Starting phenix.real_space_refine on Fri Sep 19 08:32:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rfj_19125/09_2025/8rfj_19125.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rfj_19125/09_2025/8rfj_19125.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8rfj_19125/09_2025/8rfj_19125.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rfj_19125/09_2025/8rfj_19125.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8rfj_19125/09_2025/8rfj_19125.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rfj_19125/09_2025/8rfj_19125.map" } resolution = 3.18 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= 0.027 sd= 0.079 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 Zn 1 6.06 5 P 128 5.49 5 S 85 5.16 5 C 15163 2.51 5 N 4392 2.21 5 O 4910 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24679 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2483 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 18, 'TRANS': 309} Chain breaks: 1 Chain: "B" Number of atoms: 2502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2502 Classifications: {'peptide': 331} Link IDs: {'PTRANS': 18, 'TRANS': 312} Chain breaks: 1 Chain: "C" Number of atoms: 2502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2502 Classifications: {'peptide': 331} Link IDs: {'PTRANS': 18, 'TRANS': 312} Chain breaks: 1 Chain: "D" Number of atoms: 2457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2457 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 18, 'TRANS': 305} Chain breaks: 1 Chain: "E" Number of atoms: 2153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2153 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 16, 'TRANS': 266} Chain breaks: 1 Chain: "F" Number of atoms: 1719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1719 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 208} Chain: "G" Number of atoms: 1913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1913 Classifications: {'peptide': 240} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 222} Chain: "H" Number of atoms: 1218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1218 Classifications: {'RNA': 57} Modifications used: {'5*END': 1, 'rna2p_pur': 17, 'rna2p_pyr': 9, 'rna3p_pur': 14, 'rna3p_pyr': 17} Link IDs: {'rna2p': 26, 'rna3p': 30} Chain breaks: 1 Chain: "I" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 821 Classifications: {'DNA': 40} Link IDs: {'rna3p': 39} Chain: "J" Number of atoms: 656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 656 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "K" Number of atoms: 4452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 582, 4452 Classifications: {'peptide': 582} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 29, 'TRANS': 549} Chain breaks: 5 Chain: "M" Number of atoms: 1802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1802 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 11, 'TRANS': 224} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14055 SG CYS G 30 50.393 76.687 165.137 1.00 79.46 S ATOM 14077 SG CYS G 33 54.257 76.418 165.126 1.00 78.47 S ATOM 14324 SG CYS G 66 52.468 78.632 167.652 1.00 75.02 S ATOM 14355 SG CYS G 69 52.831 79.528 164.017 1.00 77.61 S Time building chain proxies: 6.01, per 1000 atoms: 0.24 Number of scatterers: 24679 At special positions: 0 Unit cell: (100.1, 136.4, 188.1, 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) Zn 1 29.99 S 85 16.00 P 128 15.00 O 4910 8.00 N 4392 7.00 C 15163 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=0, symmetry=0 Time building additional restraints: 2.32 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN G 301 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 33 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 69 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 66 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 30 " Number of angles added : 6 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5258 Finding SS restraints... Secondary structure from input PDB file: 125 helices and 36 sheets defined 42.3% alpha, 16.7% beta 38 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 3.21 Creating SS restraints... Processing helix chain 'A' and resid 66 through 82 Processing helix chain 'A' and resid 82 through 90 removed outlier: 3.518A pdb=" N LYS A 90 " --> pdb=" O ALA A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 105 Processing helix chain 'A' and resid 106 through 110 removed outlier: 4.309A pdb=" N GLY A 109 " --> pdb=" O ASN A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 126 removed outlier: 3.506A pdb=" N ALA A 126 " --> pdb=" O VAL A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 155 No H-bonds generated for 'chain 'A' and resid 153 through 155' Processing helix chain 'A' and resid 156 through 161 Processing helix chain 'A' and resid 164 through 168 Processing helix chain 'A' and resid 183 through 188 Processing helix chain 'A' and resid 192 through 196 removed outlier: 4.103A pdb=" N VAL A 196 " --> pdb=" O ASP A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 221 Processing helix chain 'A' and resid 265 through 279 Processing helix chain 'A' and resid 280 through 282 No H-bonds generated for 'chain 'A' and resid 280 through 282' Processing helix chain 'A' and resid 318 through 332 Processing helix chain 'A' and resid 333 through 341 removed outlier: 3.988A pdb=" N PHE A 337 " --> pdb=" O THR A 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 82 Processing helix chain 'B' and resid 82 through 90 removed outlier: 3.700A pdb=" N LYS B 90 " --> pdb=" O ALA B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 105 Processing helix chain 'B' and resid 117 through 126 Processing helix chain 'B' and resid 129 through 133 removed outlier: 3.553A pdb=" N PHE B 133 " --> pdb=" O PHE B 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 129 through 133' Processing helix chain 'B' and resid 153 through 155 No H-bonds generated for 'chain 'B' and resid 153 through 155' Processing helix chain 'B' and resid 156 through 161 Processing helix chain 'B' and resid 164 through 168 Processing helix chain 'B' and resid 183 through 188 Processing helix chain 'B' and resid 192 through 196 removed outlier: 4.097A pdb=" N VAL B 196 " --> pdb=" O ASP B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 222 Processing helix chain 'B' and resid 265 through 279 Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'B' and resid 315 through 317 No H-bonds generated for 'chain 'B' and resid 315 through 317' Processing helix chain 'B' and resid 318 through 331 Processing helix chain 'B' and resid 334 through 342 Processing helix chain 'C' and resid 66 through 82 Processing helix chain 'C' and resid 82 through 90 removed outlier: 3.845A pdb=" N LYS C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 105 Processing helix chain 'C' and resid 117 through 126 Processing helix chain 'C' and resid 153 through 155 No H-bonds generated for 'chain 'C' and resid 153 through 155' Processing helix chain 'C' and resid 156 through 161 Processing helix chain 'C' and resid 164 through 168 Processing helix chain 'C' and resid 183 through 188 Processing helix chain 'C' and resid 192 through 196 removed outlier: 3.903A pdb=" N VAL C 196 " --> pdb=" O ASP C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 