 308 through 310 removed outlier: 3.871A pdb=" N PHE A 308 " --> pdb=" O GLN A 358 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A 357 " --> pdb=" O ILE A 391 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE A 391 " --> pdb=" O LEU A 357 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 404 through 405 removed outlier: 5.765A pdb=" N ILE A 404 " --> pdb=" O CYS A 436 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 499 through 500 removed outlier: 6.626A pdb=" N ARG A 499 " --> pdb=" O LYS A 543 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 51 through 58 removed outlier: 9.442A pdb=" N LEU B 119 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N THR B 35 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N ILE B 121 " --> pdb=" O THR B 35 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LYS B 37 " --> pdb=" O ILE B 121 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG B 102 " --> pdb=" O ILE B 99 " (cutoff:3.500A) 216 hydrogen bonds defined for protein. 621 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: 1.19 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.73: 8901 1.73 - 2.29: 105 2.29 - 2.84: 2 2.84 - 3.39: 0 3.39 - 3.95: 3 Bond restraints: 9011 Sorted by residual: bond pdb=" S4 F3S B 303 " pdb="FE1 F3S B 303 " ideal model delta sigma weight residual 2.233 3.947 -1.714 2.00e-02 2.50e+03 7.34e+03 bond pdb=" S2 F3S B 303 " pdb="FE3 F3S B 303 " ideal model delta sigma weight residual 2.300 3.888 -1.588 2.00e-02 2.50e+03 6.30e+03 bond pdb=" S1 F3S B 303 " pdb="FE4 F3S B 303 " ideal model delta sigma weight residual 2.258 3.822 -1.564 2.00e-02 2.50e+03 6.12e+03 bond pdb=" C CYS B 92 " pdb=" N GLY B 93 " ideal model delta sigma weight residual 1.324 1.551 -0.227 1.33e-02 5.65e+03 2.91e+02 bond pdb=" C SER A 89 " pdb=" N HIS A 90 " ideal model delta sigma weight residual 1.333 1.578 -0.245 1.47e-02 4.63e+03 2.77e+02 ... (remaining 9006 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.92: 12191 9.92 - 19.84: 19 19.84 - 29.77: 0 29.77 - 39.69: 8 39.69 - 49.61: 2 Bond angle restraints: 12220 Sorted by residual: angle pdb=" S1 F3S B 303 " pdb="FE4 F3S B 303 " pdb=" S3 F3S B 303 " ideal model delta sigma weight residual 114.75 65.14 49.61 3.00e+00 1.11e-01 2.73e+02 angle pdb=" S3 F3S B 303 " pdb="FE1 F3S B 303 " pdb=" S4 F3S B 303 " ideal model delta sigma weight residual 112.59 64.24 48.35 3.00e+00 1.11e-01 2.60e+02 angle pdb=" O CYS B 242 " pdb=" C CYS B 242 " pdb=" N THR B 243 " ideal model delta sigma weight residual 122.09 135.30 -13.21 1.08e+00 8.57e-01 1.50e+02 angle pdb="FE1 F3S B 303 " pdb=" S4 F3S B 303 " pdb="FE3 F3S B 303 " ideal model delta sigma weight residual 74.86 40.37 34.49 3.00e+00 1.11e-01 1.32e+02 angle pdb=" S1 FES B 301 " pdb="FE2 FES B 301 " pdb=" S2 FES B 301 " ideal model delta sigma weight residual 104.33 91.48 12.85 1.14e+00 7.69e-01 1.27e+02 ... (remaining 12215 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.86: 5221 34.86 - 69.72: 134 69.72 - 104.58: 7 104.58 - 139.44: 2 139.44 - 174.30: 4 Dihedral angle restraints: 5368 sinusoidal: 2189 harmonic: 3179 Sorted by residual: dihedral pdb=" CD ARG A 237 " pdb=" NE ARG A 237 " pdb=" CZ ARG A 237 " pdb=" NH1 ARG A 237 " ideal model delta sinusoidal sigma weight residual 0.00 51.02 -51.02 1 1.00e+01 1.00e-02 3.56e+01 dihedral pdb=" CA ALA A 182 " pdb=" C ALA A 182 " pdb=" N VAL A 183 " pdb=" CA VAL A 183 " ideal model delta harmonic sigma weight residual 180.00 154.00 26.00 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA ALA A 322 " pdb=" C ALA A 322 " pdb=" N PRO A 323 " pdb=" CA PRO A 323 " ideal model delta harmonic sigma weight residual -180.00 -154.09 -25.91 0 5.00e+00 4.00e-02 2.69e+01 ... (remaining 5365 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.130: 1328 4.130 - 8.260: 0 8.260 - 12.389: 0 12.389 - 16.519: 0 16.519 - 20.649: 5 Chirality restraints: 1333 Sorted by residual: chirality pdb="FE1 SF4 B 302 " pdb=" S2 SF4 B 302 " pdb=" S3 SF4 B 302 " pdb=" S4 SF4 B 302 " both_signs ideal model delta sigma weight residual False -10.55 10.09 -20.65 2.00e-01 2.50e+01 1.07e+04 chirality pdb="FE3 SF4 B 302 " pdb=" S1 SF4 B 302 " pdb=" S2 SF4 B 302 " pdb=" S4 SF4 B 302 " both_signs ideal model delta sigma weight residual False -10.55 10.07 -20.62 2.00e-01 2.50e+01 1.06e+04 chirality pdb="FE4 SF4 B 302 " pdb=" S1 SF4 B 302 " pdb=" S2 SF4 B 302 " pdb=" S3 SF4 B 302 " both_signs ideal model delta sigma weight residual False 10.55 -10.01 20.57 2.00e-01 2.50e+01 1.06e+04 ... (remaining 1330 not shown) Planarity restraints: 1544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 UQ1 D 201 " -0.006 2.00e-02 2.50e+03 2.84e-01 2.42e+03 pdb=" C2 UQ1 D 201 " 0.129 2.00e-02 2.50e+03 pdb=" C3 UQ1 D 201 " -0.078 2.00e-02 2.50e+03 pdb=" C4 UQ1 D 201 " -0.072 2.00e-02 2.50e+03 pdb=" C5 UQ1 D 201 " 0.148 2.00e-02 2.50e+03 pdb=" C6 UQ1 D 201 " -0.072 2.00e-02 2.50e+03 pdb=" C7 UQ1 D 201 " -0.445 2.00e-02 2.50e+03 pdb=" CM5 UQ1 D 201 " 0.592 2.00e-02 2.50e+03 pdb=" O1 UQ1 D 201 " -0.102 2.00e-02 2.50e+03 pdb=" O2 UQ1 D 201 " 0.452 2.00e-02 2.50e+03 pdb=" O3 UQ1 D 201 " -0.297 2.00e-02 2.50e+03 pdb=" O4 UQ1 D 201 " -0.250 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 UQ1 D 201 " -0.154 2.00e-02 2.50e+03 1.74e-01 3.78e+02 pdb=" C11 UQ1 D 201 " 0.015 2.00e-02 2.50e+03 pdb=" C7 UQ1 D 201 " -0.208 2.00e-02 2.50e+03 pdb=" C8 UQ1 D 201 " 0.283 2.00e-02 2.50e+03 pdb=" C9 UQ1 D 201 " 0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 237 " -0.837 9.50e-02 1.11e+02 3.75e-01 8.55e+01 pdb=" NE ARG A 237 " 0.051 2.00e-02 2.50e+03 pdb=" CZ ARG A 237 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG A 237 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 237 " -0.022 2.00e-02 2.50e+03 ... (remaining 1541 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1494 2.76 - 3.29: 7388 3.29 - 3.83: 13912 3.83 - 4.36: 17339 4.36 - 4.90: 29850 Nonbonded interactions: 69983 Sorted by model distance: nonbonded pdb=" S1 F3S B 303 " pdb="FE1 F3S B 303 " model vdw 2.223 2.688 nonbonded pdb=" S4 F3S B 303 " pdb="FE4 F3S B 303 " model vdw 2.247 2.688 nonbonded pdb=" S3 F3S B 303 " pdb="FE3 F3S B 303 " model vdw 2.289 2.688 nonbonded pdb=" O SER A 553 " pdb=" OG SER A 553 " model vdw 2.309 3.040 nonbonded pdb=" O VAL D 80 " pdb=" OG1 THR D 84 " model vdw 2.324 3.040 ... (remaining 69978 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: 3.960 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.730 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 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 : 0.031 1.714 9023 Z= 1.565 Angle : 1.597 49.609 12247 Z= 0.743 Chirality : 1.230 20.649 1333 Planarity : 0.017 0.375 1544 Dihedral : 16.599 174.301 3340 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 1.08 % Allowed : 9.49 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.58 (0.18), residues: 1097 helix: -4.81 (0.08), residues: 466 sheet: -1.23 (0.54), residues: 89 loop : -3.06 (0.21), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 235 TYR 0.022 0.002 TYR B 39 PHE 0.025 0.002 PHE A 69 TRP 0.023 0.002 TRP C 90 HIS 0.006 0.001 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.03086 ( 9011) covalent geometry : angle 1.51465 (12220) hydrogen bonds : bond 0.34244 ( 216) hydrogen bonds : angle 10.29684 ( 621) metal coordination : bond 0.09078 ( 11) metal coordination : angle 10.88812 ( 27) Misc. bond : bond 0.15474 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 132 time to evaluate : 0.343 Fit side-chains REVERT: A 95 GLN cc_start: 0.8276 (mp10) cc_final: 0.8045 (mp10) REVERT: A 110 TRP cc_start: 0.7864 (OUTLIER) cc_final: 0.7552 (p90) REVERT: A 237 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.8510 (ttm170) REVERT: A 417 GLU cc_start: 0.7280 (mm-30) cc_final: 0.6947 (mm-30) REVERT: A 429 MET