Starting phenix.real_space_refine on Fri Sep 19 08:25:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e8z_47737/09_2025/9e8z_47737.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e8z_47737/09_2025/9e8z_47737.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9e8z_47737/09_2025/9e8z_47737.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e8z_47737/09_2025/9e8z_47737.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9e8z_47737/09_2025/9e8z_47737.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e8z_47737/09_2025/9e8z_47737.map" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.026 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 2 6.06 5 P 121 5.49 5 S 56 5.16 5 C 15207 2.51 5 N 4250 2.21 5 O 4995 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24631 Number of models: 1 Model: "" Number of chains: 13 Chain: "C" Number of atoms: 4205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4205 Classifications: {'peptide': 534} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 18, 'TRANS': 515} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 38 Chain: "E" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1552 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 7, 'TRANS': 202} Chain breaks: 2 Unresolved non-hydrogen bonds: 181 Unresolved non-hydrogen angles: 226 Unresolved non-hydrogen dihedrals: 154 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 4, 'GLU:plan': 8, 'ARG:plan': 4, 'HIS:plan': 3, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 125 Chain: "H" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2420 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 9, 'TRANS': 296} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'TYR:plan': 1, 'PHE:plan': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "I" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 1616 Classifications: {'DNA': 79} Link IDs: {'rna3p': 78} Chain: "J" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 802 Classifications: {'RNA': 38} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 8, 'rna3p_pur': 13, 'rna3p_pyr': 13} Link IDs: {'rna2p': 11, 'rna3p': 26} Chain: "A" Number of atoms: 3969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3969 Classifications: {'peptide': 527} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 18, 'TRANS': 508} Chain breaks: 2 Unresolved non-hydrogen bonds: 266 Unresolved non-hydrogen angles: 320 Unresolved non-hydrogen dihedrals: 225 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 17, 'PHE:plan': 2, 'TYR:plan': 3, 'ASP:plan': 8, 'ARG:plan': 4, 'ASN:plan1': 3, 'GLN%COO:plan1': 1} Unresolved non-hydrogen planarities: 158 Chain: "B" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 2009 Classifications: {'peptide': 250} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 7, 'TRANS': 242} Chain breaks: 1 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "D" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3943 Classifications: {'peptide': 512} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 18, 'TRANS': 493} Chain breaks: 2 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 6, 'ASP:plan': 3, 'GLU:plan': 7, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 95 Chain: "F" Number of atoms: 4059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4059 Classifications: {'peptide': 534} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 18, 'TRANS': 515} Chain breaks: 1 Unresolved non-hydrogen bonds: 232 Unresolved non-hydrogen angles: 286 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 6, 'TYR:plan': 2, 'PHE:plan': 3, 'ARG:plan': 5, 'ASN:plan1': 6, 'ASP:plan': 5, 'HIS:plan': 1, 'GLN%COO:plan1': 1} Unresolved non-hydrogen planarities: 135 Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" 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 4521 SG CYS E 54 77.592 30.991 125.744 1.00151.03 S ATOM 4544 SG CYS E 57 77.074 31.903 122.004 1.00147.24 S ATOM 4835 SG CYS E 98 79.129 33.963 124.104 1.00153.60 S ATOM 4877 SG CYS E 116 75.186 33.772 124.622 1.00154.18 S ATOM 14981 SG CYS B 54 64.880 159.564 77.517 1.00 86.14 S ATOM 15004 SG CYS B 57 65.162 155.632 75.409 1.00 81.52 S ATOM 15290 SG CYS B 98 62.547 158.399 76.857 1.00 83.79 S Time building chain proxies: 6.89, per 1000 atoms: 0.28 Number of scatterers: 24631 At special positions: 0 Unit cell: (129.71, 191.84, 166.77, 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 2 29.99 S 56 16.00 P 121 15.00 O 4995 8.00 N 4250 7.00 C 15207 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.26 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 1.2 microseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 98 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 54 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 57 " pdb=" ZN E 501 " pdb="ZN ZN E 501 " - pdb=" SG CYS E 57 " pdb="ZN ZN E 501 " - pdb=" SG CYS E 98 " pdb="ZN ZN E 501 " - pdb=" SG CYS E 54 " pdb="ZN ZN E 501 " - pdb=" SG CYS E 116 " Number of angles added : 6 5686 Ramachandran restraints generated. 2843 Oldfield, 0 Emsley, 2843 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5468 Finding SS restraints... Secondary structure from input PDB file: 127 helices and 25 sheets defined 51.1% alpha, 10.2% beta 23 base pairs and 66 stacking pairs defined. Time for finding SS restraints: 3.03 Creating SS restraints... Processing helix chain 'C' and resid 6 through 19 Processing helix chain 'C' and resid 21 through 29 removed outlier: 3.526A pdb=" N LEU C 27 " --> pdb=" O SER C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 55 removed outlier: 3.719A pdb=" N PHE C 48 " --> pdb=" O MET C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 106 removed outlier: 3.536A pdb=" N LEU C 102 " --> pdb=" O LYS C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 118 Processing helix chain 'C' and resid 127 through 131 Processing helix chain 'C' and resid 170 through 187 removed outlier: 3.560A pdb=" N ASN C 174 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU C 175 " --> pdb=" O SER C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 205 removed outlier: 3.809A pdb=" N ASN C 204 " --> pdb=" O GLU C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 213 removed outlier: 3.937A pdb=" N ASN C 213 " --> pdb=" O ARG C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 222 removed outlier: 3.833A pdb=" N GLN C 221 " --> pdb=" O LYS C 218 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ILE C 222 " --> pdb=" O GLU C 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 218 through 222' Processing helix chain 'C' and resid 224 through 228 removed outlier: 3.698A pdb=" N ALA C 228 " --> pdb=" O LYS C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 256 Processing helix chain 'C' and resid 258 through 276 Processing helix chain 'C' and resid 276 through 286 removed outlier: 3.608A pdb=" N GLU C 285 " --> pdb=" O ALA C 281 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ASN C 286 " --> pdb=" O LEU C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 315 removed outlier: 3.559A pdb=" N TYR C 313 " --> pdb=" O LYS C 309 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER C 315 " --> pdb=" O ASN C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 332 removed outlier: 4.338A pdb=" N HIS C 322 " --> pdb=" O SER C 318 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL C 324 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE C 331 " --> pdb=" O ALA C 327 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU C 332 " --> pdb=" O MET C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 361 No H-bonds generated for 'chain 'C' and resid 359 through 361' Processing helix chain 'C' and resid 362 through 383 removed outlier: 3.911A pdb=" N THR C 367 " --> pdb=" O GLN C 363 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ILE C 368 " --> pdb=" O GLY C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 421 Processing helix chain 'C' and