222 removed outlier: 3.887A pdb=" N ALA C 204 " --> pdb=" O GLY C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 278 Processing helix chain 'C' and resid 318 through 331 Processing helix chain 'C' and resid 334 through 342 Processing helix chain 'D' and resid 24 through 28 removed outlier: 3.840A pdb=" N GLY D 27 " --> pdb=" O SER D 24 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR D 28 " --> pdb=" O LEU D 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 24 through 28' Processing helix chain 'D' and resid 66 through 82 Processing helix chain 'D' and resid 82 through 90 removed outlier: 3.509A pdb=" N LYS D 90 " --> pdb=" O ALA D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 105 Processing helix chain 'D' and resid 117 through 126 Processing helix chain 'D' and resid 129 through 134 Processing helix chain 'D' and resid 156 through 161 Processing helix chain 'D' and resid 164 through 168 removed outlier: 3.532A pdb=" N SER D 168 " --> pdb=" O ILE D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 197 removed outlier: 3.938A pdb=" N VAL D 196 " --> pdb=" O ASP D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 214 Processing helix chain 'D' and resid 265 through 278 Processing helix chain 'D' and resid 279 through 282 Processing helix chain 'D' and resid 315 through 317 No H-bonds generated for 'chain 'D' and resid 315 through 317' Processing helix chain 'D' and resid 318 through 330 Processing helix chain 'D' and resid 334 through 342 Processing helix chain 'E' and resid 66 through 82 Processing helix chain 'E' and resid 82 through 90 Processing helix chain 'E' and resid 95 through 105 Processing helix chain 'E' and resid 117 through 126 removed outlier: 3.678A pdb=" N ALA E 126 " --> pdb=" O VAL E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 134 Processing helix chain 'E' and resid 153 through 155 No H-bonds generated for 'chain 'E' and resid 153 through 155' Processing helix chain 'E' and resid 156 through 161 removed outlier: 3.543A pdb=" N GLY E 161 " --> pdb=" O GLN E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 278 Processing helix chain 'E' and resid 279 through 282 Processing helix chain 'E' and resid 288 through 292 removed outlier: 3.620A pdb=" N ASP E 291 " --> pdb=" O HIS E 288 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR E 292 " --> pdb=" O ALA E 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 288 through 292' Processing helix chain 'E' and resid 318 through 332 removed outlier: 3.581A pdb=" N PHE E 322 " --> pdb=" O THR E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 342 Processing helix chain 'F' and resid 22 through 40 Processing helix chain 'F' and resid 44 through 48 Processing helix chain 'F' and resid 89 through 99 Processing helix chain 'F' and resid 137 through 147 removed outlier: 3.919A pdb=" N GLN F 147 " --> pdb=" O ASP F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 158 Processing helix chain 'F' and resid 187 through 191 removed outlier: 3.534A pdb=" N ILE F 190 " --> pdb=" O GLU F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 212 Processing helix chain 'G' and resid 3 through 5 No H-bonds generated for 'chain 'G' and resid 3 through 5' Processing helix chain 'G' and resid 6 through 12 Processing helix chain 'G' and resid 54 through 58 Processing helix chain 'G' and resid 67 through 73 Processing helix chain 'G' and resid 74 through 81 Processing helix chain 'G' and resid 96 through 106 Processing helix chain 'G' and resid 149 through 164 Processing helix chain 'G' and resid 189 through 196 removed outlier: 3.548A pdb=" N LEU G 196 " --> pdb=" O GLY G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 206 Processing helix chain 'G' and resid 208 through 219 removed outlier: 3.542A pdb=" N TYR G 217 " --> pdb=" O TRP G 213 " (cutoff:3.500A) Processing helix chain 'G' and resid 232 through 240 Processing helix chain 'K' and resid 106 through 108 No H-bonds generated for 'chain 'K' and resid 106 through 108' Processing helix chain 'K' and resid 109 through 122 removed outlier: 3.992A pdb=" N GLU K 114 " --> pdb=" O LEU K 110 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N GLN K 115 " --> pdb=" O PRO K 111 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLU K 121 " --> pdb=" O ALA K 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 150 removed outlier: 3.566A pdb=" N MET K 139 " --> pdb=" O GLY K 135 " (cutoff:3.500A) Processing helix chain 'K' and resid 159 through 171 Processing helix chain 'K' and resid 173 through 178 Processing helix chain 'K' and resid 193 through 204 Processing helix chain 'K' and resid 205 through 215 Processing helix chain 'K' and resid 220 through 229 Processing helix chain 'K' and resid 237 through 245 removed outlier: 3.673A pdb=" N ALA K 241 " --> pdb=" O MET K 237 " (cutoff:3.500A) Processing helix chain 'K' and resid 264 through 269 Processing helix chain 'K' and resid 285 through 300 removed outlier: 3.578A pdb=" N LEU K 289 " --> pdb=" O SER K 285 " (cutoff:3.500A) Processing helix chain 'K' and resid 330 through 339 Processing helix chain 'K' and resid 344 through 355 Processing helix chain 'K' and resid 359 through 378 Processing helix chain 'K' and resid 396 through 408 removed outlier: 4.441A pdb=" N ALA K 400 " --> pdb=" O SER K 396 " (cutoff:3.500A) Processing helix chain 'K' and resid 409 through 411 No H-bonds generated for 'chain 'K' and resid 409 through 411' Processing helix chain 'K' and resid 418 through 419 No H-bonds generated for 'chain 'K' and resid 418 through 419' Processing helix chain 'K' and resid 420 through 436 removed outlier: 4.011A pdb=" N ILE K 424 " --> pdb=" O ALA K 420 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA K 427 " --> pdb=" O VAL K 423 " (cutoff:3.500A) Processing helix chain 'K' and resid 464 through 473 Processing helix chain 'K' and resid 489 through 496 Processing helix chain 'K' and resid 511 through 516 removed outlier: 4.125A pdb=" N THR K 515 " --> pdb=" O PRO K 511 " (cutoff:3.500A) Processing helix chain 'K' and resid 532 through 550 Processing helix chain 'K' and resid 560 through 575 removed outlier: 4.006A pdb=" N GLY K 569 " --> pdb=" O GLU K 565 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ARG K 570 " --> pdb=" O LEU K 566 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA K 573 " --> pdb=" O GLY K 569 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N VAL K 574 " --> pdb=" O ARG K 570 " (cutoff:3.500A) Processing helix chain 'K' and resid 590 through 601 Processing helix chain 'K' and resid 612 through 615 Processing helix chain 'K' and resid 648 through 659 Processing helix chain 'K' and resid 659 through 676 removed outlier: 4.388A pdb=" N VAL K 663 " --> pdb=" O GLY K 659 " (cutoff:3.500A) Processing helix chain 'K' and resid 693 through 698 removed outlier: 3.898A pdb=" N GLY K 697 " --> pdb=" O ASP K 693 " (cutoff:3.500A) Processing helix chain 'K' and resid 700 through 702 No H-bonds generated for 'chain 'K' and resid 700 through 702' Processing helix chain 'K' and resid 703 through 712 removed outlier: 3.622A pdb=" N ARG K 712 " --> pdb=" O LYS K 708 " (cutoff:3.500A) Processing helix chain 'M' and resid 15 through 27 removed outlier: 3.546A pdb=" N MET M 27 " --> pdb=" O VAL M 23 " (cutoff:3.500A) Processing