Starting phenix.real_space_refine on Sun Jan 26 07:22:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rfj_19125/01_2025/8rfj_19125.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rfj_19125/01_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8rfj_19125/01_2025/8rfj_19125.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rfj_19125/01_2025/8rfj_19125.map" model { file = "/net/cci-nas-00/data/ceres_data/8rfj_19125/01_2025/8rfj_19125.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rfj_19125/01_2025/8rfj_19125.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.027 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 14.33, per 1000 atoms: 0.58 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: 6.36 Conformation dependent library (CDL) restraints added in 3.0 seconds 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: 10.30 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: 12.77 Time building geometry restraints manager: 7.03 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: 0.040 Extract box with map and model: 0.950 Check model and map are aligned: 0.250 Set scattering table: 0.300 Process input model: 68.310 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.120 ------------------------------------------------------------------------------- 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 25450 Z= 0.192 Angle : 0.551 9.837 35127 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 : 10.24 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.16), 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 TRP 0.018 0.001 TRP F 127 HIS 0.009 0.001 HIS F 22 PHE 0.019 0.001 PHE M 212 TYR 0.027 0.002 TYR F 206 ARG 0.007 0.000 ARG F 60 *********************** 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 : 2.475 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: 0.4271 time to fit residues: 111.5300 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 : 2.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 250 optimal weight: 20.0000 chunk 225 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 151 optimal weight: 0.6980 chunk 120 optimal weight: 3.9990 chunk 232 optimal weight: 20.0000 chunk 90 optimal weight: 0.7980 chunk 141 optimal weight: 4.9990 chunk 173 optimal weight: 2.9990 chunk 269 optimal weight: 1.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 141 GLN ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 HIS F 147 GLN 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.073246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.056981 restraints weight = 103156.239| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 3.17 r_work: 0.3141 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 25450 Z= 0.318 Angle : 0.625 12.016 35127 Z= 0.324 Chirality : 0.044 0.286 4014 Planarity : 0.005 0.040 4099 Dihedral : 18.850 178.961 4787 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.52 % Allowed : 5.19 % Favored : 94.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.16), residues: 2839 helix: 1.58 (0.17), residues: 996 sheet: 0.69 (0.25), residues: 406 loop : -0.40 (0.16), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 255 HIS 0.005 0.001 HIS K 292 PHE 0.018 0.001 PHE E 340 TYR 0.022 0.002 TYR F 206 ARG 0.004 0.001 ARG D 138 *********************** 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 160 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 148 time to evaluate : 2.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 162 SER cc_start: 0.9182 (p) cc_final: 0.8852 (t) REVERT: E 292 TYR cc_start: 0.8713 (m-10) cc_final: 0.8224 (m-10) REVERT: F 206 TYR cc_start: 0.8063 (m-10) cc_final: 0.7804 (m-80) REVERT: K 443 MET cc_start: 0.8126 (pmm) cc_final: 0.7441 (mpp) REVERT: M 39 MET cc_start: 0.7896 (mmp) cc_final: 0.7665 (mmp) REVERT: M 207 ILE cc_start: 0.6358 (pt) cc_final: 0.6147 (pt) outliers start: 12 outliers final: 6 residues processed: 150 average time/residue: 0.3995 time to fit residues: 93.5396 Evaluate side-chains 146 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 140 time to evaluate : 2.