resid 432 through 437 removed outlier: 4.012A pdb=" N CYS C 436 " --> pdb=" O SER C 432 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N HIS C 437 " --> pdb=" O PRO C 433 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 432 through 437' Processing helix chain 'C' and resid 463 through 473 Processing helix chain 'C' and resid 481 through 495 removed outlier: 3.867A pdb=" N LEU C 493 " --> pdb=" O GLU C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 514 removed outlier: 4.028A pdb=" N ARG C 505 " --> pdb=" O SER C 501 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LYS C 506 " --> pdb=" O GLU C 502 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N HIS C 514 " --> pdb=" O THR C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 535 Processing helix chain 'E' and resid 12 through 22 Processing helix chain 'E' and resid 27 through 32 Processing helix chain 'E' and resid 36 through 50 Processing helix chain 'E' and resid 90 through 92 No H-bonds generated for 'chain 'E' and resid 90 through 92' Processing helix chain 'E' and resid 116 through 127 removed outlier: 3.659A pdb=" N LYS E 120 " --> pdb=" O CYS E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 192 Processing helix chain 'E' and resid 198 through 205 Processing helix chain 'E' and resid 207 through 214 Processing helix chain 'E' and resid 217 through 228 removed outlier: 4.296A pdb=" N LEU E 225 " --> pdb=" O LEU E 221 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU E 226 " --> pdb=" O HIS E 222 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLN E 227 " --> pdb=" O ASN E 223 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 10 removed outlier: 4.543A pdb=" N GLN H 10 " --> pdb=" O GLU H 6 " (cutoff:3.500A) Processing helix chain 'H' and resid 23 through 26 Processing helix chain 'H' and resid 49 through 62 removed outlier: 3.752A pdb=" N ILE H 53 " --> pdb=" O ARG H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 65 No H-bonds generated for 'chain 'H' and resid 63 through 65' Processing helix chain 'H' and resid 80 through 87 removed outlier: 3.692A pdb=" N ALA H 84 " --> pdb=" O ILE H 80 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N HIS H 87 " --> pdb=" O ASN H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 118 removed outlier: 3.567A pdb=" N PHE H 111 " --> pdb=" O PRO H 107 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LYS H 112 " --> pdb=" O GLU H 108 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA H 113 " --> pdb=" O LEU H 109 " (cutoff:3.500A) Processing helix chain 'H' and resid 122 through 133 Processing helix chain 'H' and resid 153 through 161 removed outlier: 3.681A pdb=" N ILE H 157 " --> pdb=" O SER H 153 " (cutoff:3.500A) Processing helix chain 'H' and resid 163 through 176 removed outlier: 3.582A pdb=" N GLU H 175 " --> pdb=" O SER H 171 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN H 176 " --> pdb=" O PHE H 172 " (cutoff:3.500A) Processing helix chain 'H' and resid 196 through 209 removed outlier: 3.527A pdb=" N ILE H 209 " --> pdb=" O LYS H 205 " (cutoff:3.500A) Processing helix chain 'H' and resid 248 through 265 removed outlier: 3.655A pdb=" N LYS H 263 " --> pdb=" O VAL H 259 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU H 264 " --> pdb=" O PHE H 260 " (cutoff:3.500A) Processing helix chain 'H' and resid 268 through 282 removed outlier: 3.600A pdb=" N ILE H 272 " --> pdb=" O SER H 268 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASN H 273 " --> pdb=" O ASN H 269 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N HIS H 274 " --> pdb=" O VAL H 270 " (cutoff:3.500A) Processing helix chain 'H' and resid 288 through 297 Processing helix chain 'H' and resid 298 through 303 Processing helix chain 'A' and resid 6 through 18 removed outlier: 3.569A pdb=" N SER A 18 " --> pdb=" O LYS A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 33 Processing helix chain 'A' and resid 34 through 38 removed outlier: 3.522A pdb=" N GLY A 37 " --> pdb=" O LYS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 54 removed outlier: 3.538A pdb=" N LYS A 54 " --> pdb=" O GLU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 117 removed outlier: 3.917A pdb=" N ILE A 101 " --> pdb=" O GLY A 97 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N HIS A 111 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU A 112 " --> pdb=" O GLY A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 185 removed outlier: 3.508A pdb=" N LEU A 176 " --> pdb=" O GLY A 172 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 205 removed outlier: 3.992A pdb=" N ARG A 202 " --> pdb=" O THR A 199 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN A 204 " --> pdb=" O GLU A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 removed outlier: 3.610A pdb=" N ILE A 211 " --> pdb=" O SER A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 252 removed outlier: 3.747A pdb=" N PHE A 242 " --> pdb=" O ASP A 238 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE A 252 " --> pdb=" O GLU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 275 Processing helix chain 'A' and resid 276 through 286 Processing helix chain 'A' and resid 289 through 313 removed outlier: 3.606A pdb=" N LEU A 295 " --> pdb=" O THR A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 332 removed outlier: 4.045A pdb=" N VAL A 324 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA A 327 " --> pdb=" O THR A 323 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N MET A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER A 330 " --> pdb=" O ASP A 326 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N PHE A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU A 332 " --> pdb=" O MET A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 361 No H-bonds generated for 'chain 'A' and resid 359 through 361' Processing helix chain 'A' and resid 362 through 383 Processing helix chain 'A' and resid 406 through 411 removed outlier: 3.518A pdb=" N GLN A 411 " --> pdb=" O PRO A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 421 removed outlier: 3.505A pdb=" N LYS A 419 " --> pdb=" O PRO A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 438 removed outlier: 3.823A pdb=" N HIS A 437 " --> pdb=" O GLN A 434 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N THR A 438 " --> pdb=" O VAL A 435 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 434 through 438' Processing helix chain 'A' and resid 440 through 442 No H-bonds generated for 'chain 'A' and resid 440 through 442' Processing helix chain 'A' and resid 463 through 472 Processing helix chain 'A' and resid 481 through 495 removed outlier: 3.856A pdb=" N PHE A 495 " --> pdb=" O LYS A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 516 removed outlier: 3.669A pdb=" N GLN A 513 " --> pdb=" O ALA A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 536 removed outlier: 4.063A pdb=" N LEU A 525 " --> pdb=" O THR A 521 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP A 536 " --> pdb=" O ARG A 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 22 removed outlier: 3.882A pdb=" N ILE B 16 " --> pdb=" O ASP B 12 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN B 22 " --> pdb=" O PHE B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 33 Processing helix chain 'B' and resid 36 through 51 Processing helix chain 'B' and resid 65 through 69 removed outlier: 4.031A pdb=" N GLU B 68 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE B 69 " --> pdb=" O GLU B 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 65 through 69' Processing helix chain 'B' and resid 90 through 92 No H-bonds generated for 'chain 'B' and resid 90 through 92' Processing helix chain 'B' and resid 117 through 128 Processing helix chain 'B' and resid 163 through 168 Processing helix chain 'B' and resid 176 through 178 No H-bonds generated for 'chain 'B' and resid 176 through 178' Processing helix