helix chain 'M' and resid 31 through 39 Processing helix chain 'M' and resid 70 through 92 Proline residue: M 82 - end of helix Processing helix chain 'M' and resid 127 through 133 removed outlier: 3.642A pdb=" N GLU M 132 " --> pdb=" O GLN M 128 " (cutoff:3.500A) Processing helix chain 'M' and resid 136 through 160 removed outlier: 4.279A pdb=" N ALA M 142 " --> pdb=" O ALA M 138 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N HIS M 143 " --> pdb=" O GLU M 139 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU M 144 " --> pdb=" O GLY M 140 " (cutoff:3.500A) Processing helix chain 'M' and resid 223 through 228 removed outlier: 3.849A pdb=" N SER M 228 " --> pdb=" O THR M 224 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 144 through 146 removed outlier: 3.669A pdb=" N TYR A 150 " --> pdb=" O LEU A 256 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 144 through 146 removed outlier: 6.854A pdb=" N GLN A 2 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LEU A 302 " --> pdb=" O GLN A 2 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLU A 4 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL A 300 " --> pdb=" O GLU A 4 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU A 6 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 21 through 23 removed outlier: 3.651A pdb=" N TYR A 21 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N GLU A 247 " --> pdb=" O PRO A 39 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N THR A 41 " --> pdb=" O GLU A 247 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N VAL A 249 " --> pdb=" O THR A 41 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 45 through 50 Processing sheet with id=AA5, first strand: chain 'A' and resid 94 through 95 removed outlier: 7.286A pdb=" N LEU A 94 " --> pdb=" O LEU F 103 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 308 through 309 Processing sheet with id=AA7, first strand: chain 'B' and resid 144 through 151 removed outlier: 4.912A pdb=" N ARG B 258 " --> pdb=" O ASP B 147 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LEU B 149 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N LEU B 256 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N LYS B 254 " --> pdb=" O PRO B 151 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP B 299 " --> pdb=" O LEU B 6 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ARG B 8 " --> pdb=" O ILE B 297 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ILE B 297 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 21 through 23 removed outlier: 7.661A pdb=" N GLU B 247 " --> pdb=" O PRO B 39 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N THR B 41 " --> pdb=" O GLU B 247 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N VAL B 249 " --> pdb=" O THR B 41 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 48 through 51 Processing sheet with id=AB1, first strand: chain 'B' and resid 134 through 135 Processing sheet with id=AB2, first strand: chain 'C' and resid 144 through 146 Processing sheet with id=AB3, first strand: chain 'C' and resid 144 through 146 removed outlier: 3.566A pdb=" N ASP C 299 " --> pdb=" O LEU C 6 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ARG C 8 " --> pdb=" O ILE C 297 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ILE C 297 " --> pdb=" O ARG C 8 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 21 through 23 removed outlier: 7.645A pdb=" N GLU C 247 " --> pdb=" O PRO C 39 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N THR C 41 " --> pdb=" O GLU C 247 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N VAL C 249 " --> pdb=" O THR C 41 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 45 through 50 Processing sheet with id=AB6, first strand: chain 'D' and resid 144 through 146 Processing sheet with id=AB7, first strand: chain 'D' and resid 144 through 146 removed outlier: 6.656A pdb=" N ARG D 8 " --> pdb=" O ILE D 297 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ILE D 297 " --> pdb=" O ARG D 8 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 21 through 23 removed outlier: 3.523A pdb=" N TYR D 21 " --> pdb=" O LEU D 40 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N GLU D 247 " --> pdb=" O PRO D 39 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR D 41 " --> pdb=" O GLU D 247 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N VAL D 249 " --> pdb=" O THR D 41 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 45 through 50 removed outlier: 3.668A pdb=" N LYS D 58 " --> pdb=" O ALA D 50 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 144 through 151 removed outlier: 5.327A pdb=" N VAL E 146 " --> pdb=" O ASN E 260 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ASN E 260 " --> pdb=" O VAL E 146 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N SER E 148 " --> pdb=" O ARG E 258 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ARG E 258 " --> pdb=" O SER E 148 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASP E 299 " --> pdb=" O LEU E 6 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ARG E 8 " --> pdb=" O ILE E 297 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ILE E 297 " --> pdb=" O ARG E 8 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 21 through 23 removed outlier: 7.672A pdb=" N GLU E 247 " --> pdb=" O PRO E 39 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N THR E 41 " --> pdb=" O GLU E 247 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL E 177 " --> pdb=" O HIS E 246 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 45 through 50 Processing sheet with id=AC4, first strand: chain 'E' and resid 308 through 309 Processing sheet with id=AC5, first strand: chain 'F' and resid 72 through 75 removed outlier: 3.549A pdb=" N THR F 131 " --> pdb=" O HIS F 72 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ASN F 74 " --> pdb=" O THR F 129 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA F 128 " --> pdb=" O LEU F 10 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU F 10 " --> pdb=" O ALA F 128 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 14 through 15 Processing sheet with id=AC7, first strand: chain 'F' and resid 56 through 58 Processing sheet with id=AC8, first strand: chain 'F' and resid 182 through 183 Processing sheet with id=AC9, first strand: chain 'G' and resid 21 through 22 Processing sheet with id=AD1, first strand: chain 'G' and resid 28 through 29 Processing sheet with id=AD2, first strand: chain 'G' and resid 91 through 93 removed outlier: 3.691A pdb=" N ALA G 84 " --> pdb=" O MET G 115 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N VAL G 114 " --> pdb=" O ARG G 140 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 181 through 182 removed outlier: 5.638A pdb=" N LEU K 323 " --> pdb=" O ALA K 476 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N VAL K 478 " --> pdb=" O LEU K 323 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N VAL K 325 " --> pdb=" O VAL K 478 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N VAL K 126 " --> pdb=" O LEU K 477 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE K 125 " --> pdb=" O ILE K 504 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 340 through 342 removed outlier: 3.575A pdb=" N GLY K 457 " --> pdb=" O ARG K 440 