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain K residue 713 TYR 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 21 optimal weight: 6.9990 chunk 203 optimal weight: 4.9990 chunk 196 optimal weight: 8.9990 chunk 207 optimal weight: 7.9990 chunk 233 optimal weight: 20.0000 chunk 174 optimal weight: 3.9990 chunk 208 optimal weight: 20.0000 chunk 155 optimal weight: 8.9990 chunk 229 optimal weight: 9.9990 chunk 202 optimal weight: 7.9990 chunk 182 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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** ** D 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 187 GLN E 33 GLN ** E 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 GLN ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 32 HIS ** K 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 56 GLN ** M 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 130 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 = 0.3654 r_free = 0.3654 target = 0.068301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.052179 restraints weight = 105474.216| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 3.04 r_work: 0.3009 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.122 25450 Z= 0.811 Angle : 0.878 22.683 35127 Z= 0.451 Chirality : 0.054 0.327 4014 Planarity : 0.007 0.102 4099 Dihedral : 19.337 176.893 4787 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.34 % Allowed : 8.83 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.15), residues: 2839 helix: 0.68 (0.16), residues: 1012 sheet: 0.16 (0.26), residues: 391 loop : -0.83 (0.16), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP K 469 HIS 0.015 0.003 HIS M 143 PHE 0.031 0.003 PHE G 52 TYR 0.026 0.003 TYR F 206 ARG 0.013 0.001 ARG A 180 *********************** 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 173 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 142 time to evaluate : 2.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 103 TYR cc_start: 0.9275 (m-80) cc_final: 0.8815 (m-80) REVERT: C 139 MET cc_start: 0.8833 (mmt) cc_final: 0.8616 (tpp) REVERT: D 188 LEU cc_start: 0.5490 (OUTLIER) cc_final: 0.5029 (mm) REVERT: E 22 TYR cc_start: 0.8018 (m-80) cc_final: 0.7529 (m-80) REVERT: E 124 MET cc_start: 0.8547 (mmt) cc_final: 0.8145 (mmt) REVERT: E 139 MET cc_start: 0.7531 (mmt) cc_final: 0.6852 (mmm) REVERT: E 292 TYR cc_start: 0.9047 (m-10) cc_final: 0.8557 (m-10) REVERT: F 86 SER cc_start: 0.9074 (OUTLIER) cc_final: 0.8870 (p) REVERT: M 39 MET cc_start: 0.8075 (mmp) cc_final: 0.7727 (mmp) REVERT: M 168 GLU cc_start: 0.7476 (mp0) cc_final: 0.7240 (mp0) REVERT: M 213 MET cc_start: 0.7787 (ppp) cc_final: 0.7134 (tmm) REVERT: M 218 TYR cc_start: 0.6372 (m-80) cc_final: 0.5759 (t80) outliers start: 31 outliers final: 15 residues processed: 163 average time/residue: 0.4402 time to fit residues: 110.8215 Evaluate side-chains 151 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 2.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain C residue 169 ILE 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 86 SER Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain G residue 225 GLN 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 235 optimal weight: 20.0000 chunk 218 optimal weight: 9.9990 chunk 132 optimal weight: 4.9990 chunk 223 optimal weight: 8.9990 chunk 166 optimal weight: 0.8980 chunk 238 optimal weight: 9.9990 chunk 80 optimal weight: 0.9980 chunk 282 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 133 optimal weight: 6.9990 chunk 0 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 339 GLN E 106 ASN E 154 GLN ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 56 GLN ** M 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.071820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.055653 restraints weight = 104359.674| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 3.08 r_work: 0.3113 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25450 Z= 0.195 Angle : 0.595 9.398 35127 Z= 0.305 Chirality : 0.042 0.253 4014 Planarity : 0.004 0.040 4099 Dihedral : 19.193 179.778 4787 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.21 % Allowed : 9.56 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.16), residues: 2839 helix: 1.30 (0.17), residues: 1013 sheet: 0.30 (0.26), residues: 398 loop : -0.58 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 255 HIS 0.007 0.001 HIS M 143 PHE 0.011 0.001 PHE E 133 TYR 0.015 0.001 TYR E 103 ARG 0.008 0.000 ARG E 8 *********************** 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 168 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 140 time to evaluate : 2.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 THR cc_start: 0.9378 (OUTLIER) cc_final: 0.8928 (p) REVERT: C 103 TYR cc_start: 0.9146 (m-80) cc_final: 0.8772 (m-80) REVERT: D 84 GLU cc_start: 0.8438 (tp30) cc_final: 0.7699 (tp30) REVERT: E 22 TYR cc_start: 0.7688 (m-80) cc_final: 0.7206 (m-80) REVERT: E 292 TYR cc_start: 0.8811 (m-10) cc_final: 0.8240 (m-10) REVERT: K 443 MET cc_start: 0.8179 (pmm) cc_final: 0.7244 (mpp) REVERT: M 1 MET cc_start: 0.7654 (mmt) cc_final: 0.7445 (mmp) REVERT: M 39 MET cc_start: 0.7911 (mmp) cc_final: 0.7592 (mmm) REVERT: M 168 GLU cc_start: 0.7282 (mp0) cc_final: 0.7077 (mp0) REVERT: M 213 MET cc_start: 0.8038 (ppp) cc_final: 0.7217 (tmm) REVERT: M 216 LYS cc_start: 0.4985 (mmtp) cc_final: 0.4366 (tttt) outliers start: 28 outliers final: 11 residues processed: 160 average time/residue: 0.3877 time to fit residues: 99.2463 Evaluate side-chains 149 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 137 time to evaluate : 2.