chain 'B' and resid 179 through 192 Processing helix chain 'B' and resid 195 through 212 removed outlier: 3.987A pdb=" N CYS B 212 " --> pdb=" O HIS B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 230 Processing helix chain 'B' and resid 236 through 247 Processing helix chain 'B' and resid 247 through 255 Processing helix chain 'D' and resid 7 through 19 removed outlier: 4.179A pdb=" N LYS D 11 " --> pdb=" O SER D 7 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS D 14 " --> pdb=" O THR D 10 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLU D 17 " --> pdb=" O ILE D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 28 removed outlier: 3.894A pdb=" N TYR D 28 " --> pdb=" O SER D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 50 Processing helix chain 'D' and resid 51 through 54 Processing helix chain 'D' and resid 97 through 117 removed outlier: 4.006A pdb=" N HIS D 111 " --> pdb=" O LYS D 107 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU D 112 " --> pdb=" O GLY D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 131 Processing helix chain 'D' and resid 181 through 185 Processing helix chain 'D' and resid 239 through 256 removed outlier: 3.709A pdb=" N ARG D 244 " --> pdb=" O LYS D 240 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TRP D 245 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN D 254 " --> pdb=" O ILE D 250 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP D 256 " --> pdb=" O ILE D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 274 removed outlier: 3.798A pdb=" N LEU D 263 " --> pdb=" O ASP D 259 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU D 274 " --> pdb=" O LYS D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 285 Processing helix chain 'D' and resid 289 through 313 removed outlier: 4.289A pdb=" N LYS D 293 " --> pdb=" O SER D 289 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU D 303 " --> pdb=" O HIS D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 332 removed outlier: 3.591A pdb=" N LEU D 332 " --> pdb=" O MET D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 383 removed outlier: 3.753A pdb=" N THR D 367 " --> pdb=" O GLN D 363 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU D 369 " --> pdb=" O GLU D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 412 removed outlier: 4.048A pdb=" N ASN D 412 " --> pdb=" O SER D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 421 removed outlier: 3.679A pdb=" N LYS D 419 " --> pdb=" O PRO D 415 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR D 420 " --> pdb=" O ARG D 416 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE D 421 " --> pdb=" O LEU D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 439 Processing helix chain 'D' and resid 463 through 472 removed outlier: 3.540A pdb=" N PHE D 472 " --> pdb=" O LEU D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 495 Processing helix chain 'D' and resid 501 through 515 Processing helix chain 'D' and resid 521 through 526 Processing helix chain 'D' and resid 528 through 535 Processing helix chain 'F' and resid 6 through 19 removed outlier: 3.741A pdb=" N LYS F 14 " --> pdb=" O THR F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 33 Processing helix chain 'F' and resid 34 through 38 Processing helix chain 'F' and resid 41 through 54 Processing helix chain 'F' and resid 100 through 117 removed outlier: 3.556A pdb=" N ARG F 115 " --> pdb=" O HIS F 111 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER F 117 " --> pdb=" O SER F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 131 Processing helix chain 'F' and resid 170 through 187 Processing helix chain 'F' and resid 200 through 205 removed outlier: 4.375A pdb=" N ASN F 204 " --> pdb=" O VAL F 200 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ASP F 205 " --> pdb=" O GLU F 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 200 through 205' Processing helix chain 'F' and resid 225 through 230 Processing helix chain 'F' and resid 238 through 249 Processing helix chain 'F' and resid 256 through 275 removed outlier: 3.680A pdb=" N ILE F 260 " --> pdb=" O ASP F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 276 through 284 Processing helix chain 'F' and resid 285 through 312 removed outlier: 3.580A pdb=" N GLU F 290 " --> pdb=" O ASN F 286 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR F 291 " --> pdb=" O LYS F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 329 removed outlier: 3.626A pdb=" N SER F 318 " --> pdb=" O TYR F 314 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS F 319 " --> pdb=" O SER F 315 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 383 Processing helix chain 'F' and resid 406 through 411 removed outlier: 3.788A pdb=" N GLN F 411 " --> pdb=" O PRO F 407 " (cutoff:3.500A) Processing helix chain 'F' and resid 413 through 421 Processing helix chain 'F' and resid 432 through 437 removed outlier: 3.799A pdb=" N CYS F 436 " --> pdb=" O SER F 432 " (cutoff:3.500A) Processing helix chain 'F' and resid 463 through 471 Processing helix chain 'F' and resid 481 through 495 Processing helix chain 'F' and resid 496 through 500 removed outlier: 5.781A pdb=" N TYR F 499 " --> pdb=" O SER F 496 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ALA F 500 " --> pdb=" O GLU F 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 496 through 500' Processing helix chain 'F' and resid 501 through 515 removed outlier: 4.272A pdb=" N ARG F 505 " --> pdb=" O SER F 501 " (cutoff:3.500A) Processing helix chain 'F' and resid 519 through 542 Processing sheet with id=AA1, first strand: chain 'C' and resid 76 through 80 removed outlier: 6.941A pdb=" N ASN C 143 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILE C 66 " --> pdb=" O ALA C 141 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ALA C 141 " --> pdb=" O ILE C 66 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LEU C 68 " --> pdb=" O SER C 139 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N SER C 139 " --> pdb=" O LEU C 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 76 through 80 removed outlier: 6.941A pdb=" N ASN C 143 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILE C 66 " --> pdb=" O ALA C 141 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ALA C 141 " --> pdb=" O ILE C 66 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LEU C 68 " --> pdb=" O SER C 139 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N SER C 139 " --> pdb=" O LEU C 68 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 428 through 429 removed outlier: 6.894A pdb=" N ILE C 89 " --> pdb=" O TRP C 445 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N LEU C 447 " --> pdb=" O ILE C 89 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL C 91 " --> pdb=" O LEU C 447 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 194 through 198 Processing sheet with id=AA5, first strand: chain 'C' and resid 336 through 341 removed outlier: 5.335A pdb=" N ASN C 337 " --> pdb=" O ASP C 350 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASP C 350 " --> pdb=" O ASN C 337 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 71 through 73 removed outlier: 3.681A pdb=" N GLU E 72 " --> pdb=" O LEU E 95 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU E 95 " --> pdb=" O GLU E 72 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'H' and resid 28 through 34 Processing sheet with id=AA8, first strand: chain 'H' and resid 178 through 181 removed outlier: 3.688A pdb=" N SER H 181 " --> pdb=" O THR H 188 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL H 224 " --> pdb=" O LYS H 95 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 135 through 136 Processing sheet with id=AB1, first strand: chain 'H' and resid 233 through 234 removed outlier: 3.508A pdb=" N VAL H 237 " --> pdb=" O VAL H 234 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 74 through 76 removed outlier: 7.011A