Starting phenix.real_space_refine on Wed Feb 4 05:32:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kps_62490/02_2026/9kps_62490.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kps_62490/02_2026/9kps_62490.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kps_62490/02_2026/9kps_62490.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kps_62490/02_2026/9kps_62490.map" model { file = "/net/cci-nas-00/data/ceres_data/9kps_62490/02_2026/9kps_62490.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kps_62490/02_2026/9kps_62490.cif" } resolution = 3.36 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= 0.003 sd= 0.088 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 5584 2.51 5 N 1515 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 81 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: 8809 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: 1905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1905 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 14, 'TRANS': 223} 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: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1041 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 10, 'TRANS': 123} 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: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5129 SG CYS B 95 32.675 34.365 55.893 1.00 31.46 S ATOM 5211 SG CYS B 107 34.972 31.728 54.697 1.00 39.29 S ATOM 5075 SG CYS B 87 37.563 35.337 51.347 1.00 41.08 S ATOM 5113 SG CYS B 92 36.512 37.959 53.109 1.00 34.37 S ATOM 5850 SG CYS B 185 39.862 39.812 68.128 1.00 29.56 S ATOM 5811 SG CYS B 179 43.659 40.677 63.323 1.00 41.60 S ATOM 6351 SG CYS B 246 42.584 34.759 66.015 1.00 37.32 S ATOM 5833 SG CYS B 182 38.028 37.514 62.656 1.00 35.76 S ATOM 6273 SG CYS B 236 43.082 41.796 79.286 1.00 37.81 S ATOM 5875 SG CYS B 189 37.339 41.425 76.337 1.00 30.74 S ATOM 6320 SG CYS B 242 41.412 37.710 74.334 1.00 36.72 S Time building chain proxies: 2.00, per 1000 atoms: 0.23 Number of scatterers: 8809 At special positions: 0 Unit cell: (82.5, 84, 132.75, 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 1515 7.00 C 5584 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: 0.50 Conformation dependent library (CDL) restraints added in 206.3 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S B 303 " pdb="FE4 F3S B 303 " - pdb=" SG CYS B 242 " pdb="FE3 F3S B 303 " - pdb=" SG CYS B 189 " pdb="FE1 F3S B 303 " - pdb=" SG CYS B 236 " pdb=" FES B 301 " pdb="FE1 FES B 301 " - pdb=" SG CYS B 95 " pdb="FE2 FES B 301 " - pdb=" SG CYS B 87 " pdb="FE2 FES B 301 " - pdb=" SG CYS B 92 " pdb="FE1 FES B 301 " - pdb=" SG CYS B 107 " pdb=" SF4 B 302 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 246 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 182 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 185 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 179 " Number of angles added : 27 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: 2036 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 8 sheets defined 37.0% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 61 through 67 removed outlier: 3.589A pdb=" N LEU A 65 " --> pdb=" O GLY A 61 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG A 66 " --> pdb=" O GLY A 62 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA A 67 " --> pdb=" O ALA A 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 61 through 67' Processing helix chain 'A' and resid 109 through 120 removed outlier: 3.766A pdb=" N HIS A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR A 115 " --> pdb=" O LYS A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 136 Processing helix chain 'A' and resid 138 through 143 Processing helix chain 'A' and resid 186 through 199 removed outlier: 3.514A pdb=" N HIS A 193 " --> pdb=" O HIS A 189 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR A 194 " --> pdb=" O ALA A 190 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY A 197 " --> pdb=" O HIS A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 273 removed outlier: 3.783A pdb=" N VAL A 271 " --> pdb=" O GLY A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 305 Processing helix chain 'A' and resid 330 through 345 removed outlier: 3.527A pdb=" N VAL A 334 " --> pdb=" O CYS A 330 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE A 338 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N MET A 340 " --> pdb=" O ARG A 336 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.617A pdb=" N ARG A 370 " --> pdb=" O VAL A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 378 removed outlier: 3.678A pdb=" N THR A 377 " --> pdb=" O GLY A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 466 removed outlier: 3.923A pdb=" N VAL A 454 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL A 460 " --> pdb=" O PHE A 456 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL A 464 " --> pdb=" O VAL A 460 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA A 465 " --> pdb=" O ALA A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 494 removed outlier: 4.088A pdb=" N ILE A 486 " --> pdb=" O GLY A 482 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A 487 " --> pdb=" O LYS A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 515 removed outlier: 3.550A pdb=" N GLN A 513 " --> pdb=" O LYS A 509 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS A 514 " --> pdb=" O GLN A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 538 removed outlier: 3.506A pdb=" N THR A 538 " --> pdb=" O ALA A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 574 removed outlier: 4.231A pdb=" N LEU A 561 " --> pdb=" O GLU A 557 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN A 562 " --> pdb=" O THR A 558 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU A 564 " --> pdb=" O GLU A 560 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR A 566 " --> pdb=" O GLN A 562 