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 518 through 521 removed outlier: 4.442A pdb=" N VAL K 691 " --> pdb=" O HIS K 521 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU K 636 " --> pdb=" O TRP K 690 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ILE K 580 " --> pdb=" O LEU K 608 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N VAL K 610 " --> pdb=" O ILE K 580 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 55 through 59 removed outlier: 3.976A pdb=" N PHE M 64 " --> pdb=" O PHE M 8 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'M' and resid 107 through 119 removed outlier: 3.620A pdb=" N SER M 107 " --> pdb=" O GLY M 205 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N ASN M 201 " --> pdb=" O ARG M 111 " (cutoff:3.500A) removed outlier: 9.714A pdb=" N TYR M 113 " --> pdb=" O ASP M 199 " (cutoff:3.500A) removed outlier: 9.300A pdb=" N ASP M 199 " --> pdb=" O TYR M 113 " (cutoff:3.500A) removed outlier: 10.410A pdb=" N LEU M 115 " --> pdb=" O VAL M 197 " (cutoff:3.500A) removed outlier: 9.253A pdb=" N VAL M 197 " --> pdb=" O LEU M 115 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ASP M 199 " --> pdb=" O PHE M 171 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N PHE M 171 " --> pdb=" O ASP M 199 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ASN M 201 " --> pdb=" O VAL M 169 " (cutoff:3.500A) removed outlier: 8.685A pdb=" N VAL M 169 " --> pdb=" O ASN M 201 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'M' and resid 122 through 123 removed outlier: 3.718A pdb=" N PHE M 178 " --> pdb=" O GLY M 192 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY M 176 " --> pdb=" O ARG M 194 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'M' and resid 207 through 209 970 hydrogen bonds defined for protein. 2688 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 97 hydrogen bonds 194 hydrogen bond angles 0 basepair planarities 38 basepair parallelities 45 stacking parallelities Total time for adding SS restraints: 5.21 Time building geometry restraints manager: 3.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6539 1.33 - 1.45: 5354 1.45 - 1.58: 13151 1.58 - 1.70: 253 1.70 - 1.82: 153 Bond restraints: 25450 Sorted by residual: bond pdb=" CG ARG A 138 " pdb=" CD ARG A 138 " ideal model delta sigma weight residual 1.520 1.484 0.036 3.00e-02 1.11e+03 1.42e+00 bond pdb=" C1' U H -6 " pdb=" N1 U H -6 " ideal model delta sigma weight residual 1.470 1.486 -0.016 1.50e-02 4.44e+03 1.14e+00 bond pdb=" C3' DG I -17 " pdb=" O3' DG I -17 " ideal model delta sigma weight residual 1.422 1.454 -0.032 3.00e-02 1.11e+03 1.13e+00 bond pdb=" O4' DA I -22 " pdb=" C1' DA I -22 " ideal model delta sigma weight residual 1.414 1.393 0.021 2.00e-02 2.50e+03 1.05e+00 bond pdb=" CG GLU C 327 " pdb=" CD GLU C 327 " ideal model delta sigma weight residual 1.516 1.491 0.025 2.50e-02 1.60e+03 9.98e-01 ... (remaining 25445 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 34586 1.97 - 3.93: 476 3.93 - 5.90: 50 5.90 - 7.87: 14 7.87 - 9.84: 1 Bond angle restraints: 35127 Sorted by residual: angle pdb=" C2' U H -6 " pdb=" C1' U H -6 " pdb=" N1 U H -6 " ideal model delta sigma weight residual 114.00 120.65 -6.65 1.50e+00 4.44e-01 1.97e+01 angle pdb=" C ARG M 78 " pdb=" N ASP M 79 " pdb=" CA ASP M 79 " ideal model delta sigma weight residual 121.94 114.82 7.12 2.00e+00 2.50e-01 1.27e+01 angle pdb=" N ASP D 54 " pdb=" CA ASP D 54 " pdb=" C ASP D 54 " ideal model delta sigma weight residual 114.04 109.85 4.19 1.24e+00 6.50e-01 1.14e+01 angle pdb=" O3' U H -6 " pdb=" C3' U H -6 " pdb=" C2' U H -6 " ideal model delta sigma weight residual 109.50 114.51 -5.01 1.50e+00 4.44e-01 1.12e+01 angle pdb=" OP1 U H -6 " pdb=" P U H -6 " pdb=" OP2 U H -6 " ideal model delta sigma weight residual 119.60 109.76 9.84 3.00e+00 1.11e-01 1.08e+01 ... (remaining 35122 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.85: 14551 35.85 - 71.69: 570 71.69 - 107.54: 39 107.54 - 143.39: 3 143.39 - 179.23: 3 Dihedral angle restraints: 15166 sinusoidal: 6987 harmonic: 8179 Sorted by residual: dihedral pdb=" C4' U H -6 " pdb=" C3' U H -6 " pdb=" C2' U H -6 " pdb=" C1' U H -6 " ideal model delta sinusoidal sigma weight residual -35.00 32.96 -67.96 1 8.00e+00 1.56e-02 9.37e+01 dihedral pdb=" C5' U H -6 " pdb=" C4' U H -6 " pdb=" C3' U H -6 " pdb=" O3' U H -6 " ideal model delta sinusoidal sigma weight residual 147.00 81.65 65.35 1 8.00e+00 1.56e-02 8.74e+01 dihedral pdb=" O4' U H -6 " pdb=" C4' U H -6 " pdb=" C3' U H -6 " pdb=" C2' U H -6 " ideal model delta sinusoidal sigma weight residual 24.00 -33.80 57.80 1 8.00e+00 1.56e-02 7.01e+01 ... (remaining 15163 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 3699 0.081 - 0.163: 307 0.163 - 0.244: 6 0.244 - 0.325: 1 0.325 - 0.407: 1 Chirality restraints: 4014 Sorted by residual: chirality pdb=" C1' U H -6 " pdb=" O4' U H -6 " pdb=" C2' U H -6 " pdb=" N1 U H -6 " both_signs ideal model delta sigma weight residual False 2.45 2.04 0.41 2.00e-01 2.50e+01 4.13e+00 chirality pdb=" C3' U H -6 " pdb=" C4' U H -6 " pdb=" O3' U H -6 " pdb=" C2' U H -6 " both_signs ideal model delta sigma weight residual False -2.74 -2.50 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" C2' U H -6 " pdb=" C3' U H -6 " pdb=" O2' U H -6 " pdb=" C1' U H -6 " both_signs ideal model delta sigma weight residual False -2.52 -2.75 0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 4011 not shown) Planarity restraints: 4099 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 206 " -0.014 2.00e-02 2.50e+03 1.40e-02 3.90e+00 pdb=" CG TYR F 206 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR F 206 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR F 206 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR F 206 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR F 206 " -0.020 2.00e-02 2.50e+03 pdb=" CZ TYR F 206 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR F 206 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A H 11 " -0.023 2.00e-02 2.50e+03 1.05e-02 3.05e+00 pdb=" N9 A H 11 " 0.025 2.00e-02 2.50e+03 pdb=" C8 A H 11 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A H 11 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A H 11 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A H 11 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A H 11 " -0.005 2.00e-02 2.50e+03 pdb=" N1 A H 11 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A H 11 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A H 11 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A H 11 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET M 213 " -0.008 2.00e-02 2.50e+03 1.54e-02 2.38e+00 pdb=" C MET M 213 " 0.027 2.00e-02 2.50e+03 pdb=" O MET M 213 " -0.010 2.00e-02 2.50e+03 pdb=" N LEU M 214 " -0.009 2.00e-02 2.50e+03 ... (remaining 4096 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 506 2.66 - 3.22: 23337 3.22 - 3.78: 40673 3.78 - 4.34: 54443 4.34 - 4.90: 88091 Nonbonded interactions: 207050 Sorted by model distance: nonbonded pdb=" OP1 G H 29 " pdb=" OG SER M 61 " model vdw 2.105 3.040 nonbonded pdb=" OG SER E 24 " pdb=" OD1 ASP E 26 " model vdw 2.133 3.040 nonbonded pdb=" O VAL E 65 " pdb=" OG SER E 148 " model vdw 2.175 3.040 nonbonded pdb=" O2' G H 33 " pdb=" O ALA M 179 " model vdw 2.189 3.040 