pdb=" N SER A 76 " --> pdb=" O GLU A 69 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N GLU A 69 " --> pdb=" O SER A 76 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N VAL A 63 " --> pdb=" O ASP A 145 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ASP A 145 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP A 65 " --> pdb=" O ASN A 143 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 79 through 80 removed outlier: 5.448A pdb=" N VAL A 63 " --> pdb=" O ASP A 145 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ASP A 145 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP A 65 " --> pdb=" O ASN A 143 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 427 through 429 removed outlier: 6.263A pdb=" N ILE A 89 " --> pdb=" O TRP A 445 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N LEU A 447 " --> pdb=" O ILE A 89 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 194 through 198 removed outlier: 5.991A pdb=" N LEU A 194 " --> pdb=" O ILE A 395 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N LEU A 397 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ALA A 196 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 335 through 340 removed outlier: 5.618A pdb=" N ASN A 337 " --> pdb=" O ASP A 350 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ASP A 350 " --> pdb=" O ASN A 337 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 70 through 73 Processing sheet with id=AB8, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AB9, first strand: chain 'D' and resid 62 through 69 removed outlier: 5.151A pdb=" N VAL D 63 " --> pdb=" O ASP D 145 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N ASP D 145 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASP D 65 " --> pdb=" O ASN D 143 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 90 through 91 removed outlier: 5.979A pdb=" N VAL D 91 " --> pdb=" O LEU D 447 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 194 through 198 removed outlier: 5.952A pdb=" N LEU D 194 " --> pdb=" O ILE D 395 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N LEU D 397 " --> pdb=" O LEU D 194 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ALA D 196 " --> pdb=" O LEU D 397 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLN D 425 " --> pdb=" O GLY D 394 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N VAL D 396 " --> pdb=" O GLN D 425 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE D 427 " --> pdb=" O VAL D 396 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 348 through 350 Processing sheet with id=AC4, first strand: chain 'F' and resid 74 through 80 removed outlier: 6.511A pdb=" N GLU F 75 " --> pdb=" O ASN F 70 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN F 143 " --> pdb=" O ALA F 64 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 74 through 80 removed outlier: 6.511A pdb=" N GLU F 75 " --> pdb=" O ASN F 70 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 194 through 198 removed outlier: 5.790A pdb=" N LEU F 194 " --> pdb=" O ILE F 395 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N LEU F 397 " --> pdb=" O LEU F 194 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ALA F 196 " --> pdb=" O LEU F 397 " (cutoff:3.500A) removed outlier: 8.521A pdb=" N ASP F 399 " --> pdb=" O ALA F 196 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N TYR F 198 " --> pdb=" O ASP F 399 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 336 through 340 removed outlier: 6.353A pdb=" N ASN F 337 " --> pdb=" O ASP F 350 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ASP F 350 " --> pdb=" O ASN F 337 " (cutoff:3.500A) 1015 hydrogen bonds defined for protein. 2910 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 59 hydrogen bonds 118 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 66 stacking parallelities Total time for adding SS restraints: 5.03 Time building geometry restraints manager: 2.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7325 1.34 - 1.46: 4366 1.46 - 1.57: 13322 1.57 - 1.69: 244 1.69 - 1.81: 85 Bond restraints: 25342 Sorted by residual: bond pdb=" C3' ADP C 601 " pdb=" C4' ADP C 601 " ideal model delta sigma weight residual 1.524 1.278 0.246 2.00e-02 2.50e+03 1.52e+02 bond pdb=" C3' ADP A 601 " pdb=" C4' ADP A 601 " ideal model delta sigma weight residual 1.524 1.278 0.246 2.00e-02 2.50e+03 1.51e+02 bond pdb=" C4' ADP C 601 " pdb=" O4' ADP C 601 " ideal model delta sigma weight residual 1.426 1.652 -0.226 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C4' ADP A 601 " pdb=" O4' ADP A 601 " ideal model delta sigma weight residual 1.426 1.650 -0.224 2.00e-02 2.50e+03 1.26e+02 bond pdb=" C1' ADP A 601 " pdb=" O4' ADP A 601 " ideal model delta sigma weight residual 1.426 1.305 0.121 2.00e-02 2.50e+03 3.66e+01 ... (remaining 25337 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 34263 2.13 - 4.27: 526 4.27 - 6.40: 60 6.40 - 8.54: 16 8.54 - 10.67: 11 Bond angle restraints: 34876 Sorted by residual: angle pdb=" N VAL H 196 " pdb=" CA VAL H 196 " pdb=" C VAL H 196 " ideal model delta sigma weight residual 113.71 108.80 4.91 9.50e-01 1.11e+00 2.67e+01 angle pdb=" C GLY D 161 " pdb=" N TYR D 162 " pdb=" CA TYR D 162 " ideal model delta sigma weight residual 121.54 129.08 -7.54 1.91e+00 2.74e-01 1.56e+01 angle pdb=" C GLU F 251 " pdb=" N ILE F 252 " pdb=" CA ILE F 252 " ideal model delta sigma weight residual 121.97 128.56 -6.59 1.80e+00 3.09e-01 1.34e+01 angle pdb=" O1B ADP A 601 " pdb=" PB ADP A 601 " pdb=" O2B ADP A 601 " ideal model delta sigma weight residual 119.90 109.23 10.67 3.00e+00 1.11e-01 1.27e+01 angle pdb=" O1A ADP A 601 " pdb=" PA ADP A 601 " pdb=" O2A ADP A 601 " ideal model delta sigma weight residual 119.90 109.24 10.66 3.00e+00 1.11e-01 1.26e+01 ... (remaining 34871 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.63: 14512 35.63 - 71.25: 582 71.25 - 106.88: 20 106.88 - 142.51: 5 142.51 - 178.13: 6 Dihedral angle restraints: 15125 sinusoidal: 6712 harmonic: 8413 Sorted by residual: dihedral pdb=" O4' U J 53 " pdb=" C1' U J 53 " pdb=" N1 U J 53 " pdb=" C2 U J 53 " ideal model delta sinusoidal sigma weight residual 232.00 53.87 178.13 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U J 54 " pdb=" C1' U J 54 " pdb=" N1 U J 54 " pdb=" C2 U J 54 " ideal model delta sinusoidal sigma weight residual -128.00 24.79 -152.79 1 1.70e+01 3.46e-03 6.28e+01 dihedral pdb=" CA ALA D 343 " pdb=" C ALA D 343 " pdb=" N PRO D 344 " pdb=" CA PRO D 344 " ideal model delta harmonic sigma weight residual 180.00 145.66 34.34 0 5.00e+00 4.00e-02 4.72e+01 ... (remaining 15122 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 3040 0.043 - 0.087: 745 0.087 - 0.130: 209 0.130 - 0.174: 17 0.174 - 0.217: 4 Chirality restraints: 4015 Sorted by residual: chirality pdb=" CB THR A 118 " pdb=" CA THR A 118 " pdb=" OG1 THR A 118 " pdb=" CG2 THR A 118 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" C1' ADP A 601 " pdb=" C2' ADP A 601 " pdb=" N9 ADP A 601 " pdb=" O4' ADP A 601 " both_signs ideal model delta sigma weight residual False 2.48 2.29 0.20 2.00e-01 2.50e+01 9.63e-01 chirality pdb=" CB ILE F 211 " pdb=" CA ILE F 211 " pdb=" CG1 ILE F 211 " pdb=" CG2 ILE F 211 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.18 2.00e-01 2.50e+01 8.35e-01 ... (remaining 4012 not shown) Planarity restraints: 4066 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 502 " -0.013 2.00e-02 2.50e+03 2.51e-02 6.32e+00 pdb=" C GLU A 502 " 0.043 2.00e-02 2.50e+03 pdb=" O GLU A 502 " -0.016 2.00e-02 2.50e+03 pdb=" N ASP A 503 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA D 455 " -0.037 5.00e-02 4.00e+02 5.65e-02 5.11e+00 pdb=" N PRO D 456 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO D 456 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 456 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER H 154 " 0.034 5.00e-02 4.00e+02 5.14e-02 4.23e+00 pdb=" N PRO H 155 