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N CYS A 567 " --> pdb=" O ASN A 563 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA A 568 " --> pdb=" O LEU A 564 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN A 570 " --> pdb=" O THR A 566 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR A 571 " --> pdb=" O CYS A 567 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA A 572 " --> pdb=" O ALA A 568 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 77 removed outlier: 3.878A pdb=" N LYS B 72 " --> pdb=" O ASP B 68 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE B 73 " --> pdb=" O ALA B 69 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS B 74 " --> pdb=" O LEU B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 removed outlier: 3.662A pdb=" N TYR B 141 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS B 145 " --> pdb=" O TYR B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 148 No H-bonds generated for 'chain 'B' and resid 146 through 148' Processing helix chain 'B' and resid 166 through 171 Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 185 through 189 Processing helix chain 'B' and resid 200 through 205 removed outlier: 4.152A pdb=" N VAL B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 246 Processing helix chain 'B' and resid 258 through 265 removed outlier: 3.553A pdb=" N PHE B 265 " --> pdb=" O LYS B 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 64 removed outlier: 3.512A pdb=" N GLU C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 73 removed outlier: 3.764A pdb=" N LYS C 70 " --> pdb=" O GLN C 66 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLN C 71 " --> pdb=" O ILE C 67 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA C 73 " --> pdb=" O ASN C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 93 removed outlier: 3.823A pdb=" N SER C 93 " --> pdb=" O THR C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 113 removed outlier: 3.656A pdb=" N PHE C 107 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE C 110 " --> pdb=" O GLY C 106 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR C 111 " --> pdb=" O PHE C 107 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 120 removed outlier: 3.593A pdb=" N LEU C 120 " --> pdb=" O VAL C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 137 removed outlier: 3.628A pdb=" N ASN C 131 " --> pdb=" O GLU C 127 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN C 135 " --> pdb=" O ASN C 131 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS C 136 " --> pdb=" O TRP C 132 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE C 137 " --> pdb=" O TYR C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 167 removed outlier: 3.764A pdb=" N TRP C 143 " --> pdb=" O LYS C 139 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS C 146 " --> pdb=" O GLU C 142 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA C 150 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N TYR C 151 " --> pdb=" O GLY C 147 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE C 153 " --> pdb=" O PHE C 149 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA C 154 " --> pdb=" O ALA C 150 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N HIS C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE C 161 " --> pdb=" O TYR C 157 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG C 162 " --> pdb=" O GLY C 158 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS C 163 " --> pdb=" O GLY C 159 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU C 164 " --> pdb=" O ALA C 160 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE C 165 " --> pdb=" O ILE C 161 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TRP C 166 " --> pdb=" O ARG C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 180 removed outlier: 3.662A pdb=" N VAL C 177 " --> pdb=" O THR C 173 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TYR C 178 " --> pdb=" O LEU C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 192 removed outlier: 3.604A pdb=" N ALA C 189 " --> pdb=" O ILE C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 198 removed outlier: 3.704A pdb=" N THR C 197 " --> pdb=" O THR C 193 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU C 198 " --> pdb=" O TYR C 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 193 through 198' Processing helix chain 'D' and resid 65 through 74 removed outlier: 3.519A pdb=" N TRP D 69 " --> pdb=" O GLY D 65 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR D 70 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS D 73 " --> pdb=" O TRP D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 80 removed outlier: 3.697A pdb=" N VAL D 79 " --> pdb=" O PHE D 75 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL D 80 " --> pdb=" O ALA D 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 75 through 80' Processing helix chain 'D' and resid 80 through 85 Processing helix chain 'D' and resid 94 through 114 removed outlier: 4.100A pdb=" N PHE D 101 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N MET D 104 " --> pdb=" O PHE D 100 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU D 106 " --> pdb=" O SER D 102 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU D 112 " --> pdb=" O TYR D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 121 removed outlier: 3.710A pdb=" N TYR D 120 " --> pdb=" O CYS D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 133 Processing helix chain 'D' and resid 142 through 153 removed outlier: 3.740A pdb=" N PHE D 146 " --> pdb=" O ALA D 142 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR D 149 " --> pdb=" O LEU D 145 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU D 151 " --> pdb=" O GLY D 147 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR D 153 " --> pdb=" O TYR D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 166 removed outlier: 3.942A pdb=" N TRP D 166 " --> pdb=" O VAL D 162 