nonbonded pdb=" OG1 THR B 69 " pdb=" OP1 A H 7 " model vdw 2.216 3.040 ... (remaining 207045 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 179 or resid 242 through 343)) selection = (chain 'B' and (resid 1 through 179 or resid 242 through 343)) selection = (chain 'C' and (resid 1 through 179 or resid 242 through 343)) selection = (chain 'D' and (resid 1 through 179 or resid 242 through 343)) selection = (chain 'E' and resid 1 through 343) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.260 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: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 29.090 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25454 Z= 0.138 Angle : 0.553 9.837 35133 Z= 0.281 Chirality : 0.041 0.407 4014 Planarity : 0.004 0.035 4099 Dihedral : 16.982 179.234 9908 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.48 % 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 aren not related in a simple way. whole: 0.80 (0.16), residues: 2839 helix: 1.62 (0.17), residues: 981 sheet: 0.77 (0.24), residues: 450 loop : -0.28 (0.17), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 60 TYR 0.027 0.002 TYR F 206 PHE 0.019 0.001 PHE M 212 TRP 0.018 0.001 TRP F 127 HIS 0.009 0.001 HIS F 22 Details of bonding type rmsd covalent geometry : bond 0.00302 (25450) covalent geometry : angle 0.55050 (35127) hydrogen bonds : bond 0.17757 ( 1061) hydrogen bonds : angle 7.16024 ( 2882) metal coordination : bond 0.00849 ( 4) metal coordination : angle 4.03384 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 162 SER cc_start: 0.8685 (p) cc_final: 0.8390 (t) REVERT: E 292 TYR cc_start: 0.8178 (m-10) cc_final: 0.7791 (m-10) REVERT: K 284 CYS cc_start: 0.8342 (p) cc_final: 0.8035 (m) REVERT: M 216 LYS cc_start: 0.5026 (mmtm) cc_final: 0.4746 (tttt) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.1877 time to fit residues: 48.5849 Evaluate side-chains 142 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.0060 chunk 183 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 overall best weight: 3.5202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 GLN B 260 ASN ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 HIS D 288 HIS E 106 ASN E 141 GLN ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 HIS F 147 GLN ** K 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 525 ASN M 56 GLN ** M 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.071351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.055170 restraints weight = 104448.946| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 3.09 r_work: 0.3087 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 25454 Z= 0.338 Angle : 0.713 13.489 35133 Z= 0.367 Chirality : 0.047 0.360 4014 Planarity : 0.005 0.065 4099 Dihedral : 19.010 179.781 4787 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.48 % Allowed : 6.06 % Favored : 93.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.48 % 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 aren not related in a simple way. whole: 0.46 (0.16), residues: 2839 helix: 1.30 (0.17), residues: 997 sheet: 0.78 (0.25), residues: 386 loop : -0.49 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 180 TYR 0.025 0.002 TYR F 206 PHE 0.018 0.002 PHE G 52 TRP 0.013 0.002 TRP K 469 HIS 0.007 0.002 HIS G 220 Details of bonding type rmsd covalent geometry : bond 0.00749 (25450) covalent geometry : angle 0.70989 (35127) hydrogen bonds : bond 0.04946 ( 1061) hydrogen bonds : angle 5.72951 ( 2882) metal coordination : bond 0.01494 ( 4) metal coordination : angle 4.74208 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 151 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 MET cc_start: 0.7739 (OUTLIER) cc_final: 0.7504 (ttm) REVERT: E 292 TYR cc_start: 0.8771 (m-10) cc_final: 0.8295 (m-10) REVERT: F 206 TYR cc_start: 0.8159 (m-10) cc_final: 0.7956 (m-80) REVERT: K 443 MET cc_start: 0.8155 (pmm) cc_final: 0.7455 (mpp) REVERT: M 39 MET cc_start: 0.7931 (mmp) cc_final: 0.7663 (mmp) REVERT: M 207 ILE cc_start: 0.6461 (pt) cc_final: 0.6215 (pt) outliers start: 11 outliers final: 6 residues processed: 154 average time/residue: 0.1993 time to fit residues: 47.1812 Evaluate side-chains 148 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 141 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain K residue 713 TYR Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 56 GLN Chi-restraints excluded: chain M residue 97 ILE Chi-restraints excluded: chain M residue 204 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 92 optimal weight: 2.9990 chunk 167 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 146 optimal weight: 5.9990 chunk 96 optimal weight: 0.6980 chunk 37 optimal weight: 0.0770 chunk 267 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 overall best weight: 0.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 339 GLN ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 GLN ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 123 HIS ** K 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 521 HIS M 56 GLN ** M 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.073266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.056951 restraints weight = 102982.508| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 3.16 r_work: 0.3143 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25454 Z= 0.138 Angle : 0.570 9.021 35133 Z= 0.292 Chirality : 0.041 0.248 4014 Planarity : 0.004 0.033 4099 Dihedral : 18.954 179.558 4787 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.74 % Allowed : 7.66 % Favored : 91.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.48 % 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 aren not related in a simple way. whole: 0.63 (0.16), residues: 2839 helix: 1.58 (0.17), residues: 999 sheet: 0.68 (0.25), residues: 390 loop : -0.45 (0.16), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 191 TYR 0.018 0.001 TYR F 206 PHE 0.009 0.001 PHE E 133 TRP 0.011 0.001 TRP C 255 HIS 0.005 0.001 HIS M 143 Details of bonding type rmsd covalent geometry : bond 0.00299 (25450) covalent geometry : angle 0.56740 (35127) hydrogen bonds : bond 0.03879 ( 1061) hydrogen bonds : angle 5.33559 ( 2882) metal coordination : bond 0.00752 ( 4) metal coordination : angle 4.35802 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 145 MET cc_start: 0.8481 (mtt) cc_final: 0.8255 (mtt) REVERT: E 292 TYR cc_start: 0.8828 (m-10) cc_final: 0.8188 (m-10) REVERT: M 39 MET cc_start: 0.8008 (mmp) cc_final: 0.7719 (mmp) outliers start: 17 outliers final: 8 residues processed: 157 average time/residue: 0.1891 time to fit residues: 46.8559 Evaluate side-chains 147 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 139 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain E residue 8 ARG Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 713 TYR Chi-restraints excluded: chain M residue 31 GLN Chi-restraints excluded: chain M residue 97 ILE Chi-restraints excluded: chain M residue 204 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 32 optimal weight: 6.9990 chunk 216 optimal weight: 10.0000 chunk 2 optimal weight: 0.7980 chunk 115 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 60 optimal weight: 0.6980 chunk 263 optimal weight: 10.0000 chunk 143 optimal weight: 4.9990 chunk 195 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 262 optimal weight: 7.