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO H 155 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO H 155 " 0.029 5.00e-02 4.00e+02 ... (remaining 4063 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 786 2.71 - 3.26: 24933 3.26 - 3.80: 38878 3.80 - 4.35: 49046 4.35 - 4.90: 78140 Nonbonded interactions: 191783 Sorted by model distance: nonbonded pdb=" OG SER A 16 " pdb=" OG SER A 24 " model vdw 2.159 3.040 nonbonded pdb=" O SER A 114 " pdb=" OG1 THR A 118 " model vdw 2.166 3.040 nonbonded pdb=" OD1 ASN H 83 " pdb=" OG SER H 181 " model vdw 2.205 3.040 nonbonded pdb=" O ASN F 288 " pdb=" OG1 THR F 292 " model vdw 2.233 3.040 nonbonded pdb=" O2' U J 74 " pdb=" O4' G J 75 " model vdw 2.246 3.040 ... (remaining 191778 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 5 through 7 or (resid 8 and (name N or name CA or name C o \ r name O or name CB )) or resid 9 through 11 or (resid 12 and (name N or name CA \ or name C or name O or name CB )) or resid 13 through 25 or (resid 26 through 2 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 28 through 4 \ 2 or (resid 43 through 44 and (name N or name CA or name C or name O or name CB \ )) or resid 45 through 84 or (resid 85 and (name N or name CA or name C or name \ O or name CB )) or resid 86 through 106 or (resid 107 and (name N or name CA or \ name C or name O or name CB )) or resid 108 through 114 or (resid 115 and (name \ N or name CA or name C or name O or name CB )) or resid 116 through 118 or (resi \ d 119 and (name N or name CA or name C or name O or name CB )) or resid 123 or ( \ resid 124 and (name N or name CA or name C or name O or name CB )) or resid 125 \ through 126 or (resid 127 through 129 and (name N or name CA or name C or name O \ or name CB )) or resid 130 through 131 or (resid 132 through 133 and (name N or \ name CA or name C or name O or name CB )) or resid 134 through 136 or (resid 13 \ 7 through 138 and (name N or name CA or name C or name O or name CB )) or resid \ 139 through 149 or (resid 150 and (name N or name CA or name C or name O or name \ CB )) or resid 151 through 161 or (resid 162 and (name N or name CA or name C o \ r name O or name CB )) or resid 163 through 175 or (resid 176 and (name N or nam \ e CA or name C or name O or name CB )) or resid 177 through 203 or (resid 204 an \ d (name N or name CA or name C or name O or name CB )) or resid 223 through 237 \ or (resid 238 and (name N or name CA or name C or name O or name CB )) or resid \ 239 or (resid 240 through 241 and (name N or name CA or name C or name O or name \ CB )) or resid 242 through 243 or (resid 244 and (name N or name CA or name C o \ r name O or name CB )) or resid 245 through 262 or (resid 263 through 266 and (n \ ame N or name CA or name C or name O or name CB )) or resid 267 through 269 or ( \ resid 270 through 273 and (name N or name CA or name C or name O or name CB )) o \ r resid 274 through 292 or (resid 293 through 295 and (name N or name CA or name \ C or name O or name CB )) or resid 296 or (resid 297 through 299 and (name N or \ name CA or name C or name O or name CB )) or resid 300 or (resid 301 and (name \ N or name CA or name C or name O or name CB )) or resid 302 or (resid 303 throug \ h 310 and (name N or name CA or name C or name O or name CB )) or resid 311 thro \ ugh 324 or (resid 325 and (name N or name CA or name C or name O or name CB )) o \ r resid 326 through 327 or (resid 328 and (name N or name CA or name C or name O \ or name CB )) or resid 329 through 331 or (resid 332 and (name N or name CA or \ name C or name O or name CB )) or resid 333 through 334 or (resid 335 and (name \ N or name CA or name C or name O or name CB )) or resid 336 or (resid 337 throug \ h 343 and (name N or name CA or name C or name O or name CB )) or resid 344 or ( \ resid 345 through 347 and (name N or name CA or name C or name O or name CB )) o \ r resid 348 or (resid 349 through 353 and (name N or name CA or name C or name O \ or name CB )) or resid 354 through 355 or (resid 356 and (name N or name CA or \ name C or name O or name CB )) or resid 357 or (resid 358 through 360 and (name \ N or name CA or name C or name O or name CB )) or resid 361 through 415 or (resi \ d 416 and (name N or name CA or name C or name O or name CB )) or resid 417 thro \ ugh 452 or (resid 453 and (name N or name CA or name C or name O or name CB )) o \ r resid 454 through 490 or (resid 491 and (name N or name CA or name C or name O \ or name CB )) or resid 492 through 501 or (resid 502 through 506 and (name N or \ name CA or name C or name O or name CB )) or resid 507 through 518 or (resid 51 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 520 through \ 536)) selection = (chain 'C' and (resid 5 through 7 or (resid 8 and (name N or name CA or name C o \ r name O or name CB )) or resid 9 through 10 or (resid 11 through 12 and (name N \ or name CA or name C or name O or name CB )) or resid 13 or (resid 14 through 1 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 16 through 2 \ 5 or (resid 26 through 27 and (name N or name CA or name C or name O or name CB \ )) or resid 28 or (resid 29 and (name N or name CA or name C or name O or name C \ B )) or resid 30 or (resid 31 and (name N or name CA or name C or name O or name \ CB )) or resid 32 through 33 or (resid 34 through 36 and (name N or name CA or \ name C or name O or name CB )) or resid 37 through 38 or (resid 39 and (name N o \ r name CA or name C or name O or name CB )) or resid 40 or (resid 41 through 44 \ and (name N or name CA or name C or name O or name CB )) or resid 45 or (resid 4 \ 6 through 48 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 9 through 50 or (resid 51 and (name N or name CA or name C or name O or name CB \ )) or resid 52 through 84 or (resid 85 and (name N or name CA or name C or name \ O or name CB )) or resid 86 through 106 or (resid 107 and (name N or name CA or \ name C or name O or name CB )) or resid 108 through 114 or (resid 115 and (name \ N or name CA or name C or name O or name CB )) or resid 116 through 118 or (resi \ d 119 and (name N or name CA or name C or name O or name CB )) or resid 123 or ( \ resid 124 and (name N or name CA or name C or name O or name CB )) or resid 125 \ through 126 or (resid 127 through 129 and (name N or name CA or name C or name O \ or name CB )) or resid 130 through 131 or (resid 132 through 133 and (name N or \ name CA or name C or name O or name CB )) or resid 134 through 136 or (resid 13 \ 7 through 138 and (name N or name CA or name C or name O or name CB )) or resid \ 139 through 149 or (resid 150 and (name N or name CA or name C or name O or name \ CB )) or resid 151 through 158 or (resid 159 and (name N or name CA or name C o \ r name O or name CB )) or resid 160 through 161 or (resid 162 and (name N or nam \ e CA or name C or name O or name CB )) or resid 163 or (resid 164 and (name N or \ name CA or name C or name O or name CB )) or resid 165 through 174 or (resid 17 \ 5 through 176 and (name N or name CA or name C or name O or name CB )) or resid \ 177 through 180 or (resid 181 and (name N or name CA or name C or name O or name \ CB )) or resid 182 through 203 or (resid 204 and (name N or name CA or name C o \ r name O or name CB )) or resid 223 through 237 or (resid 238 and (name N or nam \ e CA or name C or name O or name CB )) or resid 239 or (resid 240 through 241 an \ d (name N or name CA or name C or name O or name CB )) or resid 242 through 243 \ or (resid 244 and (name N or name CA or name C or name O or name CB )) or resid \ 245 through 247 or (resid 248 and (name N or name CA or name C or name O or name \ CB )) or resid 249 through 253 or resid 261 through 272 or (resid 273 and (name \ N or name CA or name C or name O or name CB )) or resid 274 or (resid 275 throu \ gh 276 and (name N or name CA or name C or name O or name CB )) or resid 277 or \ (resid 278 through 288 and (name N or name