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 50 removed outlier: 6.537A pdb=" N ILE A 49 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N THR A 234 " --> pdb=" O ASN A 229 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N VAL A 222 " --> pdb=" O HIS A 218 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N HIS A 218 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY A 224 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP A 214 " --> pdb=" O ILE A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 205 through 207 removed outlier: 7.429A pdb=" N THR A 78 " --> pdb=" O HIS A 205 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N PHE A 207 " --> pdb=" O THR A 78 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N CYS A 80 " --> pdb=" O PHE A 207 " (cutoff:3.500A) removed outlier: 11.074A pdb=" N THR A 414 " --> pdb=" O PRO A 426 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N LEU A 428 " --> pdb=" O ALA A 412 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 278 through 279 removed outlier: 3.528A pdb=" N ARG A 618 " --> pdb=" O HIS A 601 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 284 through 290 removed outlier: 7.336A pdb=" N VAL A 284 " --> pdb=" O ASN A 400 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ASN A 400 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N PHE A 286 " --> pdb=" O HIS A 398 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N HIS A 398 " --> pdb=" O PHE A 286 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N THR A 396 " --> pdb=" O PRO A 288 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 308 through 310 removed outlier: 4.230A pdb=" N PHE A 308 " --> pdb=" O GLN A 358 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL A 310 " --> pdb=" O TYR A 356 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR A 356 " --> pdb=" O VAL A 310 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 404 through 405 removed outlier: 6.000A 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: 6.823A 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: 3.866A pdb=" N ARG B 102 " --> pdb=" O ILE B 99 " (cutoff:3.500A) 198 hydrogen bonds defined for protein. 570 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: 1.06 Time building geometry restraints manager: 0.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.68: 8916 1.68 - 2.22: 85 2.22 - 2.77: 22 2.77 - 3.31: 0 3.31 - 3.85: 3 Bond restraints: 9026 Sorted by residual: bond pdb=" S4 F3S B 303 " pdb="FE1 F3S B 303 " ideal model delta sigma weight residual 2.233 3.852 -1.619 2.00e-02 2.50e+03 6.55e+03 bond pdb=" S1 F3S B 303 " pdb="FE4 F3S B 303 " ideal model delta sigma weight residual 2.258 3.851 -1.593 2.00e-02 2.50e+03 6.34e+03 bond pdb=" S2 F3S B 303 " pdb="FE3 F3S B 303 " ideal model delta sigma weight residual 2.300 3.818 -1.518 2.00e-02 2.50e+03 5.76e+03 bond pdb=" C38 PEE D 201 " pdb=" C39 PEE D 201 " ideal model delta sigma weight residual 1.523 1.304 0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" C18 PEE D 201 " pdb=" C19 PEE D 201 " ideal model delta sigma weight residual 1.523 1.337 0.186 2.00e-02 2.50e+03 8.66e+01 ... (remaining 9021 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.66: 12220 9.66 - 19.32: 13 19.32 - 28.98: 0 28.98 - 38.64: 8 38.64 - 48.30: 2 Bond angle restraints: 12243 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 66.45 48.30 3.00e+00 1.11e-01 2.59e+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 66.68 45.91 3.00e+00 1.11e-01 2.34e+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 90.25 14.08 1.14e+00 7.69e-01 1.53e+02 angle pdb=" S1 FES B 301 " pdb="FE1 FES B 301 " pdb=" S2 FES B 301 " ideal model delta sigma weight residual 104.33 90.26 14.07 1.20e+00 6.94e-01 1.38e+02 angle pdb=" S1 F3S B 303 " pdb="FE4 F3S B 303 " pdb=" S2 F3S B 303 " ideal model delta sigma weight residual 103.63 68.80 34.83 3.00e+00 1.11e-01 1.35e+02 ... (remaining 12238 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.39: 5190 33.39 - 66.79: 164 66.79 - 100.18: 21 100.18 - 133.57: 1 133.57 - 166.96: 2 Dihedral angle restraints: 5378 sinusoidal: 2187 harmonic: 3191 Sorted by residual: dihedral pdb=" C ILE B 239 " pdb=" N ILE B 239 " pdb=" CA ILE B 239 " pdb=" CB ILE B 239 " ideal model delta harmonic sigma weight residual -122.00 -102.25 -19.75 0 2.50e+00 1.60e-01 6.24e+01 dihedral pdb=" CD ARG B 235 " pdb=" NE ARG B 235 " pdb=" CZ ARG B 235 " pdb=" NH1 ARG B 235 " ideal model delta sinusoidal sigma weight residual 0.00 -62.45 62.45 1 1.00e+01 1.00e-02 5.16e+01 dihedral pdb=" C CYS B 189 " pdb=" N CYS B 189 " pdb=" CA CYS B 189 " pdb=" CB CYS B 189 " ideal model delta harmonic sigma weight residual -122.60 -105.69 -16.91 0 2.50e+00 1.60e-01 4.57e+01 ... (remaining 5375 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.221: 1334 4.221 - 8.443: 0 8.443 - 12.664: 0 12.664 - 16.885: 0 16.885 - 21.107: 5 Chirality restraints: 1339 Sorted by residual: 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 -10.55 21.11 2.00e-01 2.50e+01 1.11e+04 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 10.55 -21.10 2.00e-01 2.50e+01 1.11e+04 chirality pdb="FE2 SF4 B 302 " pdb=" S1 SF4 B 302 " pdb=" S3 SF4 B 302 " pdb=" S4 SF4 B 302 " both_signs ideal model delta sigma weight residual False 10.55 -10.55 21.10 2.00e-01 2.50e+01 1.11e+04 ... (remaining 1336 not shown) Planarity restraints: 1548 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 235 " -0.978 9.50e-02 1.11e+02 4.38e-01 1.16e+02 pdb=" NE ARG B 235 " 0.057 2.00e-02 2.50e+03 pdb=" CZ ARG B 235 " 0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG B 235 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 235 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 210 " 0.806 9.50e-02 1.11e+02 3.61e-01 7.93e+01 pdb=" NE ARG B 210 " -0.049 2.00e-02 2.50e+03 pdb=" CZ ARG B 210 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG B 210 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 