cc_start: 0.8827 (mtp) cc_final: 0.8604 (mtt) REVERT: B 65 MET cc_start: 0.8952 (mmt) cc_final: 0.8544 (mmt) REVERT: B 218 GLN cc_start: 0.7935 (pt0) cc_final: 0.7299 (pp30) REVERT: B 231 MET cc_start: 0.8169 (mtp) cc_final: 0.7946 (mtt) REVERT: D 150 LYS cc_start: 0.8475 (mmtt) cc_final: 0.8108 (mmtt) REVERT: D 154 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8190 (mt-10) REVERT: D 166 TRP cc_start: 0.7344 (OUTLIER) cc_final: 0.6677 (m-90) outliers start: 10 outliers final: 5 residues processed: 140 average time/residue: 0.1094 time to fit residues: 20.2699 Evaluate side-chains 116 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 110 TRP Chi-restraints excluded: chain A residue 164 PHE Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 242 CYS Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 166 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.0980 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 HIS ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 HIS A 219 ASN A 279 GLN A 469 GLN A 507 ASN A 577 ASN B 53 GLN B 142 GLN B 152 GLN B 198 GLN D 68 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.128260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.099535 restraints weight = 10935.840| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.07 r_work: 0.3002 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.243 9023 Z= 0.334 Angle : 2.449 87.273 12247 Z= 1.181 Chirality : 0.358 6.523 1333 Planarity : 0.005 0.059 1544 Dihedral : 13.719 167.219 1325 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 2.05 % Allowed : 12.41 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.49 (0.20), residues: 1097 helix: -3.63 (0.16), residues: 468 sheet: -1.06 (0.53), residues: 86 loop : -2.65 (0.23), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 88 TYR 0.014 0.001 TYR B 39 PHE 0.015 0.001 PHE A 69 TRP 0.015 0.001 TRP A 110 HIS 0.004 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00942 ( 9011) covalent geometry : angle 1.95735 (12220) hydrogen bonds : bond 0.06223 ( 216) hydrogen bonds : angle 5.56891 ( 621) metal coordination : bond 0.02745 ( 11) metal coordination : angle 31.39561 ( 27) Misc. bond : bond 0.00132 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.342 Fit side-chains REVERT: A 95 GLN cc_start: 0.8595 (mp10) cc_final: 0.8324 (mp10) REVERT: A 320 ARG cc_start: 0.5955 (OUTLIER) cc_final: 0.5749 (pmt170) REVERT: A 371 LEU cc_start: 0.5859 (OUTLIER) cc_final: 0.5641 (pp) REVERT: B 65 MET cc_start: 0.9242 (mmt) cc_final: 0.8796 (mmt) REVERT: B 218 GLN cc_start: 0.8087 (pt0) cc_final: 0.7198 (pp30) REVERT: B 231 MET cc_start: 0.8519 (mtp) cc_final: 0.8213 (mtt) REVERT: C 134 HIS cc_start: 0.8000 (m170) cc_final: 0.7701 (m-70) REVERT: C 135 GLN cc_start: 0.7926 (mp10) cc_final: 0.7544 (mp10) REVERT: D 61 ASN cc_start: 0.9077 (t0) cc_final: 0.8846 (t0) REVERT: D 154 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8455 (mt-10) outliers start: 19 outliers final: 10 residues processed: 135 average time/residue: 0.0821 time to fit residues: 15.5151 Evaluate side-chains 123 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 164 PHE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 551 TRP Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 242 CYS Chi-restraints excluded: chain D residue 52 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 45 optimal weight: 7.9990 chunk 98 optimal weight: 0.0570 chunk 86 optimal weight: 5.9990 chunk 64 optimal weight: 0.6980 chunk 49 optimal weight: 0.4980 chunk 84 optimal weight: 0.0060 chunk 58 optimal weight: 0.0570 chunk 72 optimal weight: 5.9990 chunk 76 optimal weight: 0.6980 chunk 51 optimal weight: 0.4980 chunk 32 optimal weight: 6.9990 overall best weight: 0.2232 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 GLN A 230 GLN A 577 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.134499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.104637 