CA or name C or name O or name CB )) \ or resid 289 or (resid 290 and (name N or name CA or name C or name O or name CB \ )) or resid 291 through 292 or (resid 293 through 295 and (name N or name CA or \ name C or name O or name CB )) or resid 296 through 297 or (resid 298 through 2 \ 99 and (name N or name CA or name C or name O or name CB )) or resid 300 through \ 304 or (resid 305 through 310 and (name N or name CA or name C or name O or nam \ e CB )) or resid 311 through 312 or (resid 313 and (name N or name CA or name C \ or name O or name CB )) or resid 314 through 318 or (resid 319 and (name N or na \ me CA or name C or name O or name CB )) or resid 320 through 324 or (resid 325 a \ nd (name N or name CA or name C or name O or name CB )) or resid 326 through 327 \ or (resid 328 and (name N or name CA or name C or name O or name CB )) or resid \ 329 through 331 or (resid 332 and (name N or name CA or name C or name O or nam \ e CB )) or resid 333 through 334 or (resid 335 and (name N or name CA or name C \ or name O or name CB )) or resid 336 or (resid 337 through 343 and (name N or na \ me CA or name C or name O or name CB )) or resid 344 or (resid 345 through 347 a \ nd (name N or name CA or name C or name O or name CB )) or resid 348 or (resid 3 \ 49 through 353 and (name N or name CA or name C or name O or name CB )) or resid \ 354 through 355 or (resid 356 and (name N or name CA or name C or name O or nam \ e CB )) or resid 357 or (resid 358 through 360 and (name N or name CA or name C \ or name O or name CB )) or resid 361 through 364 or (resid 365 and (name N or na \ me CA or name C or name O or name CB )) or resid 366 through 415 or (resid 416 a \ nd (name N or name CA or name C or name O or name CB )) or resid 417 through 447 \ or (resid 448 and (name N or name CA or name C or name O or name CB )) or resid \ 449 through 452 or (resid 453 and (name N or name CA or name C or name O or nam \ e CB )) or resid 454 through 456 or (resid 457 and (name N or name CA or name C \ or name O or name CB )) or resid 458 through 490 or (resid 491 and (name N or na \ me CA or name C or name O or name CB )) or resid 492 through 496 or (resid 497 a \ nd (name N or name CA or name C or name O or name CB )) or resid 498 through 501 \ or (resid 502 through 506 and (name N or name CA or name C or name O or name CB \ )) or resid 507 through 518 or (resid 519 and (name N or name CA or name C or n \ ame O or name CB )) or resid 520 through 525 or (resid 526 and (name N or name C \ A or name C or name O or name CB )) or resid 527 through 529 or (resid 530 throu \ gh 532 and (name N or name CA or name C or name O or name CB )) or resid 533 thr \ ough 534 or (resid 535 and (name N or name CA or name C or name O or name CB )) \ or resid 536)) selection = (chain 'D' and (resid 5 through 10 or (resid 11 through 12 and (name N or name C \ A or name C or name O or name CB )) or resid 13 through 16 or (resid 17 and (nam \ e N or name CA or name C or name O or name CB )) or resid 18 through 25 or (resi \ d 26 through 27 and (name N or name CA or name C or name O or name CB )) or resi \ d 28 or (resid 29 and (name N or name CA or name C or name O or name CB )) or re \ sid 30 or (resid 31 and (name N or name CA or name C or name O or name CB )) or \ resid 32 through 33 or (resid 34 through 36 and (name N or name CA or name C or \ name O or name CB )) or resid 37 through 38 or (resid 39 and (name N or name CA \ or name C or name O or name CB )) or resid 40 or (resid 41 through 44 and (name \ N or name CA or name C or name O or name CB )) or resid 45 or (resid 46 through \ 48 and (name N or name CA or name C or name O or name CB )) or resid 49 through \ 50 or (resid 51 and (name N or name CA or name C or name O or name CB )) or resi \ d 52 through 163 or (resid 164 and (name N or name CA or name C or name O or nam \ e CB )) or resid 165 through 180 or (resid 181 and (name N or name CA or name C \ or name O or name CB )) or resid 182 through 203 or (resid 204 and (name N or na \ me CA or name C or name O or name CB )) or resid 223 through 237 or (resid 238 a \ nd (name N or name CA or name C or name O or name CB )) or resid 239 or (resid 2 \ 40 through 241 and (name N or name CA or name C or name O or name CB )) or resid \ 242 through 243 or (resid 244 and (name N or name CA or name C or name O or nam \ e CB )) or resid 245 through 247 or (resid 248 and (name N or name CA or name C \ or name O or name CB )) or resid 249 through 253 or resid 261 through 262 or (re \ sid 263 through 266 and (name N or name CA or name C or name O or name CB )) or \ resid 267 or (resid 268 through 273 and (name N or name CA or name C or name O o \ r name CB )) or resid 274 or (resid 275 through 276 and (name N or name CA or na \ me C or name O or name CB )) or resid 277 or (resid 278 through 288 and (name N \ or name CA or name C or name O or name CB )) or resid 289 or (resid 290 and (nam \ e N or name CA or name C or name O or name CB )) or resid 291 through 294 or (re \ sid 295 and (name N or name CA or name C or name O or name CB )) or resid 296 th \ rough 297 or (resid 298 through 299 and (name N or name CA or name C or name O o \ r name CB )) or resid 300 through 302 or (resid 303 through 310 and (name N or n \ ame CA or name C or name O or name CB )) or resid 311 through 312 or (resid 313 \ and (name N or name CA or name C or name O or name CB )) or resid 314 through 31 \ 8 or (resid 319 and (name N or name CA or name C or name O or name CB )) or resi \ d 320 through 324 or (resid 325 and (name N or name CA or name C or name O or na \ me CB )) or resid 326 through 327 or (resid 328 and (name N or name CA or name C \ or name O or name CB )) or resid 329 through 331 or (resid 332 and (name N or n \ ame CA or name C or name O or name CB )) or resid 333 through 334 or (resid 335 \ and (name N or name CA or name C or name O or name CB )) or resid 336 or (resid \ 337 through 343 and (name N or name CA or name C or name O or name CB )) or resi \ d 344 or (resid 345 through 347 and (name N or name CA or name C or name O or na \ me CB )) or resid 348 or (resid 349 through 353 and (name N or name CA or name C \ or name O or name CB )) or resid 354 through 355 or (resid 356 and (name N or n \ ame CA or name C or name O or name CB )) or resid 357 through 358 or (resid 359 \ through 360 and (name N or name CA or name C or name O or name CB )) or resid 36 \ 1 through 364 or (resid 365 and (name N or name CA or name C or name O or name C \ B )) or resid 366 through 415 or (resid 416 and (name N or name CA or name C or \ name O or name CB )) or resid 417 through 447 or (resid 448 and (name N or name \ CA or name C or name O or name CB )) or resid 449 through 456 or (resid 457 and \ (name N or name CA or name C or name O or name CB )) or resid 458 through 496 or \ (resid 497 and (name N or name CA or name C or name O or name CB )) or resid 49 \ 8 through 525 or (resid 526 and (name N or name CA or name C or name O or name C \ B )) or resid 527 through 529 or (resid 530 through 532 and (name N or name CA o \ r name C or name O or name CB )) or resid 533 through 534 or (resid 535 and (nam \ e N or name CA or name C or name O or name CB )) or resid 536)) selection = (chain 'F' and (resid 5 through 7 or (resid 8 and (name N or name CA or name C o \ r name O or name CB )) or resid 9 through 14 or (resid 15 and (name N or name CA \ or name C or name O or name CB )) or resid 16 or (resid 17 and (name N or name \ CA or name C or name O or name CB )) or resid 18 through 30 or (resid 31 and (na \ me N or name CA or name C or name O or name CB )) or resid 32 through 40 or (res \ id 41 through 44 and (name N or name CA or name C or name O or name CB )) or res \ id 45 or (resid 46 through 48 and (name N or name CA or name C or name O or name \ CB )) or resid 49 through 84 or (resid 85 and (name N or name CA or name C or n \ ame O or name CB )) or resid 86 through 106 or (resid 107 and (name N or name CA \ or name C or name O or name CB )) or resid 108 through 114 or (resid 115 and (n \ ame N or name CA or name C or name O or name CB )) or resid 116 through 119 or r \ esid 123 or (resid 124 and (name N or name CA or name C or name O or name CB )) \ or resid 125 through 126 or (resid 127 through 129 and (name N or name CA or nam \ e C or name O or name CB )) or resid 130 through 131 or (resid 132 through 133 a \ nd (name N or name CA or name C or name O or name CB )) or resid 134 through 136 \ or (resid 137 through 138 and (name N or name CA or name C or name O or name CB \ )) or resid 139 through 149 or (resid 150 and (name N or name CA or name C or n \ ame O or name CB )) or resid 151 through 158 or (resid 159 and (name N or name C \ A or name C or name O or name CB )) or resid 160 through 161 or (resid 162 and ( \ name N or name CA or name C or name O or name CB )) or resid 163 or (resid 164 a \ nd (name N or name CA or name C or name O or name CB )) or resid 165 through 174 \ or (resid 175 through 176 and (name N or name CA or name C or name O or name CB \ )) or resid 177 through 180 or (resid 181 and (name N or name CA or name C or n \ ame O or name CB )) or resid 182 through 204 or resid 223 through 247 or (resid \ 248 and (name N or name CA or name C or name O or name CB )) or resid 249 throug \ h 253 or resid 261 through 262 or (resid 263 through 266 and (name N or name CA \ or name C or name O or name CB )) or resid 267 or (resid 268 through 273 and (na \ me N or name CA or name C or name O or name CB )) or resid 274 or (resid 275 thr \ ough 276 and (name N or name CA or name C or name O or name CB )) or resid 277 o \ r (resid 278 through 288 and (name N or name CA or name C or name O or name CB ) \ ) or resid 289 or (resid 290 and (name N or name CA or name C or name O or name \ CB )) or resid 291 through 292 or (resid 293 through 295 and (name N or name CA \ or name C or name O or name CB )) or resid 296 or (resid 297 through 299 and (na \ me N or name CA or name C or name O or name CB )) or resid 300 or (resid 301 and \ (name N or name CA or name C or name O or name CB )) or resid 302 or (resid 303 \ through 310 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 11 through 312 or (resid 313 and (name N or name CA or name C or name O or name \ CB )) or resid 314 through 318 or (resid 319 and (name N or name CA or name C or \ name O or name CB )) or resid 320 through 364 or (resid 365 and (name N or name \ CA or name C or name O or name CB )) or resid 366 through 447 or (resid 448 and \ (name N or name CA or name C or name O or name CB )) or resid 449 through 452 o \ r (resid 453 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 54 through 456 or (resid 457 and (name N or name CA or name C or name O or name \ CB )) or resid 458 through 490 or (resid 491 and (name N or name CA or name C or \ name O or name CB )) or resid 492 through 496 or (resid 497 and (name N or name \ CA or name C or name O or name CB )) or resid 498 through 501 or (resid 502 thr \ ough 506 and (name N or name CA or name C or name O or name CB )) or resid 507 t \ hrough 518 or (resid 519 and (name N or name CA or name C or name O or name CB ) \ ) or resid 520 through 525 or (resid 526 and (name N or name CA or name C or nam \ e O or name CB )) or resid 527 through 529 or (resid 530 through 532 and (name N \ or name CA or name C or name O or name CB )) or resid 533 through 534 or (resid \ 535 and (name N or name CA or name C or name O or name CB )) or resid 536)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 29.820 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6475 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.246 25349 Z= 0.227 Angle : 0.661 10.674 34882 Z= 0.339 Chirality : 0.041 0.217 4015 Planarity : 0.005 0.057 4066 Dihedral : 17.639 178.131 9657 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.78 % Favored : 89.98 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.06 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.16), residues: 2843 helix: 0.96 (0.15), residues: 1270 sheet: -1.15 (0.31), residues: 310 loop : -1.77 (0.18), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 253 TYR 0.018 0.001 TYR A 490 PHE 0.024 0.002 PHE D 426 TRP 0.031 0.002 TRP F 245 HIS 0.015 0.001 HIS D 299 Details of bonding type rmsd covalent geometry : bond 0.00470 (25342) covalent geometry : angle 0.65724 (34876) hydrogen bonds : bond 0.16439 ( 1057) hydrogen bonds : angle 6.28669 ( 3028) metal coordination : bond 0.00598 ( 7) metal coordination : angle 5.30605 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5686 Ramachandran restraints generated. 2843 Oldfield, 0 Emsley, 2843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5686 Ramachandran restraints generated. 2843 Oldfield, 0 Emsley, 2843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 623 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 60 GLN cc_start: 0.7121 (mp10) cc_final: 0.6858 (mp10) REVERT: C 69 GLU cc_start: 0.7014 (tt0) cc_final: 0.6800 (tt0) REVERT: C 75 GLU cc_start: 0.7200 (tp30) cc_final: 0.6153 (mm-30) REVERT: C 80 ASP cc_start: 0.6774 (t70) cc_final: 0.6553 (t0) REVERT: C 99 SER cc_start: 0.7425 (m) cc_final: 0.6722 (p) REVERT: C 132 ARG cc_start: 0.7386 (ttt-90) cc_final: 0.6632 (ttp80) REVERT: C 157 THR cc_start: 0.7996 (t) cc_final: 0.7762 (p) REVERT: C 236 LYS cc_start: 0.7577 (mtmt) cc_final: 0.7240 (mtmt) REVERT: C 326 ASP cc_start: 0.8296 (t70) cc_final: 0.7935 (t70) REVERT: C 349 VAL cc_start: 0.7011 (p) cc_final: 0.6600 (m) REVERT: C 473 GLU cc_start: 0.6550 (mm-30) cc_final: 0.6318 (mm-30) REVERT: C 477 ARG cc_start: 0.8101 (mtt90) cc_final: 0.7842 (ttm170) REVERT: C 498 LYS cc_start: 0.7489 (mppt) cc_final: 0.7153 (mptt) REVERT: C 506 LYS cc_start: 0.7805 (ptmt) cc_final: 0.7515 (ptmt) REVERT: C 529 ILE cc_start: 0.7338 (tp) cc_final: 0.7104 (tt) REVERT: C 530 GLU cc_start: 0.7068 (tm-30) cc_final: 0.6596 (tt0) REVERT: E 200 ASN cc_start: 0.7606 (m110) cc_final: 0.7398 (m110) REVERT: E 223 ASN cc_start: 0.6391 (m-40) cc_final: 0.5754 (m-40) REVERT: H 57 ILE cc_start: 0.7315 (tt) cc_final: 0.7028 (tt) REVERT: H 163 SER cc_start: 0.7496 (t) cc_final: 0.7286 (p) REVERT: H 175 GLU cc_start: 0.6767 (mm-30) cc_final: 0.6358 (mp0) REVERT: H 191 THR cc_start: 0.7175 (t) cc_final: 0.6659 (m) REVERT: H 253 ARG cc_start: 0.7846 (mtp85) cc_final: 0.7118 (mtp85) REVERT: H 283 TYR cc_start: 0.7108 (m-80) cc_final: 0.6859 (m-80) REVERT: H 292 ARG cc_start: 0.7926 (mtp-110) cc_final: 0.7570 (mtp-110) REVERT: A 60 GLN cc_start: 0.7093 (mp10) cc_final: 0.6512 (mp10) REVERT: A 62 ARG cc_start: 0.7594 (mmt180) cc_final: 0.7310 (mmt-90) REVERT: A 63 VAL cc_start: 0.8276 (m) cc_final: 0.7889 (t) REVERT: A 69 GLU cc_start: 0.7124 (tt0) cc_final: 0.6915 (tt0) REVERT: A 71 TYR cc_start: 0.7224 (t80) cc_final: 0.6330 (t80) REVERT: A 77 LEU cc_start: 0.8125 (tp) cc_final: 0.7597 (tp) REVERT: A 78 ILE cc_start: 0.7658 (mp) cc_final: 0.7304 (tp) REVERT: A 103 ASP cc_start: 0.6696 (t70) cc_final: 0.6284 (t70) REVERT: A 133 LYS cc_start: 0.7921 (tttm) cc_final: 0.7714 (mtpp) REVERT: A 191 SER cc_start: 0.8282 (m) cc_final: 0.7838 (p) REVERT: A 227 LYS cc_start: 0.7169 (mmmt) cc_final: 0.6080 (mmmt) REVERT: A 338 LEU cc_start: 0.7698 (tp) cc_final: 0.7443 (tt) REVERT: A 339 LYS cc_start: 0.7135 (mmtt) cc_final: 0.6455 (mttt) REVERT: A 417 LEU cc_start: 0.8266 (tp) cc_final: 0.8013 (tp) REVERT: B 72 GLU cc_start: 0.7390 (pp20) cc_final: 0.6737 (pp20) REVERT: B 199 ASN cc_start: 0.6810 (m-40) cc_final: 0.6524 (m-40) REVERT: D 35 GLU cc_start: 0.6944 (pm20) cc_final: 0.6542 (pm20) REVERT: D 44 MET cc_start: 0.3000 (ptp) cc_final: 0.2709 (ppp) REVERT: D 87 SER cc_start: 0.6438 (p) cc_final: 0.6230 (m) REVERT: D 143 ASN cc_start: 0.6937 (t0) cc_final: 0.6713 (t0) REVERT: D 144 TYR cc_start: 0.7370 (m-80) cc_final: 0.6904 (m-10) REVERT: D 145 