210 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 189 " 0.023 2.00e-02 2.50e+03 4.52e-02 2.04e+01 pdb=" C CYS B 189 " -0.078 2.00e-02 2.50e+03 pdb=" O CYS B 189 " 0.029 2.00e-02 2.50e+03 pdb=" N PRO B 190 " 0.026 2.00e-02 2.50e+03 ... (remaining 1545 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 714 2.72 - 3.26: 7696 3.26 - 3.81: 13239 3.81 - 4.35: 16671 4.35 - 4.90: 29706 Nonbonded interactions: 68026 Sorted by model distance: nonbonded pdb=" O ILE B 239 " pdb=" CB ILE B 239 " model vdw 2.174 2.776 nonbonded pdb=" O CYS B 95 " pdb=" CB CYS B 95 " model vdw 2.211 2.752 nonbonded pdb=" S3 F3S B 303 " pdb="FE3 F3S B 303 " model vdw 2.259 2.688 nonbonded pdb=" S1 F3S B 303 " pdb="FE1 F3S B 303 " model vdw 2.260 2.688 nonbonded pdb=" S4 F3S B 303 " pdb="FE4 F3S B 303 " model vdw 2.260 2.688 ... (remaining 68021 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: 5.340 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.160 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 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 : 0.032 1.619 9038 Z= 1.632 Angle : 1.630 48.299 12270 Z= 0.788 Chirality : 1.257 21.107 1339 Planarity : 0.017 0.438 1548 Dihedral : 17.187 166.963 3342 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.17 % Favored : 90.74 % Rotamer: Outliers : 2.04 % Allowed : 13.63 % Favored : 84.33 % Cbeta Deviations : 0.39 % 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: -5.92 (0.17), residues: 1101 helix: -4.94 (0.07), residues: 450 sheet: -2.48 (0.50), residues: 93 loop : -3.28 (0.21), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 72 TYR 0.027 0.003 TYR C 84 PHE 0.039 0.003 PHE A 69 TRP 0.025 0.003 TRP B 194 HIS 0.010 0.002 HIS A 354 Details of bonding type rmsd covalent geometry : bond 0.03174 ( 9026) covalent geometry : angle 1.60273 (12243) hydrogen bonds : bond 0.34350 ( 198) hydrogen bonds : angle 10.74549 ( 570) metal coordination : bond 0.07958 ( 11) metal coordination : angle 6.49030 ( 27) Misc. bond : bond 0.42481 ( 1) *********************** 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 130 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.300 Fit side-chains REVERT: A 346 ARG cc_start: 0.7134 (mtt90) cc_final: 0.6587 (mtp180) REVERT: A 355 MET cc_start: 0.8035 (mmm) cc_final: 0.7384 (tpp) REVERT: A 411 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8151 (mt-10) REVERT: A 577 ASN cc_start: 0.8365 (t0) cc_final: 0.7527 (t0) REVERT: A 625 LEU cc_start: 0.8621 (mt) cc_final: 0.8351 (mp) REVERT: B 65 MET cc_start: 0.8969 (mmt) cc_final: 0.8749 (mmt) REVERT: B 171 LYS cc_start: 0.8740 (ttmt) cc_final: 0.8340 (tptp) REVERT: B 190 PRO cc_start: 0.9071 (OUTLIER) cc_final: 0.8695 (Cg_exo) REVERT: C 132 TRP cc_start: 0.8799 (t60) cc_final: 0.8520 (t60) REVERT: D 131 LYS cc_start: 0.8329 (mttm) cc_final: 0.8038 (mmtt) outliers start: 19 outliers final: 14 residues processed: 129 average time/residue: 0.1117 time to fit residues: 19.1217 Evaluate side-chains 117 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain B residue 29 HIS Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 190 PRO Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 242 CYS Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain D residue 56 VAL 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: 2.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.1980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.4980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 HIS A 167 GLN A 176 GLN A 202 HIS A 268 ASN B 142 GLN B 152 GLN C 131 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.128464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.094944 restraints weight = 11348.126| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.09 r_work: 0.2883 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.240 9038 Z= 0.352 Angle : 2.328 65.053 12270 Z= 1.187 Chirality : 0.354 6.463 1339 Planarity : 0.005 0.065 1548 Dihedral : 13.410 167.453 1329 Min Nonbonded Distance : 1.501 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.90 % Favored : 94.01 % Rotamer: Outliers : 2.36 % Allowed : 15.24 % Favored : 82.40 % 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: -4.85 (0.20), residues: 1101 helix: -3.83 (0.15), residues: 445 sheet: -2.03 (0.53), residues: 89 loop : -2.88 (0.22), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 102 TYR 0.013 0.001 TYR B 39 PHE 0.016 0.001 PHE A 69 TRP 0.011 0.001 TRP B 194 HIS 0.004 0.001 HIS A 354 Details of bonding type rmsd covalent geometry : bond 0.00958 ( 9026) covalent geometry : angle 1.99556 (12243) hydrogen bonds : bond 0.05336 ( 198) hydrogen bonds : angle 5.67880 ( 570) metal coordination : bond 0.01960 ( 11) metal coordination : angle 25.63232 ( 27) Misc. bond : bond 0.00156 ( 1) *********************** 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 136 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.298 Fit side-chains REVERT: A 98 ILE cc_start: 0.8536 (OUTLIER) cc_final: 0.8293 (mt) REVERT: A 346 ARG cc_start: 0.7184 (mtt90) cc_final: 0.6277 (mtp180) REVERT: A 355 MET cc_start: 0.7299 (mmm) cc_final: 0.6768 (tpp) REVERT: A 577 ASN cc_start: 0.8727 (t0) cc_final: 0.7816 (t0) REVERT: A 599 MET cc_start: 0.9083 (tpp) cc_final: 0.8848 (tpt) REVERT: A 625 LEU cc_start: 0.8559 (mt) cc_final: 0.8131 (mp) REVERT: B 88 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.6626 (ptt-90) REVERT: B 91 ILE cc_start: 0.9319 (OUTLIER) cc_final: 0.8749 (tt) REVERT: B 171 LYS cc_start: 0.9046 (ttmt) cc_final: 0.8487 (tptp) REVERT: B 210 ARG cc_start: 0.9173 (OUTLIER) cc_final: 0.8856 (tmt170) REVERT: C 132 TRP cc_start: 0.8880 (t60) cc_final: 0.8678 (t60) REVERT: D 64 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7943 (mt-10) REVERT: D 131 LYS cc_start: 0.8535 (mttm) cc_final: 0.8120 (mmtt) outliers start: 22 outliers final: 13 residues processed: 133 average time/residue: 0.1091 time to