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain K residue 713 TYR Chi-restraints excluded: chain M residue 4 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 266 optimal weight: 8.9990 chunk 256 optimal weight: 8.9990 chunk 44 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 137 optimal weight: 0.6980 chunk 207 optimal weight: 8.9990 chunk 125 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 69 optimal weight: 5.9990 chunk 151 optimal weight: 0.7980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 260 ASN ** K 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 56 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.071719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.055555 restraints weight = 104288.480| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 3.08 r_work: 0.3112 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25450 Z= 0.218 Angle : 0.582 11.250 35127 Z= 0.296 Chirality : 0.042 0.264 4014 Planarity : 0.004 0.037 4099 Dihedral : 19.128 179.649 4787 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.08 % Allowed : 10.73 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.16), residues: 2839 helix: 1.49 (0.17), residues: 1009 sheet: 0.34 (0.26), residues: 398 loop : -0.51 (0.16), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 255 HIS 0.010 0.001 HIS K 292 PHE 0.014 0.001 PHE M 178 TYR 0.011 0.001 TYR K 287 ARG 0.003 0.000 ARG E 8 *********************** 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 167 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 2.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 THR cc_start: 0.9374 (OUTLIER) cc_final: 0.8981 (p) REVERT: C 103 TYR cc_start: 0.9169 (m-80) cc_final: 0.8689 (m-80) REVERT: E 22 TYR cc_start: 0.7721 (m-80) cc_final: 0.7292 (m-80) REVERT: E 292 TYR cc_start: 0.8810 (m-10) cc_final: 0.8238 (m-10) REVERT: M 39 MET cc_start: 0.7958 (mmp) cc_final: 0.7572 (mmm) REVERT: M 92 MET cc_start: 0.8824 (mmm) cc_final: 0.8612 (mmm) REVERT: M 207 ILE cc_start: 0.7096 (pt) cc_final: 0.6804 (pt) REVERT: M 216 LYS cc_start: 0.4925 (mmtp) cc_final: 0.4437 (tttt) outliers start: 25 outliers final: 10 residues processed: 160 average time/residue: 0.4098 time to fit residues: 104.5896 Evaluate side-chains 144 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 133 time to evaluate : 3.367 ------------------------------------------------------------------------------- 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 193 ASP 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 54 THR 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 140 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 236 optimal weight: 3.9990 chunk 241 optimal weight: 9.9990 chunk 228 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 172 optimal weight: 2.9990 chunk 285 optimal weight: 9.9990 chunk 294 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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** D 187 GLN D 244 ASN ** E 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 56 GLN ** M 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 177 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.069520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.053365 restraints weight = 104503.766| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 3.05 r_work: 0.3050 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 25450 Z= 0.466 Angle : 0.686 16.244 35127 Z= 0.348 Chirality : 0.045 0.297 4014 Planarity : 0.005 0.046 4099 Dihedral : 19.267 178.730 4787 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.43 % Allowed : 11.60 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.16), residues: 2839 helix: 1.29 (0.17), residues: 1007 sheet: 0.20 (0.25), residues: 405 loop : -0.58 (0.17), residues: 1427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 702 HIS 0.011 0.002 HIS G 32 PHE 0.019 0.002 PHE G 52 TYR 0.026 0.002 TYR M 218 ARG 0.007 0.001 ARG A 180 *********************** 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 170 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 137 time to evaluate : 2.