restraints weight = 11185.638| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.95 r_work: 0.3090 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.243 9023 Z= 0.316 Angle : 2.369 81.791 12247 Z= 1.171 Chirality : 0.347 6.285 1333 Planarity : 0.004 0.050 1544 Dihedral : 11.486 148.403 1315 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 1.51 % Allowed : 13.38 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.56 (0.22), residues: 1097 helix: -2.72 (0.20), residues: 463 sheet: -0.62 (0.54), residues: 86 loop : -2.29 (0.24), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 97 TYR 0.012 0.001 TYR B 141 PHE 0.011 0.001 PHE C 137 TRP 0.010 0.001 TRP C 90 HIS 0.003 0.000 HIS B 237 Details of bonding type rmsd covalent geometry : bond 0.00910 ( 9011) covalent geometry : angle 1.92091 (12220) hydrogen bonds : bond 0.03387 ( 216) hydrogen bonds : angle 4.70159 ( 621) metal coordination : bond 0.01812 ( 11) metal coordination : angle 29.57697 ( 27) Misc. bond : bond 0.00045 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.259 Fit side-chains REVERT: A 357 LEU cc_start: 0.5031 (tt) cc_final: 0.4813 (tp) REVERT: B 65 MET cc_start: 0.9228 (mmt) cc_final: 0.8801 (mmt) REVERT: B 75 ASP cc_start: 0.8021 (m-30) cc_final: 0.7775 (m-30) REVERT: B 218 GLN cc_start: 0.8006 (pt0) cc_final: 0.7323 (pp30) REVERT: B 231 MET cc_start: 0.8429 (mtp) cc_final: 0.8200 (mtt) REVERT: C 109 LEU cc_start: 0.8869 (tt) cc_final: 0.8230 (mp) REVERT: C 134 HIS cc_start: 0.7741 (m170) cc_final: 0.7540 (m-70) REVERT: D 61 ASN cc_start: 0.8877 (t0) cc_final: 0.8611 (t0) REVERT: D 150 LYS cc_start: 0.7793 (mmtt) cc_final: 0.7560 (mmmt) outliers start: 14 outliers final: 7 residues processed: 136 average time/residue: 0.0944 time to fit residues: 18.0111 Evaluate side-chains 121 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 114 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 164 PHE Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 551 TRP Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 139 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 103 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 105 optimal weight: 0.0060 chunk 37 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 overall best weight: 1.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 HIS A 268 ASN A 563 ASN A 577 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.128136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.098276 restraints weight = 11087.337| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.64 r_work: 0.2952 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.241 9023 Z= 0.357 Angle : 2.368 81.098 12247 Z= 1.180 Chirality : 0.353 6.387 1333 Planarity : 0.004 0.042 1544 Dihedral : 10.769 147.537 1313 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 2.70 % Allowed : 13.92 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.39 (0.23), residues: 1097 helix: -2.48 (0.21), residues: 461 sheet: -0.57 (0.53), residues: 88 loop : -2.28 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 587 TYR 0.018 0.001 TYR B 39 PHE 0.018 0.001 PHE A 69 TRP 0.013 0.001 TRP C 90 HIS 0.005 0.001 HIS A 601 Details of bonding type rmsd covalent geometry : bond 0.00990 ( 9011) covalent geometry : angle 1.94504 (12220) hydrogen bonds : bond 0.04624 ( 216) hydrogen bonds : angle 4.76305 ( 621) metal coordination : bond 0.02459 ( 11) metal coordination : angle 28.81371 ( 27) Misc. bond : bond 0.00099 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 0.350 Fit side-chains REVERT: A 619 ARG cc_start: 0.8122 (ttp-170) cc_final: 0.7780 (ttp-170) REVERT: B 65 MET cc_start: 0.9274 (mmt) cc_final: 0.8780 (mmt) REVERT: B 88 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.7645 (pmt-80) REVERT: B 218 GLN cc_start: 0.8177 (pt0) cc_final: 0.7273 (pp30) REVERT: B 231 MET cc_start: 0.8674 (mtp) cc_final: 0.8354 (mtt) REVERT: D 150 LYS cc_start: 0.7921 (mmtt) cc_final: 0.7635 (mmmt) outliers start: 25 outliers final: 14 residues processed: 135 average time/residue: 0.0993 time to fit residues: 18.6599 Evaluate side-chains 123 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 164 PHE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 551 TRP Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain B residue 88 ARG Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 196 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 70 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 74 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 98 optimal weight: 0.0030 chunk 106 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 42 optimal weight: 0.0000 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 ASN A 577 ASN A 597 HIS ** D 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.130484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.101291 restraints weight = 10947.963| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.16 r_work: 0.3039 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.242 9023 Z= 0.316 Angle : 2.308 80.723 12247 Z= 1.168 Chirality : 0.351 6.351 1333 Planarity : 0.004 0.033 1544 Dihedral : 9.782 137.695 1313 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.37 % Allowed : 15.21 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.91 (0.23), residues: 1097 helix: -2.02 (0.22), residues: 458 sheet: -0.39 (0.55), residues: 86 loop : -2.07 (0.25), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 88 TYR 0.012 0.001 TYR B 141 PHE 0.010 0.001 PHE A 69 TRP 0.011 0.001 TRP C 90 HIS 0.003 0.000 HIS A 354 Details of bonding type rmsd covalent geometry : bond 0.00909 ( 9011) covalent geometry : angle 1.91947 (12220) hydrogen bonds : bond 0.03307 ( 216) hydrogen bonds : angle 4.49104 ( 621) metal coordination : bond 0.01553 ( 11) metal coordination : angle 27.35932 ( 27) Misc. bond : bond 0.00022 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.328 Fit side-chains REVERT: A 619 ARG cc_start: 0.8108 (ttp-170) cc_final: 0.7760 (ttp-170) REVERT: B 65 MET cc_start: 0.9250 (mmt) cc_final: 0.8808 (mmt) REVERT: B 88 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.7798 (pmt-80) REVERT: B 218 GLN cc_start: 0.8057 (pt0) cc_final: 0.7194 (pp30) REVERT: B 231 MET cc_start: 0.8499 (mtp) cc_final: 0.8188 (mtt) REVERT: C 134 HIS cc_start: 0.7742 (m170) cc_final: 0.7495 (m-70) outliers start: 22 outliers final: 13 residues processed: 131 average time/residue: 0.0901 time to fit residues: 16.4404 Evaluate side-chains 123 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 164 PHE Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 551 TRP Chi-restraints excluded: chain B residue 88 ARG Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 154 GLU Chi-restraints excluded: chain D residue 158 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 8 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 72 optimal weight: 0.0870 chunk 26 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 66 optimal weight: 0.0870 chunk 58 optimal weight: 0.0050 chunk 75 optimal weight: 0.7980 chunk 34 optimal weight: 0.0770 chunk 48 optimal weight: 0.9990 overall best weight: 0.1908 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 462 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.138450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.108203 restraints weight = 11476.875| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.98 r_work: 0.3143 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.242 9023 Z= 0.313 Angle : 2.252 81.667 12247 Z= 1.165 Chirality : 0.350 6.408 1333 Planarity : 0.003 0.031 1544 Dihedral : 9.121 115.273 1313 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 1.73 % Allowed : 16.61 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.24), residues: 1097 helix: -1.52 (0.23), residues: 