fit residues: 19.1462 Evaluate side-chains 119 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 167 GLN Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 361 HIS Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain B residue 29 HIS Chi-restraints excluded: chain B residue 88 ARG Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain B residue 242 CYS Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 166 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 106 optimal weight: 6.9990 chunk 76 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 81 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.129066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.095604 restraints weight = 11219.633| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.11 r_work: 0.2858 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.243 9038 Z= 0.321 Angle : 2.364 85.997 12270 Z= 1.175 Chirality : 0.348 6.324 1339 Planarity : 0.004 0.058 1548 Dihedral : 11.833 149.796 1318 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 3.00 % Allowed : 16.09 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % 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: -4.07 (0.22), residues: 1101 helix: -2.98 (0.20), residues: 439 sheet: -1.92 (0.56), residues: 82 loop : -2.59 (0.23), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 102 TYR 0.011 0.001 TYR B 39 PHE 0.017 0.001 PHE A 69 TRP 0.010 0.001 TRP B 194 HIS 0.003 0.001 HIS A 354 Details of bonding type rmsd covalent geometry : bond 0.00919 ( 9026) covalent geometry : angle 1.93865 (12243) hydrogen bonds : bond 0.04052 ( 198) hydrogen bonds : angle 4.86995 ( 570) metal coordination : bond 0.02052 ( 11) metal coordination : angle 28.89922 ( 27) Misc. bond : bond 0.00081 ( 1) *********************** 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 136 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 0.404 Fit side-chains REVERT: A 98 ILE cc_start: 0.8520 (mt) cc_final: 0.8318 (mt) REVERT: A 346 ARG cc_start: 0.7090 (mtt90) cc_final: 0.6238 (mtp180) REVERT: A 355 MET cc_start: 0.7097 (mmm) cc_final: 0.6636 (tpp) REVERT: A 577 ASN cc_start: 0.8693 (t0) cc_final: 0.7787 (t0) REVERT: A 625 LEU cc_start: 0.8513 (mt) cc_final: 0.8098 (mp) REVERT: B 91 ILE cc_start: 0.9355 (OUTLIER) cc_final: 0.8744 (tt) REVERT: B 171 LYS cc_start: 0.9073 (ttmt) cc_final: 0.8500 (tptp) REVERT: B 210 ARG cc_start: 0.9144 (OUTLIER) cc_final: 0.8729 (tmt170) REVERT: D 131 LYS cc_start: 0.8470 (mttm) cc_final: 0.8063 (mmtt) outliers start: 28 outliers final: 20 residues processed: 129 average time/residue: 0.1103 time to fit residues: 18.8455 Evaluate side-chains 123 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 361 HIS Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 551 TRP Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 242 CYS Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 166 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 67 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 82 optimal weight: 8.9990 chunk 97 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.126677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.093356 restraints weight = 11497.217| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.09 r_work: 0.2790 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.241 9038 Z= 0.351 Angle : 2.397 83.900 12270 Z= 1.179 Chirality : 0.350 6.359 1339 Planarity : 0.005 0.059 1548 Dihedral : 11.152 143.280 1312 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 3.86 % Allowed : 15.88 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % 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: -3.70 (0.23), residues: 1101 helix: -2.56 (0.22), residues: 440 sheet: -1.79 (0.55), residues: 90 loop : -2.46 (0.24), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 102 TYR 0.015 0.001 TYR C 84 PHE 0.024 0.001 PHE A 69 TRP 0.011 0.001 TRP D 129 HIS 0.004 0.001 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00978 ( 9026) covalent geometry : angle 1.94502 (12243) hydrogen bonds : bond 0.04420 ( 198) hydrogen bonds : angle 4.69588 ( 570) metal coordination : bond 0.02299 ( 11) metal coordination : angle 29.92357 ( 27) Misc. bond : bond 0.00126 ( 1) *********************** 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 140 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 104 time to evaluate : 0.322 Fit side-chains REVERT: A 346 ARG cc_start: 0.7116 (mtt90) cc_final: 0.6264 (mtp180) REVERT: A 355 MET cc_start: 0.7128 (mmm) cc_final: 0.6717 (tpp) REVERT: A 551 TRP cc_start: 0.9139 (OUTLIER) cc_final: 0.7658 (t60) REVERT: A 577 ASN cc_start: 0.8634 (t0) cc_final: 0.7828 (t0) REVERT: A 625 LEU cc_start: 0.8491 (mt) cc_final: 0.8028 (mp) REVERT: B 49 LYS cc_start: 0.8797 (mmtm) cc_final: 0.8336 (mmmt) REVERT: B 171 LYS cc_start: 0.9091 (ttmt) cc_final: 0.8504 (tptp) REVERT: B 231 MET cc_start: 0.9019 (ptm) cc_final: 0.8815 (ptp) REVERT: C 179 ARG cc_start: 0.8993 (ptt-90) cc_final: 0.8775 (ptt-90) REVERT: D 131 LYS cc_start: 0.8390 (mttm) cc_final: 0.7973 (mmtt) REVERT: D 154 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7408 (mp0) outliers start: 36 outliers final: 27 residues processed: 129 average time/residue: 0.1062 time to fit residues: 18.3233 Evaluate side-chains 126 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 97 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 361 HIS Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 551 TRP Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 242 CYS Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 154 GLU Chi-restraints excluded: chain D residue 166 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 106 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 GLN ** 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 = 0.3455 r_free = 0.3455 target = 0.125274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.091934 restraints weight = 