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 THR cc_start: 0.9433 (OUTLIER) cc_final: 0.8958 (p) REVERT: C 103 TYR cc_start: 0.9265 (m-80) cc_final: 0.8855 (m-80) REVERT: C 145 MET cc_start: 0.8401 (mtt) cc_final: 0.7983 (mtt) REVERT: D 188 LEU cc_start: 0.4926 (OUTLIER) cc_final: 0.4560 (mm) REVERT: E 22 TYR cc_start: 0.7931 (m-80) cc_final: 0.7473 (m-80) REVERT: E 124 MET cc_start: 0.8561 (mmt) cc_final: 0.8236 (mmt) REVERT: E 292 TYR cc_start: 0.8951 (m-10) cc_final: 0.8400 (m-10) REVERT: M 39 MET cc_start: 0.7994 (mmp) cc_final: 0.7601 (mmm) REVERT: M 92 MET cc_start: 0.9014 (mmm) cc_final: 0.8771 (mmm) outliers start: 33 outliers final: 23 residues processed: 160 average time/residue: 0.3900 time to fit residues: 97.8551 Evaluate side-chains 159 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 2.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain D residue 82 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 46 MET Chi-restraints excluded: chain E residue 254 LYS Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain F residue 129 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 56 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 296 optimal weight: 10.0000 chunk 200 optimal weight: 1.9990 chunk 264 optimal weight: 7.9990 chunk 45 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 279 optimal weight: 0.6980 chunk 205 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 286 optimal weight: 8.9990 chunk 237 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 188 GLN ** K 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 56 GLN ** M 220 GLN ** 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 = 0.3722 r_free = 0.3722 target = 0.070999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.054882 restraints weight = 104191.392| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 3.12 r_work: 0.3093 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25450 Z= 0.224 Angle : 0.599 12.012 35127 Z= 0.304 Chirality : 0.042 0.265 4014 Planarity : 0.004 0.039 4099 Dihedral : 19.223 179.581 4787 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.21 % Allowed : 11.81 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.16), residues: 2839 helix: 1.46 (0.17), residues: 1008 sheet: 0.19 (0.25), residues: 411 loop : -0.50 (0.17), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 255 HIS 0.007 0.001 HIS M 143 PHE 0.010 0.001 PHE E 133 TYR 0.011 0.001 TYR K 339 ARG 0.005 0.000 ARG E 8 *********************** 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 166 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 138 time to evaluate : 2.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 THR cc_start: 0.9365 (OUTLIER) cc_final: 0.8925 (p) REVERT: C 103 TYR cc_start: 0.9175 (m-80) cc_final: 0.8769 (m-80) REVERT: C 145 MET cc_start: 0.8541 (mtt) cc_final: 0.8274 (mtt) REVERT: D 188 LEU cc_start: 0.4638 (OUTLIER) cc_final: 0.3973 (mm) REVERT: E 22 TYR cc_start: 0.7996 (m-80) cc_final: 0.7449 (m-80) REVERT: E 254 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8461 (mptt) REVERT: E 292 TYR cc_start: 0.8895 (m-10) cc_final: 0.8302 (m-10) REVERT: K 443 MET cc_start: 0.8120 (pmm) cc_final: 0.6944 (mpp) REVERT: M 39 MET cc_start: 0.7929 (mmp) cc_final: 0.7704 (mmm) REVERT: M 92 MET cc_start: 0.8921 (mmm) cc_final: 0.8686 (mmm) REVERT: M 216 LYS cc_start: 0.5242 (mmtp) cc_final: 0.4707 (tttt) outliers start: 28 outliers final: 13 residues processed: 157 average time/residue: 0.3867 time to fit residues: 96.9932 Evaluate side-chains 150 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 2.697 ------------------------------------------------------------------------------- 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 C residue 272 ILE Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain E residue 254 LYS 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 128 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 163 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 179 optimal weight: 2.9990 chunk 146 optimal weight: 0.6980 chunk 219 optimal weight: 20.0000 chunk 107 optimal weight: 5.9990 chunk 135 optimal weight: 5.