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 188 GLN ** K 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 372 GLN ** M 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.070800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.054495 restraints weight = 105150.882| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 3.08 r_work: 0.3078 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 25454 Z= 0.285 Angle : 0.650 17.981 35133 Z= 0.331 Chirality : 0.044 0.292 4014 Planarity : 0.005 0.048 4099 Dihedral : 19.062 179.411 4787 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.08 % Allowed : 9.00 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.48 % 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 aren not related in a simple way. whole: 0.45 (0.16), residues: 2839 helix: 1.36 (0.17), residues: 1001 sheet: 0.55 (0.26), residues: 390 loop : -0.50 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 180 TYR 0.015 0.002 TYR G 141 PHE 0.016 0.002 PHE G 52 TRP 0.025 0.002 TRP B 257 HIS 0.008 0.001 HIS M 143 Details of bonding type rmsd covalent geometry : bond 0.00632 (25450) covalent geometry : angle 0.64745 (35127) hydrogen bonds : bond 0.04265 ( 1061) hydrogen bonds : angle 5.38439 ( 2882) metal coordination : bond 0.01407 ( 4) metal coordination : angle 4.54774 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8043 (OUTLIER) cc_final: 0.7658 (tpp) REVERT: C 41 THR cc_start: 0.9422 (OUTLIER) cc_final: 0.8959 (p) REVERT: C 145 MET cc_start: 0.8606 (mtt) cc_final: 0.8273 (mtt) REVERT: C 174 THR cc_start: 0.8978 (OUTLIER) cc_final: 0.8763 (t) REVERT: D 188 LEU cc_start: 0.4922 (OUTLIER) cc_final: 0.4330 (mm) REVERT: E 22 TYR cc_start: 0.7638 (m-80) cc_final: 0.7246 (m-80) REVERT: E 292 TYR cc_start: 0.8783 (m-10) cc_final: 0.8208 (m-10) REVERT: G 115 MET cc_start: 0.8457 (mpp) cc_final: 0.7095 (mmt) REVERT: K 443 MET cc_start: 0.8223 (pmm) cc_final: 0.7196 (mpp) REVERT: M 39 MET cc_start: 0.8055 (mmp) cc_final: 0.7717 (mmm) REVERT: M 213 MET cc_start: 0.7915 (ppp) cc_final: 0.7325 (tmm) REVERT: M 214 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8593 (mp) REVERT: M 216 LYS cc_start: 0.5284 (mmtp) cc_final: 0.4759 (tttt) REVERT: M 218 TYR cc_start: 0.5829 (m-80) cc_final: 0.5556 (t80) outliers start: 25 outliers final: 12 residues processed: 154 average time/residue: 0.1855 time to fit residues: 45.0895 Evaluate side-chains 147 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain E residue 8 ARG Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain K residue 469 TRP Chi-restraints excluded: chain K residue 713 TYR Chi-restraints excluded: chain M residue 31 GLN Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 97 ILE Chi-restraints excluded: chain M residue 102 LYS Chi-restraints excluded: chain M residue 204 LEU Chi-restraints excluded: chain M residue 214 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 102 optimal weight: 0.4980 chunk 265 optimal weight: 20.0000 chunk 31 optimal weight: 2.9990 chunk 138 optimal weight: 0.7980 chunk 119 optimal weight: 8.9990 chunk 225 optimal weight: 10.0000 chunk 210 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 145 optimal weight: 0.8980 chunk 191 optimal weight: 0.8980 chunk 209 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 154 GLN ** F 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 286 HIS ** 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 = 0.3761 r_free = 0.3761 target = 0.072816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.056642 restraints weight = 102754.307| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 3.12 r_work: 0.3140 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25454 Z= 0.126 Angle : 0.561 9.800 35133 Z= 0.284 Chirality : 0.041 0.245 4014 Planarity : 0.004 0.033 4099 Dihedral : 19.033 179.758 4787 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.13 % Allowed : 9.61 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.48 % 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 aren not related in a simple way. whole: 0.66 (0.16), residues: 2839 helix: 1.62 (0.17), residues: 1003 sheet: 0.49 (0.26), residues: 390 loop : -0.39 (0.16), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 88 TYR 0.015 0.001 TYR G 141 PHE 0.009 0.001 PHE M 178 TRP 0.014 0.001 TRP K 469 HIS 0.005 0.001 HIS M 143 Details of bonding type rmsd covalent geometry : bond 0.00273 (25450) covalent geometry : angle 0.55745 (35127) hydrogen bonds : bond 0.03433 ( 1061) hydrogen bonds : angle 5.06565 ( 2882) metal coordination : bond 0.00743 ( 4) metal coordination : angle 4.50705 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 THR cc_start: 0.9329 (OUTLIER) cc_final: 0.8970 (p) REVERT: C 145 MET cc_start: 0.8837 (mtt) cc_final: 0.8524 (mtt) REVERT: D 188 LEU cc_start: 0.4885 (OUTLIER) cc_final: 0.4150 (mm) REVERT: E 292 TYR cc_start: 0.8793 (m-10) cc_final: 0.8199 (m-10) REVERT: G 115 MET cc_start: 0.8358 (mpp) cc_final: 0.7476 (mpp) REVERT: G 141 TYR cc_start: 0.8926 (t80) cc_final: 0.8643 (t80) REVERT: K 443 MET cc_start: 0.8121 (pmm) cc_final: 0.7208 (mpp) REVERT: M 39 MET cc_start: 0.7931 (mmp) cc_final: 0.7596 (mmm) REVERT: M 213 MET cc_start: 0.8347 (ppp) cc_final: 0.8076 (ppp) REVERT: M 216 LYS cc_start: 0.5229 (mmtp) cc_final: 0.4768 (tttt) outliers start: 26 outliers final: 9 residues processed: 162 average time/residue: 0.1838 time to fit residues: 47.2701 Evaluate side-chains 146 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 135 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain K residue 713 TYR Chi-restraints excluded: chain M residue 31 GLN Chi-restraints excluded: chain M residue 97 ILE Chi-restraints excluded: chain M residue 204 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 53 optimal weight: 8.9990 chunk 57 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 133 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 168 optimal weight: 0.5980 chunk 144 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 238 optimal weight: 8.9990 chunk 51 optimal weight: 5.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 244 ASN E 154 GLN ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 56 GLN M 177 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.071373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.055165 restraints weight = 104100.440| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 3.05 r_work: 0.3093 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 25454 Z= 0.231 Angle : 0.606 12.292 35133 Z= 0.307 Chirality : 0.042 0.281 4014 Planarity : 0.004 0.036 4099 Dihedral : 19.061 179.391 4787 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.13 % Allowed : 10.69 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.48 % 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 aren not related in a simple way. whole: 0.58 (0.16), residues: 2839 helix: 1.58 (0.17), residues: 999 sheet: 0.49 (0.26), residues: 392 loop : -0.46 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 180 TYR 0.011 0.001 TYR K 339 PHE 0.012 0.001 PHE G 52 TRP 0.011 0.001 TRP K 702 HIS 0.007 0.001 HIS M 143 Details of bonding type rmsd covalent geometry : bond 0.00510 (25450) covalent geometry : angle 0.60317 (35127) hydrogen