11470.938| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 2.06 r_work: 0.2788 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.239 9038 Z= 0.387 Angle : 2.424 83.471 12270 Z= 1.185 Chirality : 0.351 6.355 1339 Planarity : 0.005 0.060 1548 Dihedral : 10.944 143.152 1312 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 3.65 % Allowed : 16.95 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % 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: -3.67 (0.23), residues: 1101 helix: -2.44 (0.22), residues: 442 sheet: -1.80 (0.53), residues: 99 loop : -2.54 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 102 TYR 0.017 0.001 TYR C 84 PHE 0.027 0.002 PHE A 69 TRP 0.010 0.001 TRP D 129 HIS 0.004 0.001 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.01053 ( 9026) covalent geometry : angle 1.95694 (12243) hydrogen bonds : bond 0.04662 ( 198) hydrogen bonds : angle 4.79687 ( 570) metal coordination : bond 0.02542 ( 11) metal coordination : angle 30.56203 ( 27) Misc. bond : bond 0.00181 ( 1) *********************** 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 137 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 103 time to evaluate : 0.234 Fit side-chains REVERT: A 318 MET cc_start: 0.6734 (tmm) cc_final: 0.6509 (tmm) REVERT: A 346 ARG cc_start: 0.7189 (mtt90) cc_final: 0.6381 (mtp180) REVERT: A 355 MET cc_start: 0.7330 (mmm) cc_final: 0.6883 (tpp) REVERT: A 551 TRP cc_start: 0.9188 (OUTLIER) cc_final: 0.7697 (t60) REVERT: A 577 ASN cc_start: 0.8684 (t0) cc_final: 0.7939 (t0) REVERT: A 625 LEU cc_start: 0.8559 (mt) cc_final: 0.8093 (mp) REVERT: B 49 LYS cc_start: 0.8814 (mmtm) cc_final: 0.8359 (mmmt) REVERT: B 171 LYS cc_start: 0.9123 (ttmt) cc_final: 0.8546 (tptp) REVERT: B 231 MET cc_start: 0.9018 (ptm) cc_final: 0.8777 (ptm) REVERT: C 179 ARG cc_start: 0.9002 (ptt-90) cc_final: 0.8733 (ptt-90) REVERT: D 131 LYS cc_start: 0.8429 (mttm) cc_final: 0.8018 (mmtt) REVERT: D 154 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7402 (mp0) outliers start: 34 outliers final: 28 residues processed: 125 average time/residue: 0.0981 time to fit residues: 16.4934 Evaluate side-chains 128 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 98 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 361 HIS Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 551 TRP Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 242 CYS Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 154 GLU Chi-restraints excluded: chain D residue 166 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 75 optimal weight: 0.0010 chunk 26 optimal weight: 0.0970 chunk 76 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 overall best weight: 0.4184 ------------------------------------------------------------------------------- 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 577 ASN C 156 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.129659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.096459 restraints weight = 11296.448| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.10 r_work: 0.2880 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.242 9038 Z= 0.314 Angle : 2.357 83.321 12270 Z= 1.168 Chirality : 0.349 6.313 1339 Planarity : 0.004 0.056 1548 Dihedral : 10.186 137.881 1312 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.00 % Allowed : 17.70 % Favored : 79.29 % 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: -3.18 (0.24), residues: 1101 helix: -2.05 (0.23), residues: 443 sheet: -1.37 (0.58), residues: 82 loop : -2.27 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 102 TYR 0.009 0.001 TYR B 39 PHE 0.011 0.001 PHE A 69 TRP 0.011 0.001 TRP C 132 HIS 0.003 0.001 HIS A 354 Details of bonding type rmsd covalent geometry : bond 0.00906 ( 9026) covalent geometry : angle 1.91964 (12243) hydrogen bonds : bond 0.03182 ( 198) hydrogen bonds : angle 4.37356 ( 570) metal coordination : bond 0.01266 ( 11) metal coordination : angle 29.22873 ( 27) Misc. bond : bond 0.00056 ( 1) *********************** 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 134 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 0.280 Fit side-chains REVERT: A 346 ARG cc_start: 0.7087 (mtt90) cc_final: 0.6002 (mtp180) REVERT: A 355 MET cc_start: 0.7109 (mmm) cc_final: 0.6627 (tpp) REVERT: A 551 TRP cc_start: 0.9161 (OUTLIER) cc_final: 0.7686 (t60) REVERT: A 577 ASN cc_start: 0.8688 (t0) cc_final: 0.7808 (t0) REVERT: A 625 LEU cc_start: 0.8565 (mt) cc_final: 0.8079 (mp) REVERT: B 49 LYS cc_start: 0.8824 (mmtm) cc_final: 0.8366 (mmmt) REVERT: B 91 ILE cc_start: 0.9331 (OUTLIER) cc_final: 0.8916 (tp) REVERT: B 171 LYS cc_start: 0.9078 (ttmt) cc_final: 0.8501 (tptp) REVERT: B 197 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8168 (mp0) REVERT: D 131 LYS cc_start: 0.8381 (mttm) cc_final: 0.7973 (mmtt) outliers start: 28 outliers final: 20 residues processed: 125 average time/residue: 0.1043 time to fit residues: 17.3936 Evaluate side-chains 123 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 361 HIS Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 551 TRP Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain B residue 29 HIS Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 242 CYS Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 166 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 7 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 42 optimal weight: 0.3980 chunk 77 optimal weight: 2.