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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 154 GLN ** 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** ** M 85 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 = 0.3719 r_free = 0.3719 target = 0.070357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.054470 restraints weight = 104586.049| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 3.01 r_work: 0.3097 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 25450 Z= 0.339 Angle : 0.635 14.022 35127 Z= 0.320 Chirality : 0.043 0.287 4014 Planarity : 0.004 0.040 4099 Dihedral : 19.234 179.528 4787 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.25 % Allowed : 12.16 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.16), residues: 2839 helix: 1.42 (0.17), residues: 1009 sheet: 0.10 (0.25), residues: 410 loop : -0.51 (0.17), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 207 HIS 0.008 0.001 HIS M 143 PHE 0.012 0.001 PHE G 112 TYR 0.025 0.001 TYR M 218 ARG 0.005 0.000 ARG E 8 *********************** 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 164 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 135 time to evaluate : 2.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 THR cc_start: 0.9399 (OUTLIER) cc_final: 0.8917 (p) REVERT: C 103 TYR cc_start: 0.9222 (m-80) cc_final: 0.8815 (m-80) REVERT: C 145 MET cc_start: 0.8612 (mtt) cc_final: 0.8249 (mtt) REVERT: D 188 LEU cc_start: 0.4902 (OUTLIER) cc_final: 0.4341 (mm) REVERT: E 22 TYR cc_start: 0.7986 (m-80) cc_final: 0.7480 (m-80) REVERT: E 292 TYR cc_start: 0.8896 (m-10) cc_final: 0.8319 (m-10) REVERT: G 35 ARG cc_start: 0.9383 (OUTLIER) cc_final: 0.7476 (ttm-80) REVERT: K 443 MET cc_start: 0.8145 (pmm) cc_final: 0.7047 (mpp) REVERT: M 39 MET cc_start: 0.8025 (mmp) cc_final: 0.7811 (mmm) REVERT: M 92 MET cc_start: 0.8954 (mmm) cc_final: 0.8723 (mmm) outliers start: 29 outliers final: 19 residues processed: 157 average time/residue: 0.4050 time to fit residues: 99.0373 Evaluate side-chains 155 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 2.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 THR 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 169 ILE Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain E residue 46 MET Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain G residue 35 ARG 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 90 optimal weight: 2.9990 chunk 265 optimal weight: 8.9990 chunk 122 optimal weight: 0.0770 chunk 66 optimal weight: 2.9990 chunk 264 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 220 optimal weight: 10.0000 chunk 289 optimal weight: 0.0980 chunk 131 optimal weight: 10.0000 chunk 42 optimal weight: 0.8980 overall best weight: 1.4142 ------------------------------------------------------------------------------- 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 154 GLN ** F 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 188 GLN ** K 286 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 = 0.3739 r_free = 0.3739 target = 0.071242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.055288 restraints weight = 104521.338| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 3.07 r_work: 0.3123 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 25450 Z= 0.233 Angle : 0.599 13.055 35127 Z= 0.301 Chirality : 0.042 0.262 4014 Planarity : 0.004 0.036 4099 Dihedral : 19.194 179.975 4787 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.00 % Allowed : 12.81 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.16), residues: 2839 helix: 1.56 (0.17), residues: 1009 sheet: 0.25 (0.26), residues: 395 loop : -0.46 (0.17), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 469 HIS 0.007 0.001 HIS M 143 PHE 0.010 0.001 PHE D 133 TYR 0.019 0.001 TYR M 218 ARG 0.005 0.000 ARG D 88 *********************** 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 162 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 2.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 174 THR cc_start: 0.9243 (OUTLIER) cc_final: 0.8942 (t) REVERT: C 41 THR cc_start: 0.9378 (OUTLIER) cc_final: 0.8926 (p) REVERT: C 103 TYR cc_start: 0.9209 (m-80) cc_final: 0.8728 (m-80) REVERT: C 145 MET cc_start: 0.8587 (mtt) cc_final: 0.8238 (mtt) REVERT: D 2 GLN cc_start: 0.8399 (mt0) cc_final: 0.8166 (mt0) REVERT: D 188 LEU cc_start: 0.4680 (OUTLIER) cc_final: 0.4005 (mm) REVERT: E 22 TYR cc_start: 0.7860 (m-80) cc_final: 0.7353 (m-80) REVERT: E 124 MET cc_start: 0.8454 (mmt) cc_final: 0.8242 (mmt) REVERT: E 292 TYR cc_start: 0.8832 (m-10) cc_final: 0.8199 (m-10) REVERT: K 443 MET cc_start: 0.8106 (pmm) cc_final: 0.7012 (mpp) REVERT: M 39 MET cc_start: 0.7967 (mmp) cc_final: 0.7739 (mmm) REVERT: M 92 MET cc_start: 0.8940 (mmm) cc_final: 0.8690 (mmm) REVERT: M 213 MET cc_start: 0.8776 (ppp) cc_final: 0.7889 (ppp) outliers start: 23 outliers final: 17 residues processed: 155 average time/residue: 0.3856 time to fit residues: 95.3970 Evaluate side-chains 156 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 2.