bonds : bond 0.03778 ( 1061) hydrogen bonds : angle 5.12308 ( 2882) metal coordination : bond 0.01171 ( 4) metal coordination : angle 4.51278 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 THR cc_start: 0.9406 (OUTLIER) cc_final: 0.8952 (p) REVERT: C 145 MET cc_start: 0.8922 (mtt) cc_final: 0.8627 (mtt) REVERT: D 188 LEU cc_start: 0.4799 (OUTLIER) cc_final: 0.4192 (mm) REVERT: E 22 TYR cc_start: 0.7720 (m-80) cc_final: 0.7295 (m-80) REVERT: E 292 TYR cc_start: 0.8742 (m-10) cc_final: 0.8161 (m-10) REVERT: M 39 MET cc_start: 0.7971 (mmp) cc_final: 0.7576 (mmm) REVERT: M 213 MET cc_start: 0.8523 (ppp) cc_final: 0.8091 (ppp) REVERT: M 216 LYS cc_start: 0.5085 (mmtp) cc_final: 0.4604 (tttt) outliers start: 26 outliers final: 15 residues processed: 157 average time/residue: 0.1837 time to fit residues: 45.3386 Evaluate side-chains 147 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 244 ASN Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain K residue 713 TYR Chi-restraints excluded: chain M residue 31 GLN Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 55 VAL Chi-restraints excluded: chain M residue 97 ILE Chi-restraints excluded: chain M residue 204 LEU Chi-restraints excluded: chain M residue 218 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 225 optimal weight: 0.0020 chunk 95 optimal weight: 0.8980 chunk 108 optimal weight: 4.9990 chunk 182 optimal weight: 6.9990 chunk 142 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 220 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 89 optimal weight: 0.5980 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 260 ASN ** F 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 286 HIS ** 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 = 0.3750 r_free = 0.3750 target = 0.072160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.055893 restraints weight = 103642.743| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 3.17 r_work: 0.3126 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25454 Z= 0.133 Angle : 0.567 11.186 35133 Z= 0.286 Chirality : 0.041 0.251 4014 Planarity : 0.004 0.033 4099 Dihedral : 19.037 179.589 4787 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.04 % Allowed : 11.03 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.48 % 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 aren not related in a simple way. whole: 0.70 (0.16), residues: 2839 helix: 1.71 (0.17), residues: 996 sheet: 0.44 (0.25), residues: 404 loop : -0.38 (0.16), residues: 1439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 88 TYR 0.012 0.001 TYR E 103 PHE 0.009 0.001 PHE D 243 TRP 0.012 0.001 TRP E 255 HIS 0.005 0.001 HIS M 143 Details of bonding type rmsd covalent geometry : bond 0.00293 (25450) covalent geometry : angle 0.56352 (35127) hydrogen bonds : bond 0.03349 ( 1061) hydrogen bonds : angle 4.98945 ( 2882) metal coordination : bond 0.00824 ( 4) metal coordination : angle 4.57000 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 THR cc_start: 0.9355 (OUTLIER) cc_final: 0.8946 (p) REVERT: C 103 TYR cc_start: 0.9200 (m-80) cc_final: 0.8788 (m-80) REVERT: C 145 MET cc_start: 0.8884 (mtt) cc_final: 0.8609 (mtt) REVERT: D 1 MET cc_start: 0.8301 (tmm) cc_final: 0.8057 (ttp) REVERT: D 188 LEU cc_start: 0.4801 (OUTLIER) cc_final: 0.4159 (mm) REVERT: E 22 TYR cc_start: 0.7728 (m-80) cc_final: 0.7256 (m-80) REVERT: E 292 TYR cc_start: 0.8821 (m-10) cc_final: 0.8231 (m-10) REVERT: M 39 MET cc_start: 0.7936 (mmp) cc_final: 0.7509 (mmm) REVERT: M 213 MET cc_start: 0.8501 (ppp) cc_final: 0.7928 (ppp) REVERT: M 216 LYS cc_start: 0.5200 (mmtp) cc_final: 0.4683 (tttt) outliers start: 24 outliers final: 13 residues processed: 154 average time/residue: 0.1884 time to fit residues: 45.6771 Evaluate side-chains 145 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain K residue 713 TYR Chi-restraints excluded: chain M residue 31 GLN Chi-restraints excluded: chain M residue 97 ILE Chi-restraints excluded: chain M residue 102 LYS Chi-restraints excluded: chain M residue 204 LEU Chi-restraints excluded: chain M residue 218 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 1 optimal weight: 0.9980 chunk 279 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 19 optimal weight: 0.4980 chunk 59 optimal weight: 0.9990 chunk 268 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 84 optimal weight: 0.0980 chunk 136 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 525 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.072734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.056542 restraints weight = 103119.556| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 3.15 r_work: 0.3146 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25454 Z= 0.120 Angle : 0.572 18.310 35133 Z= 0.286 Chirality : 0.041 0.245 4014 Planarity : 0.004 0.032 4099 Dihedral : 18.995 179.915 4787 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.74 % Allowed : 11.55 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.48 % 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 aren not related in a simple way. whole: 0.78 (0.16), residues: 2839 helix: 1.76 (0.17), residues: 997 sheet: 0.43 (0.25), residues: 410 loop : -0.30 (0.17), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 88 TYR 0.013 0.001 TYR K 287 PHE 0.040 0.001 PHE K 295 TRP 0.013 0.001 TRP E 255 HIS 0.011 0.001 HIS K 292 Details of bonding type rmsd covalent geometry : bond 0.00262 (25450) covalent geometry : angle 0.56827 (35127) hydrogen bonds : bond 0.03171 ( 1061) hydrogen bonds : angle 4.89790 ( 2882) metal coordination : bond 0.00763 ( 4) metal coordination : angle 4.69655 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 THR cc_start: 0.9330 (OUTLIER) cc_final: 0.8961 (p) REVERT: C 103 TYR cc_start: 0.9199 (m-80) cc_final: 0.8816 (m-80) REVERT: C 145 MET cc_start: 0.8907 (mtt) cc_final: 0.8604 (mtt) REVERT: D 1 MET cc_start: 0.8136 (tmm) cc_final: 0.7857 (ttp) REVERT: D 80 LYS cc_start: 0.9154 (mttt) cc_final: 0.8863 (mtpt) REVERT: D 188 LEU cc_start: 0.4400 (OUTLIER) cc_final: 0.3718 (mm) REVERT: E 22 TYR cc_start: 0.7701 (m-80) cc_final: 0.7212 (m-80) REVERT: E 90 LYS cc_start: 0.9055 (ttmm) cc_final: 0.8761 (ttpt) REVERT: E 124 MET cc_start: 0.8337 (mmt) cc_final: 0.8099 (mmt) REVERT: E 292 TYR cc_start: 0.8744 (m-10) cc_final: 0.8138 (m-10) REVERT: G 115 MET cc_start: 0.8238 (mpp) cc_final: 0.7923 (mpp) REVERT: M 39 MET cc_start: 0.7942 (mmp) cc_final: 0.7557 (mmm) REVERT: M 207 ILE cc_start: 0.6785 (pt) cc_final: 0.6524 (pp) REVERT: M 213 MET cc_start: 0.8503 (ppp) cc_final: 0.7852 (ppp) REVERT: M 216 LYS cc_start: 0.5434 (mmtp) cc_final: 0.4961 (tttt) outliers start: 17 outliers final: 11 residues processed: 151 average time/residue: 0.1791 time to fit residues: 41.9693 Evaluate side-chains 146 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain K residue 713 TYR Chi-restraints excluded: chain M residue 97 ILE Chi-restraints excluded: chain M residue 102 LYS Chi-restraints excluded: chain M residue 204 LEU Chi-restraints excluded: chain M residue 218 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 126 optimal weight: 1.9990 chunk 288 optimal weight: 7.9990 chunk 59 optimal weight: 0.6980 chunk 200 optimal weight: 3.9990 chunk 164 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 