461 sheet: 0.07 (0.55), residues: 88 loop : -1.91 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 320 TYR 0.014 0.001 TYR B 141 PHE 0.007 0.001 PHE D 100 TRP 0.009 0.001 TRP C 90 HIS 0.003 0.000 HIS A 354 Details of bonding type rmsd covalent geometry : bond 0.00904 ( 9011) covalent geometry : angle 1.91688 (12220) hydrogen bonds : bond 0.02726 ( 216) hydrogen bonds : angle 4.22720 ( 621) metal coordination : bond 0.01139 ( 11) metal coordination : angle 25.24452 ( 27) Misc. bond : bond 0.00026 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.227 Fit side-chains REVERT: A 619 ARG cc_start: 0.7944 (ttp-170) cc_final: 0.7657 (ttp-170) REVERT: B 65 MET cc_start: 0.9189 (mmt) cc_final: 0.8803 (mmt) REVERT: B 88 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.8589 (ptt-90) REVERT: B 231 MET cc_start: 0.8405 (mtp) cc_final: 0.8200 (mtt) REVERT: C 134 HIS cc_start: 0.7644 (m170) cc_final: 0.7439 (m-70) REVERT: D 150 LYS cc_start: 0.8048 (mmtt) cc_final: 0.7805 (mmmt) outliers start: 16 outliers final: 11 residues processed: 130 average time/residue: 0.0902 time to fit residues: 16.6732 Evaluate side-chains 122 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 164 PHE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 551 TRP Chi-restraints excluded: chain B residue 88 ARG Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 154 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 103 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 69 optimal weight: 0.2980 chunk 64 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 78 optimal weight: 0.4980 chunk 102 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 ASN ** D 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.130024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.101558 restraints weight = 11128.976| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.21 r_work: 0.3053 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.241 9023 Z= 0.331 Angle : 2.285 82.171 12247 Z= 1.172 Chirality : 0.351 6.359 1333 Planarity : 0.004 0.032 1544 Dihedral : 9.053 109.872 1313 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 2.05 % Allowed : 16.40 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.24), residues: 1097 helix: -1.50 (0.23), residues: 463 sheet: 0.03 (0.55), residues: 88 loop : -1.96 (0.25), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 88 TYR 0.015 0.001 TYR B 141 PHE 0.014 0.001 PHE A 69 TRP 0.012 0.001 TRP C 90 HIS 0.004 0.001 HIS A 601 Details of bonding type rmsd covalent geometry : bond 0.00940 ( 9011) covalent geometry : angle 1.93150 (12220) hydrogen bonds : bond 0.03711 ( 216) hydrogen bonds : angle 4.36782 ( 621) metal coordination : bond 0.01873 ( 11) metal coordination : angle 26.07105 ( 27) Misc. bond : bond 0.00095 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.344 Fit side-chains REVERT: A 619 ARG cc_start: 0.8057 (ttp-170) cc_final: 0.7757 (ttp-170) REVERT: B 65 MET cc_start: 0.9246 (mmt) cc_final: 0.8844 (mmt) REVERT: B 88 ARG cc_start: 0.8941 (OUTLIER) cc_final: 0.8720 (ptt-90) REVERT: B 231 MET cc_start: 0.8592 (mtp) cc_final: 0.8313 (mtt) REVERT: C 131 ASN cc_start: 0.9151 (m-40) cc_final: 0.8911 (m110) REVERT: C 137 PHE cc_start: 0.8304 (m-10) cc_final: 0.8088 (m-10) REVERT: D 150 LYS cc_start: 0.8129 (mmtt) cc_final: 0.7794 (mmmt) outliers start: 19 outliers final: 13 residues processed: 124 average time/residue: 0.0977 time to fit residues: 16.9270 Evaluate side-chains 119 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 164 PHE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 551 TRP Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain B residue 88 ARG Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 158 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 22 optimal weight: 3.9990 chunk 58 optimal weight: 0.0060 chunk 28 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 