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 GLN ** 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 = 0.3465 r_free = 0.3465 target = 0.126216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.092866 restraints weight = 11485.319| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.07 r_work: 0.2798 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.239 9038 Z= 0.365 Angle : 2.400 83.243 12270 Z= 1.180 Chirality : 0.351 6.350 1339 Planarity : 0.004 0.058 1548 Dihedral : 10.297 140.146 1311 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 3.65 % Allowed : 17.70 % Favored : 78.65 % 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: -3.23 (0.24), residues: 1101 helix: -2.02 (0.23), residues: 446 sheet: -1.50 (0.57), residues: 90 loop : -2.35 (0.25), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 102 TYR 0.017 0.001 TYR C 84 PHE 0.024 0.001 PHE A 69 TRP 0.012 0.001 TRP C 132 HIS 0.005 0.001 HIS A 354 Details of bonding type rmsd covalent geometry : bond 0.01008 ( 9026) covalent geometry : angle 1.94563 (12243) hydrogen bonds : bond 0.04194 ( 198) hydrogen bonds : angle 4.53073 ( 570) metal coordination : bond 0.02185 ( 11) metal coordination : angle 30.03016 ( 27) Misc. bond : bond 0.00165 ( 1) *********************** 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 138 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 104 time to evaluate : 0.399 Fit side-chains REVERT: A 318 MET cc_start: 0.6663 (tmm) cc_final: 0.6460 (tmm) REVERT: A 346 ARG cc_start: 0.7187 (mtt90) cc_final: 0.6214 (mtp180) REVERT: A 355 MET cc_start: 0.7235 (mmm) cc_final: 0.6777 (tpp) REVERT: A 519 PHE cc_start: 0.8482 (m-80) cc_final: 0.8082 (m-80) REVERT: A 551 TRP cc_start: 0.9192 (OUTLIER) cc_final: 0.7732 (t60) REVERT: A 577 ASN cc_start: 0.8722 (t0) cc_final: 0.7878 (t0) REVERT: A 625 LEU cc_start: 0.8549 (mt) cc_final: 0.8040 (mp) REVERT: B 49 LYS cc_start: 0.8819 (mmtm) cc_final: 0.8369 (mmmt) REVERT: B 171 LYS cc_start: 0.9128 (ttmt) cc_final: 0.8539 (tptp) REVERT: C 179 ARG cc_start: 0.8973 (ptt-90) cc_final: 0.8718 (ptt-90) REVERT: D 63 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8644 (tt) REVERT: D 131 LYS cc_start: 0.8408 (mttm) cc_final: 0.7994 (mmtt) outliers start: 34 outliers final: 29 residues processed: 128 average time/residue: 0.1109 time to fit residues: 19.1586 Evaluate side-chains 132 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 101 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 361 HIS Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 551 TRP Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 242 CYS Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 166 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 13 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 88 optimal weight: 0.1980 chunk 61 optimal weight: 0.2980 chunk 97 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.129694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.096428 restraints weight = 11295.266| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.11 r_work: 0.2907 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.242 9038 Z= 0.316 Angle : 2.346 83.036 12270 Z= 1.169 Chirality : 0.349 6.313 1339 Planarity : 0.004 0.055 1548 Dihedral : 9.599 139.045 1311 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.11 % Allowed : 18.35 % Favored : 78.54 % 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: -2.85 (0.24), residues: 1101 helix: -1.69 (0.24), residues: 448 sheet: -1.26 (0.59), residues: 82 loop : -2.14 (0.25), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 102 TYR 0.009 0.001 TYR B 39 PHE 0.013 0.001 PHE A 69 TRP 0.014 0.001 TRP C 132 HIS 0.003 0.001 HIS A 354 Details of bonding type rmsd covalent geometry : bond 0.00910 ( 9026) covalent geometry : angle 1.92180 (12243) hydrogen bonds : bond 0.03131 ( 198) hydrogen bonds : angle 4.33656 ( 570) metal coordination : bond 0.01283 ( 11) metal coordination : angle 28.74170 ( 27) Misc. bond : bond 0.00091 ( 1) *********************** 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 135 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 106 time to evaluate : 0.350 Fit side-chains REVERT: A 346 ARG cc_start: 0.7058 (mtt90) cc_final: 0.6024 (mtp180) REVERT: A 355 MET cc_start: 0.7082 (mmm) cc_final: 0.6613 (tpp) REVERT: A 519 PHE cc_start: 0.8430 (m-80) cc_final: 0.8044 (m-80) REVERT: A 551 TRP cc_start: 0.9168 (OUTLIER) cc_final: 0.7702 (t60) REVERT: A 577 ASN cc_start: 0.8711 (t0) cc_final: 0.7909 (t0) REVERT: A 625 LEU cc_start: 0.8542 (mt) cc_final: 0.8030 (mp) REVERT: B 171 LYS cc_start: 0.9109 (ttmt) cc_final: 0.8523 (tptp) REVERT: B 197 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8212 (mp0) REVERT: C 179 ARG cc_start: 0.8996 (ptt-90) cc_final: 0.8736 (ptt-90) REVERT: D 131 LYS cc_start: 0.8363 (mttm) cc_final: 0.7945 (mmtt) outliers start: 29 outliers final: 24 residues processed: 129 average time/residue: 0.0998 time to fit residues: 17.4510 Evaluate side-chains 128 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 361 HIS Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 551 TRP Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain B residue 29 HIS Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 242 CYS Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 166 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 104 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 106 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 87 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 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 29 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.128188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.094812 restraints weight = 11334.024| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.11 r_work: 0.2883 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.240 9038 Z= 0.330 Angle : 2.354 82.715 12270 Z= 1.173 Chirality : 0.350 6.332 1339 Planarity : 0.004 0.055 1548 Dihedral : 9.453 142.331 1309 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 2.90 % Allowed : 18.56 % Favored : 78.54 % 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: -2.75 (0.24), residues: 1101 helix: -1.53 (0.24), residues: 448 sheet: -1.30 (0.57), residues: 90 loop : -2.15 (0.25), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 102 TYR 0.012 0.001 TYR B 39 PHE 0.019 0.001 PHE A 69 TRP 0.015 0.001 TRP C 132 HIS 0.003 0.001 HIS