275 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 157 optimal weight: 0.5980 chunk 284 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 286 HIS ** 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 = 0.3769 r_free = 0.3769 target = 0.072933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.056761 restraints weight = 103777.721| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 3.19 r_work: 0.3152 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25454 Z= 0.121 Angle : 0.563 12.947 35133 Z= 0.282 Chirality : 0.041 0.243 4014 Planarity : 0.004 0.039 4099 Dihedral : 18.965 179.780 4787 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.52 % Allowed : 11.94 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.48 % 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 aren not related in a simple way. whole: 0.83 (0.16), residues: 2839 helix: 1.79 (0.17), residues: 996 sheet: 0.42 (0.25), residues: 412 loop : -0.25 (0.17), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 402 TYR 0.012 0.001 TYR E 103 PHE 0.050 0.001 PHE K 295 TRP 0.012 0.001 TRP B 257 HIS 0.006 0.001 HIS K 292 Details of bonding type rmsd covalent geometry : bond 0.00266 (25450) covalent geometry : angle 0.56005 (35127) hydrogen bonds : bond 0.03116 ( 1061) hydrogen bonds : angle 4.87108 ( 2882) metal coordination : bond 0.00779 ( 4) metal coordination : angle 4.76643 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 138 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 THR cc_start: 0.9327 (OUTLIER) cc_final: 0.8952 (p) REVERT: C 103 TYR cc_start: 0.9211 (m-80) cc_final: 0.8838 (m-80) REVERT: C 145 MET cc_start: 0.8904 (mtt) cc_final: 0.8611 (mtt) REVERT: D 1 MET cc_start: 0.8218 (tmm) cc_final: 0.7955 (ttp) REVERT: D 188 LEU cc_start: 0.4440 (OUTLIER) cc_final: 0.3712 (mm) REVERT: E 22 TYR cc_start: 0.7677 (m-80) cc_final: 0.7203 (m-80) REVERT: E 90 LYS cc_start: 0.9002 (ttmm) cc_final: 0.8725 (ttpt) REVERT: E 292 TYR cc_start: 0.8762 (m-10) cc_final: 0.8128 (m-10) REVERT: F 151 ILE cc_start: 0.9324 (mm) cc_final: 0.9118 (mm) REVERT: G 115 MET cc_start: 0.8229 (mpp) cc_final: 0.7923 (mpp) REVERT: K 288 MET cc_start: 0.8254 (mmt) cc_final: 0.8034 (mmt) REVERT: M 39 MET cc_start: 0.7965 (mmp) cc_final: 0.7546 (mmm) REVERT: M 216 LYS cc_start: 0.5423 (mmtp) cc_final: 0.5115 (tttt) outliers start: 12 outliers final: 9 residues processed: 147 average time/residue: 0.1965 time to fit residues: 45.2894 Evaluate side-chains 145 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 134 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain K residue 713 TYR Chi-restraints excluded: chain M residue 97 ILE Chi-restraints excluded: chain M residue 102 LYS Chi-restraints excluded: chain M residue 204 LEU Chi-restraints excluded: chain M residue 218 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 48 optimal weight: 0.9980 chunk 221 optimal weight: 7.9990 chunk 125 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 231 optimal weight: 0.0670 chunk 163 optimal weight: 2.9990 chunk 230 optimal weight: 8.9990 chunk 274 optimal weight: 8.9990 chunk 92 optimal weight: 5.9990 overall best weight: 1.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 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 = 0.3737 r_free = 0.3737 target = 0.071550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.055299 restraints weight = 104099.133| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 3.18 r_work: 0.3108 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 25454 Z= 0.191 Angle : 0.602 14.733 35133 Z= 0.302 Chirality : 0.042 0.269 4014 Planarity : 0.004 0.033 4099 Dihedral : 19.031 179.228 4787 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.52 % Allowed : 12.12 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.48 % 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 aren not related in a simple way. whole: 0.75 (0.16), residues: 2839 helix: 1.71 (0.17), residues: 1002 sheet: 0.37 (0.25), residues: 418 loop : -0.30 (0.17), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 180 TYR 0.012 0.001 TYR E 103 PHE 0.056 0.001 PHE K 295 TRP 0.013 0.001 TRP K 702 HIS 0.010 0.001 HIS K 292 Details of bonding type rmsd covalent geometry : bond 0.00425 (25450) covalent geometry : angle 0.59868 (35127) hydrogen bonds : bond 0.03460 ( 1061) hydrogen bonds : angle 4.94796 ( 2882) metal coordination : bond 0.01121 ( 4) metal coordination : angle 4.62770 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 THR cc_start: 0.9405 (OUTLIER) cc_final: 0.8905 (p) REVERT: C 103 TYR cc_start: 0.9236 (m-80) cc_final: 0.8871 (m-80) REVERT: C 145 MET cc_start: 0.8932 (mtt) cc_final: 0.8636 (mtt) REVERT: D 188 LEU cc_start: 0.4800 (OUTLIER) cc_final: 0.4074 (mm) REVERT: E 22 TYR cc_start: 0.7886 (m-80) cc_final: 0.7355 (m-80) REVERT: E 90 LYS cc_start: 0.8997 (ttmm) cc_final: 0.8726 (ttpt) REVERT: E 292 TYR cc_start: 0.8773 (m-10) cc_final: 0.8146 (m-10) REVERT: G 115 MET cc_start: 0.8286 (mpp) cc_final: 0.8033 (mpp) REVERT: M 39 MET cc_start: 0.8018 (mmp) cc_final: 0.7775 (mmm) REVERT: M 216 LYS cc_start: 0.5210 (mmtp) cc_final: 0.4681 (tttt) outliers start: 12 outliers final: 10 residues processed: 141 average time/residue: 0.1873 time to fit residues: 41.7463 Evaluate side-chains 142 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain K residue 713 TYR Chi-restraints excluded: chain M residue 97 ILE Chi-restraints excluded: chain M residue 102 LYS Chi-restraints excluded: chain M residue 204 LEU Chi-restraints excluded: chain M residue 218 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 170 optimal weight: 0.8980 chunk 162 optimal weight: 5.9990 chunk 296 optimal weight: 8.9990 chunk 234 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 259 optimal weight: 9.9990 chunk 260 optimal weight: 6.9990 chunk 283 optimal weight: 5.9990 chunk 207 optimal weight: 7.9990 chunk 256 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 288 HIS C 141 GLN D 244 ASN ** K 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.069344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.053432 restraints weight = 104967.866| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 3.00 r_work: 0.3065 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.081 25454 Z= 0.353 Angle : 0.717 11.225 35133 Z= 0.365 Chirality : 0.046 0.305 4014 Planarity : 0.005 0.042 4099 Dihedral : 19.347 178.401 4787 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.82 % Allowed : 11.77 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.48 % 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 aren not related in a simple way. whole: 0.33 (0.16), residues: 2839 helix: 1.27 (0.17), residues: 1020 sheet: 0.19 (0.25), residues: 400 loop : -0.51 (0.17), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 180 TYR 0.014 0.002 TYR E 22 PHE 0.066 0.002 PHE K 295 TRP 0.018 0.002 TRP K 702 HIS 0.014 0.002 HIS M 143 Details of bonding type rmsd covalent geometry : bond 0.00783 (25450) covalent geometry : angle 0.71446 (35127) hydrogen bonds : bond 0.04415 ( 1061) hydrogen bonds : angle 5.36900 ( 2882) metal coordination : bond 0.01913 ( 4) metal coordination : angle 4.61260 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5889.12 seconds wall clock time: 101 minutes 48.81 seconds (6108.81 seconds total)