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain B residue 174 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 C residue 272 ILE Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain E residue 46 MET Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 157 VAL 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 45 THR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 35 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 194 optimal weight: 4.9990 chunk 275 optimal weight: 9.9990 chunk 58 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 153 optimal weight: 8.9990 chunk 182 optimal weight: 4.9990 chunk 279 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 258 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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** ** F 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 188 GLN ** K 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.070710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.054678 restraints weight = 104263.851| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 3.07 r_work: 0.3106 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 25450 Z= 0.292 Angle : 0.616 14.718 35127 Z= 0.310 Chirality : 0.042 0.275 4014 Planarity : 0.004 0.037 4099 Dihedral : 19.206 179.534 4787 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.17 % Allowed : 12.94 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.16), residues: 2839 helix: 1.53 (0.17), residues: 1009 sheet: 0.17 (0.25), residues: 400 loop : -0.47 (0.17), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 257 HIS 0.008 0.001 HIS M 143 PHE 0.011 0.001 PHE G 112 TYR 0.020 0.001 TYR M 218 ARG 0.005 0.000 ARG E 8 ********************** 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 160 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 133 time to evaluate : 2.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 174 THR cc_start: 0.9245 (OUTLIER) cc_final: 0.8933 (t) REVERT: C 41 THR cc_start: 0.9382 (OUTLIER) cc_final: 0.8899 (p) REVERT: C 103 TYR cc_start: 0.9216 (m-80) cc_final: 0.8745 (m-80) REVERT: D 2 GLN cc_start: 0.8437 (mt0) cc_final: 0.8204 (mt0) REVERT: D 188 LEU cc_start: 0.5080 (OUTLIER) cc_final: 0.4414 (mm) REVERT: E 22 TYR cc_start: 0.7910 (m-80) cc_final: 0.7408 (m-80) REVERT: E 124 MET cc_start: 0.8493 (mmt) cc_final: 0.8291 (mmt) REVERT: E 292 TYR cc_start: 0.8836 (m-10) cc_final: 0.8197 (m-10) REVERT: K 443 MET cc_start: 0.8123 (pmm) cc_final: 0.7036 (mpp) REVERT: M 39 MET cc_start: 0.7966 (mmp) cc_final: 0.7751 (mmm) REVERT: M 92 MET cc_start: 0.8962 (mmm) cc_final: 0.8721 (mmm) REVERT: M 213 MET cc_start: 0.8949 (ppp) cc_final: 0.8102 (ppp) outliers start: 27 outliers final: 21 residues processed: 153 average time/residue: 0.3846 time to fit residues: 94.7075 Evaluate side-chains 155 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 2.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain B residue 174 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 244 ASN Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain E residue 46 MET Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 188 GLN 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 45 THR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 88 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 chunk 289 optimal weight: 0.8980 chunk 269 optimal weight: 10.0000 chunk 205 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 209 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 231 optimal weight: 0.0980 chunk 56 optimal weight: 4.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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** D 244 ASN ** F 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.070448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.054412 restraints weight = 104442.626| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 3.06 r_work: 0.3098 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 25450 Z= 0.318 Angle : 0.625 14.975 35127 Z= 0.315 Chirality : 0.043 0.276 4014 Planarity : 0.004 0.038 4099 Dihedral : 19.242 179.409 4787 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.43 % Allowed : 12.89 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.16), residues: 2839 helix: 1.49 (0.17), residues: 1011 sheet: 0.09 (0.25), residues: 410 loop : -0.46 (0.17), residues: 1418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 207 HIS 0.009 0.001 HIS M 143 PHE 0.011 0.001 PHE G 112 TYR 0.020 0.001 TYR M 218 ARG 0.005 0.000 ARG E 8 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11066.89 seconds wall clock time: 200 minutes 2.81 seconds (12002.81 seconds total)