A 354 Details of bonding type rmsd covalent geometry : bond 0.00939 ( 9026) covalent geometry : angle 1.93309 (12243) hydrogen bonds : bond 0.03610 ( 198) hydrogen bonds : angle 4.32953 ( 570) metal coordination : bond 0.01680 ( 11) metal coordination : angle 28.70576 ( 27) Misc. bond : bond 0.00122 ( 1) *********************** 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 128 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 0.351 Fit side-chains REVERT: A 346 ARG cc_start: 0.7083 (mtt90) cc_final: 0.6097 (mtp180) REVERT: A 355 MET cc_start: 0.7113 (mmm) cc_final: 0.6668 (tpp) REVERT: A 551 TRP cc_start: 0.9174 (OUTLIER) cc_final: 0.7663 (t60) REVERT: A 577 ASN cc_start: 0.8714 (t0) cc_final: 0.7891 (t0) REVERT: A 625 LEU cc_start: 0.8534 (mt) cc_final: 0.8015 (mp) REVERT: B 171 LYS cc_start: 0.9131 (ttmt) cc_final: 0.8554 (tptp) REVERT: C 179 ARG cc_start: 0.9002 (ptt-90) cc_final: 0.8731 (ptt-90) REVERT: D 63 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8415 (tt) REVERT: D 131 LYS cc_start: 0.8383 (mttm) cc_final: 0.7949 (mmtt) REVERT: D 163 LYS cc_start: 0.8185 (mttt) cc_final: 0.7968 (mttt) outliers start: 27 outliers final: 23 residues processed: 122 average time/residue: 0.1073 time to fit residues: 17.6522 Evaluate side-chains 123 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 98 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 361 HIS Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 551 TRP Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 242 CYS Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 166 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 51 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 GLN ** A 176 GLN ** 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 = 0.3493 r_free = 0.3493 target = 0.128787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.095568 restraints weight = 11185.497| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.08 r_work: 0.2877 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.241 9038 Z= 0.322 Angle : 2.340 82.644 12270 Z= 1.172 Chirality : 0.349 6.327 1339 Planarity : 0.004 0.055 1548 Dihedral : 9.220 143.644 1309 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.00 % Allowed : 18.99 % Favored : 78.00 % 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: -2.53 (0.25), residues: 1101 helix: -1.34 (0.24), residues: 447 sheet: -1.19 (0.57), residues: 90 loop : -2.04 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 102 TYR 0.010 0.001 TYR B 39 PHE 0.016 0.001 PHE A 69 TRP 0.016 0.001 TRP C 132 HIS 0.003 0.001 HIS A 354 Details of bonding type rmsd covalent geometry : bond 0.00924 ( 9026) covalent geometry : angle 1.93123 (12243) hydrogen bonds : bond 0.03350 ( 198) hydrogen bonds : angle 4.27012 ( 570) metal coordination : bond 0.01519 ( 11) metal coordination : angle 28.22570 ( 27) Misc. bond : bond 0.00110 ( 1) ********************** 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 128 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 100 time to evaluate : 0.392 Fit side-chains REVERT: A 346 ARG cc_start: 0.7086 (mtt90) cc_final: 0.6106 (mtp180) REVERT: A 355 MET cc_start: 0.7083 (mmm) cc_final: 0.6640 (tpp) REVERT: A 519 PHE cc_start: 0.8452 (m-80) cc_final: 0.8106 (m-80) REVERT: A 551 TRP cc_start: 0.9169 (OUTLIER) cc_final: 0.7689 (t60) REVERT: A 577 ASN cc_start: 0.8720 (t0) cc_final: 0.7924 (t0) REVERT: A 625 LEU cc_start: 0.8527 (mt) cc_final: 0.7995 (mp) REVERT: B 91 ILE cc_start: 0.9352 (OUTLIER) cc_final: 0.8923 (tp) REVERT: B 171 LYS cc_start: 0.9126 (ttmt) cc_final: 0.8530 (tptp) REVERT: B 197 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8225 (mp0) REVERT: C 179 ARG cc_start: 0.9003 (ptt-90) cc_final: 0.8737 (ptt-90) REVERT: D 131 LYS cc_start: 0.8391 (mttm) cc_final: 0.7961 (mmtt) REVERT: D 163 LYS cc_start: 0.8192 (mttt) cc_final: 0.7945 (mttt) outliers start: 28 outliers final: 25 residues processed: 122 average time/residue: 0.1136 time to fit residues: 18.3390 Evaluate side-chains 126 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 99 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 361 HIS Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 551 TRP Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 242 CYS Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 166 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 2 optimal weight: 0.3980 chunk 78 optimal weight: 4.9990 chunk 33 optimal weight: 0.2980 chunk 30 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 101 optimal weight: 10.0000 chunk 51 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 GLN ** 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 = 0.3505 r_free = 0.3505 target = 0.129865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.096610 restraints weight = 11079.983| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.09 r_work: 0.2901 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.241 9038 Z= 0.318 Angle : 2.313 82.541 12270 Z= 1.169 Chirality : 0.349 6.318 1339 Planarity : 0.004 0.054 1548 Dihedral : 8.894 148.607 1309 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.68 % Allowed : 19.42 % Favored : 77.90 % 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: -2.31 (0.25), residues: 1101 helix: -1.12 (0.25), residues: 448 sheet: -0.87 (0.60), residues: 80 loop : -1.97 (0.25), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 102 TYR 0.010 0.001 TYR B 39 PHE 0.013 0.001 PHE A 69 TRP 0.016 0.001 TRP C 132 HIS 0.003 0.001 HIS A 354 Details of bonding type rmsd covalent geometry : bond 0.00916 ( 9026) covalent geometry : angle 1.92622 (12243) hydrogen bonds : bond 0.03138 ( 198) hydrogen bonds : angle 4.17110 ( 570) metal coordination : bond 0.01360 ( 11) metal coordination : angle 27.37630 ( 27) Misc. bond : bond 0.00093 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2167.91 seconds wall clock time: 37 minutes 50.64 seconds (2270.64 seconds total)