49 optimal weight: 0.0050 chunk 85 optimal weight: 0.7980 overall best weight: 0.5210 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 597 HIS ** D 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.133973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.103774 restraints weight = 11285.484| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.96 r_work: 0.3053 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.240 9023 Z= 0.315 Angle : 2.262 82.223 12247 Z= 1.167 Chirality : 0.351 6.388 1333 Planarity : 0.003 0.031 1544 Dihedral : 8.683 114.019 1313 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 1.51 % Allowed : 17.04 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.24), residues: 1097 helix: -1.14 (0.23), residues: 464 sheet: 0.21 (0.55), residues: 88 loop : -1.82 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 88 TYR 0.016 0.001 TYR B 141 PHE 0.009 0.001 PHE A 69 TRP 0.011 0.001 TRP C 90 HIS 0.003 0.001 HIS A 354 Details of bonding type rmsd covalent geometry : bond 0.00907 ( 9011) covalent geometry : angle 1.92291 (12220) hydrogen bonds : bond 0.03052 ( 216) hydrogen bonds : angle 4.26859 ( 621) metal coordination : bond 0.01460 ( 11) metal coordination : angle 25.42490 ( 27) Misc. bond : bond 0.00039 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 0.333 Fit side-chains REVERT: A 619 ARG cc_start: 0.8022 (ttp-170) cc_final: 0.7689 (ttp-170) REVERT: B 65 MET cc_start: 0.9235 (mmt) cc_final: 0.8805 (mmt) REVERT: B 88 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.8640 (ptt-90) REVERT: B 231 MET cc_start: 0.8509 (mtp) cc_final: 0.8236 (mtt) REVERT: C 131 ASN cc_start: 0.9098 (m-40) cc_final: 0.8766 (m110) REVERT: D 150 LYS cc_start: 0.8077 (mmtt) cc_final: 0.7845 (mmmt) outliers start: 14 outliers final: 11 residues processed: 119 average time/residue: 0.0988 time to fit residues: 16.3866 Evaluate side-chains 115 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 164 PHE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 551 TRP Chi-restraints excluded: chain B residue 88 ARG Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain D residue 119 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 22 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 59 optimal weight: 0.0970 chunk 25 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 104 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 overall best weight: 1.0780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 443 ASN ** D 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.131917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.101602 restraints weight = 11194.303| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.95 r_work: 0.3028 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.240 9023 Z= 0.330 Angle : 2.288 82.325 12247 Z= 1.171 Chirality : 0.351 6.371 1333 Planarity : 0.004 0.032 1544 Dihedral : 8.682 112.213 1313 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 1.62 % Allowed : 16.83 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.24), residues: 1097 helix: -1.14 (0.23), residues: 468 sheet: 0.09 (0.54), residues: 88 loop : -1.88 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 88 TYR 0.016 0.001 TYR B 141 PHE 0.016 0.001 PHE C 137 TRP 0.012 0.001 TRP C 90 HIS 0.004 0.001 HIS A 601 Details of bonding type rmsd covalent geometry : bond 0.00938 ( 9011) covalent geometry : angle 1.93211 (12220) hydrogen bonds : bond 0.03574 ( 216) hydrogen bonds : angle 4.34175 ( 621) metal coordination : bond 0.01854 ( 11) metal coordination : angle 26.17151 ( 27) Misc. bond : bond 0.00084 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: A 619 ARG cc_start: 0.8087 (ttp-170) cc_final: 0.7795 (ttp-170) REVERT: B 65 MET cc_start: 0.9252 (mmt) cc_final: 0.8846 (mmt) REVERT: B 88 ARG cc_start: 0.8954 (OUTLIER) cc_final: 0.8738 (ptt-90) REVERT: B 231 MET cc_start: 0.8592 (mtp) cc_final: 0.8303 (mtt) REVERT: C 131 ASN cc_start: 0.9094 (m-40) cc_final: 0.8765 (m110) outliers start: 15 outliers final: 13 residues processed: 115 average time/residue: 0.1008 time to fit residues: 16.0914 Evaluate side-chains 117 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 164 PHE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 551 TRP Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain B residue 88 ARG Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 158 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 67 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 15 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 577 ASN A 597 HIS ** D 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.130603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.100584 restraints weight = 11145.134| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.91 r_work: 0.3019 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.241 9023 Z= 0.337 Angle : 2.317 82.457 12247 Z= 1.176 Chirality : 0.351 6.371 1333 Planarity : 0.004 0.032 1544 Dihedral : 8.679 113.534 1313 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 1.73 % Allowed : 16.72 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.24), residues: 1097 helix: -1.14 (0.23), residues: 466 sheet: -0.01 (0.54), residues: 88 loop : -1.81 (0.26), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 88 TYR 0.015 0.001 TYR B 141 PHE 0.017 0.001 PHE C 137 TRP 0.013 0.001 TRP C 90 HIS 0.004 0.001 HIS A 601 Details of bonding type rmsd covalent geometry : bond 0.00952 ( 9011) covalent geometry : angle 1.93999 (12220) hydrogen bonds : bond 0.03864 ( 216) hydrogen bonds : angle 4.46709 ( 621) metal coordination : bond 0.01999 ( 11) metal coordination : angle 27.03681 ( 27) Misc. bond : bond 0.00094 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.374 Fit side-chains REVERT: A 619 ARG cc_start: 0.8070 (ttp-170) cc_final: 0.7694 (ttp-170) REVERT: B 65 MET cc_start: 0.9257 (mmt) cc_final: 0.8880 (mmt) REVERT: B 231 MET cc_start: 0.8611 (mtp) cc_final: 0.8328 (mtt) REVERT: C 131 ASN cc_start: 0.9073 (m-40) cc_final: 0.8760 (m110) REVERT: D 150 LYS cc_start: 0.8168 (mmtt) cc_final: 0.7819 (mmmt) outliers start: 16 outliers final: 12 residues processed: 116 average time/residue: 0.1008 time to fit residues: 16.2333 Evaluate side-chains 113 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 164 PHE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 551 TRP Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain D residue 158 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 29 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 79 optimal weight: 0.0870 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.132207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.102532 restraints weight = 10952.241| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.89 r_work: 0.3045 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.241 9023 Z= 0.320 Angle : 2.292 82.452 12247 Z= 1.171 Chirality : 0.350 6.385 1333 Planarity : 0.003 0.031 1544 Dihedral : 8.436 115.595 1313 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 1.19 % Allowed : 17.26 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.25), residues: 1097 helix: -0.95 (0.23), residues: 470 sheet: 0.07 (0.54), residues: 88 loop : -1.75 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 88 TYR 0.016 0.001 TYR B 141 PHE 0.015 0.001 PHE C 137 TRP 0.012 0.001 TRP C 90 HIS 0.003 0.001 HIS A 354 Details of bonding type rmsd covalent geometry : bond 0.00919 ( 9011) covalent geometry : angle 1.92983 (12220) hydrogen bonds : bond 0.03332 ( 216) hydrogen bonds : angle 4.34583 ( 621) metal coordination : bond 0.01669 ( 11) metal coordination : angle 26.40918 ( 27) Misc. bond : bond 0.00058 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2324.31 seconds wall clock time: 40 minutes 38.22 seconds (2438.22 seconds total)