ASP cc_start: 0.6358 (m-30) cc_final: 0.6098 (m-30) REVERT: D 266 GLU cc_start: 0.7249 (tm-30) cc_final: 0.6680 (tm-30) REVERT: D 306 LEU cc_start: 0.8399 (tp) cc_final: 0.8045 (tp) REVERT: D 330 SER cc_start: 0.8203 (m) cc_final: 0.7787 (p) REVERT: D 422 LYS cc_start: 0.6481 (pttt) cc_final: 0.6264 (pttt) REVERT: D 460 ARG cc_start: 0.7356 (ttt180) cc_final: 0.6943 (ttt180) REVERT: D 473 GLU cc_start: 0.6075 (tp30) cc_final: 0.5637 (tp30) REVERT: D 474 VAL cc_start: 0.8135 (t) cc_final: 0.7699 (p) REVERT: D 532 ARG cc_start: 0.6824 (mmm-85) cc_final: 0.6494 (mmm-85) REVERT: F 82 SER cc_start: 0.7752 (t) cc_final: 0.7249 (m) REVERT: F 83 MET cc_start: 0.7116 (mmm) cc_final: 0.6722 (mmm) REVERT: F 110 THR cc_start: 0.6827 (m) cc_final: 0.6583 (m) REVERT: F 115 ARG cc_start: 0.8332 (mtt90) cc_final: 0.8098 (mtt-85) REVERT: F 124 ASP cc_start: 0.6626 (m-30) cc_final: 0.6416 (m-30) REVERT: F 143 ASN cc_start: 0.7053 (m-40) cc_final: 0.6605 (m-40) REVERT: F 146 TYR cc_start: 0.6421 (t80) cc_final: 0.6173 (t80) REVERT: F 151 PHE cc_start: 0.7167 (m-10) cc_final: 0.6861 (m-10) REVERT: F 153 MET cc_start: 0.6798 (ttm) cc_final: 0.6573 (ttm) REVERT: F 270 LYS cc_start: 0.8838 (mtmt) cc_final: 0.8393 (mtmt) REVERT: F 321 LEU cc_start: 0.7554 (mt) cc_final: 0.7204 (mt) REVERT: F 368 ILE cc_start: 0.7656 (tp) cc_final: 0.7434 (tp) REVERT: F 369 LEU cc_start: 0.8267 (mm) cc_final: 0.8051 (mm) REVERT: F 371 LEU cc_start: 0.8778 (tp) cc_final: 0.8566 (tp) REVERT: F 382 LEU cc_start: 0.8349 (mt) cc_final: 0.8125 (mt) REVERT: F 404 HIS cc_start: 0.6523 (m170) cc_final: 0.6258 (m170) REVERT: F 456 PRO cc_start: 0.5230 (Cg_exo) cc_final: 0.5004 (Cg_endo) REVERT: F 520 GLU cc_start: 0.7844 (mp0) cc_final: 0.7500 (mp0) REVERT: F 524 GLU cc_start: 0.7299 (tm-30) cc_final: 0.6969 (tm-30) REVERT: F 530 GLU cc_start: 0.6764 (mm-30) cc_final: 0.6500 (mm-30) outliers start: 0 outliers final: 0 residues processed: 623 average time/residue: 0.1878 time to fit residues: 179.6265 Evaluate side-chains 550 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 550 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.3980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 ASN C 431 HIS E 22 ASN ** E 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 ASN E 50 GLN E 222 HIS H 64 HIS H 66 HIS H 201 HIS ** H 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 269 ASN A 143 ASN ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 HIS A 352 ASN A 360 GLN B 73 HIS B 127 ASN F 111 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.188412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.153231 restraints weight = 36677.206| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 2.56 r_work: 0.3753 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 25349 Z= 0.164 Angle : 0.655 10.925 34882 Z= 0.340 Chirality : 0.043 0.249 4015 Planarity : 0.005 0.065 4066 Dihedral : 18.872 177.872 4527 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.39 % Favored : 90.40 % Rotamer: Outliers : 1.50 % Allowed : 9.01 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.06 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.16), residues: 2843 helix: 0.94 (0.15), residues: 1303 sheet: -1.08 (0.30), residues: 316 loop : -1.76 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 216 TYR 0.018 0.002 TYR F 25 PHE 0.032 0.002 PHE D 515 TRP 0.027 0.002 TRP E 228 HIS 0.014 0.001 HIS E 122 Details of bonding type rmsd covalent geometry : bond 0.00364 (25342) covalent geometry : angle 0.65189 (34876) hydrogen bonds : bond 0.04259 ( 1057) hydrogen bonds : angle 4.73448 ( 3028) metal coordination : bond 0.00824 ( 7) metal coordination : angle 5.22965 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5686 Ramachandran restraints generated. 2843 Oldfield, 0 Emsley, 2843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5686 Ramachandran restraints generated. 2843 Oldfield, 0 Emsley, 2843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 592 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 99 SER cc_start: 0.7583 (m) cc_final: 0.7209 (m) REVERT: C 236 LYS cc_start: 0.7843 (mtmt) cc_final: 0.7495 (mtmt) REVERT: C 241 LEU cc_start: 0.7672 (mp) cc_final: 0.7455 (mp) REVERT: C 349 VAL cc_start: 0.7164 (p) cc_final: 0.6806 (m) REVERT: C 356 LEU cc_start: 0.7757 (mt) cc_final: 0.7548 (mt) REVERT: C 400 GLU cc_start: 0.7008 (mm-30) cc_final: 0.6776 (mm-30) REVERT: C 477 ARG cc_start: 0.8355 (mtt90) cc_final: 0.8030 (ttm170) REVERT: C 506 LYS cc_start: 0.8042 (ptmt) cc_final: 0.7717 (ptmt) REVERT: C 518 ASP cc_start: 0.6984 (p0) cc_final: 0.6443 (p0) REVERT: C 529 ILE cc_start: 0.7753 (tp) cc_final: 0.7441 (tt) REVERT: E 220 LYS cc_start: 0.8514 (tppt) cc_final: 0.8220 (tppt) REVERT: E 229 ASN cc_start: 0.6007 (p0) cc_final: 0.5592 (p0) REVERT: H 156 PHE cc_start: 0.7439 (OUTLIER) cc_final: 0.7236 (m-80) REVERT: H 168 GLU cc_start: 0.5992 (tt0) cc_final: 0.5764 (tt0) REVERT: H 191 THR cc_start: 0.7017 (t) cc_final: 0.6550 (m) REVERT: H 211 PHE cc_start: 0.7081 (m-10) cc_final: 0.6736 (m-10) REVERT: H 212 PHE cc_start: 0.6836 (t80) cc_final: 0.6583 (t80) REVERT: H 215 ARG cc_start: 0.8049 (tpp80) cc_final: 0.7596 (tpp-160) REVERT: H 253 ARG cc_start: 0.7849 (mtp85) cc_final: 0.6973 (mtp85) REVERT: H 292 ARG cc_start: 0.8405 (mtp-110) cc_final: 0.8027 (mtp-110) REVERT: A 66 ILE cc_start: 0.7976 (tt) cc_final: 0.7485 (pt) REVERT: A 69 GLU cc_start: 0.7849 (tt0) cc_final: 0.7305 (tt0) REVERT: A 77 LEU cc_start: 0.8347 (tp) cc_final: 0.7744 (tp) REVERT: A 103 ASP cc_start: 0.7132 (t70) cc_final: 0.6793 (t70) REVERT: A 130 GLU cc_start: 0.6445 (mt-10) cc_final: 0.6218 (mt-10) REVERT: A 153 MET cc_start: 0.7505 (ttp) cc_final: 0.7289 (ttp) REVERT: A 191 SER cc_start: 0.8456 (m) cc_final: 0.7956 (p) REVERT: A 193 PRO cc_start: 0.8461 (Cg_exo) cc_final: 0.8237 (Cg_endo) REVERT: A 201 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7436 (mm-30) REVERT: A 227 LYS cc_start: 0.7622 (mmmt) cc_final: 0.6648 (mmmt) REVERT: A 270 LYS cc_start: 0.7993 (ptmm) cc_final: 0.7678 (ptmm) REVERT: A 410 GLN cc_start: 0.8100 (mt0) cc_final: 0.7813 (mt0) REVERT: A 416 ARG cc_start: 0.8181 (ttm110) cc_final: 0.7848 (tpp80) REVERT: B 14 PHE cc_start: 0.7350 (p90) cc_final: 0.6644 (p90) REVERT: B 40 LYS cc_start: 0.7717 (ptpp) cc_final: 0.7455 (ptpp) REVERT: B 72 GLU cc_start: 0.7564 (pp20) cc_final: 0.7252 (pp20) REVERT: B 199 ASN cc_start: 0.7064 (m-40) cc_final: 0.6858 (m-40) REVERT: D 35 GLU cc_start: 0.6955 (pm20) cc_final: 0.6545 (pm20) REVERT: D 44 MET cc_start: 0.3301 (ptp) cc_final: 0.2824 (ppp) REVERT: D 144 TYR cc_start: 0.7890 (m-80) cc_final: 0.7679 (m-10) REVERT: D 163 GLU cc_start: 0.7002 (tp30) cc_final: 0.6742 (tp30) REVERT: D 251 GLU cc_start: 0.6367 (tp30) cc_final: 0.5058 (tp30) REVERT: D 266 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7265 (tm-30) REVERT: D 306 LEU cc_start: 0.8639 (tp) cc_final: 0.8367 (tp) REVERT: D 317 ASN cc_start: 0.7974 (t0) cc_final: 0.7603 (t0) REVERT: D 330 SER cc_start: 0.8102 (m) cc_final: 0.7803 (t) REVERT: D 398 ILE cc_start: 0.6777 (mt) cc_final: 0.6257 (mt) REVERT: D 460 ARG cc_start: 0.7896 (ttt180) cc_final: 0.7638 (tpp80) REVERT: D 473 GLU cc_start: 0.6619 (tp30) cc_final: 0.6082 (tp30) REVERT: D 474 VAL cc_start: 0.8257 (t) cc_final: 0.7809 (p) REVERT: D 532 ARG cc_start: 0.7184 (mmm-85) cc_final: 0.6787 (mmm-85) REVERT: F 76 SER cc_start: 0.7401 (t) cc_final: 0.7124 (p) REVERT: F 82 SER cc_start: 0.7895 (t) cc_final: 0.7452 (m) REVERT: F 83 MET cc_start: 0.7742 (mmm) cc_final: 0.7498 (mmm) REVERT: F 115 ARG cc_start: 0.8448 (mtt90) cc_final: 0.8067 (mtt-85) REVERT: F 124 ASP cc_start: 0.7411 (m-30) cc_final: 0.7080 (m-30) REVERT: F 135 GLN cc_start: 0.7911 (mm-40) cc_final: 0.7544 (mp10) REVERT: F 145 ASP cc_start: 0.7266 (t0) cc_final: 0.7002 (t0) REVERT: F 146 TYR cc_start: 0.7010 (t80) cc_final: 0.6728 (t80) REVERT: F 189 ASN cc_start: 0.8378 (p0) cc_final: 0.7989 (p0) REVERT: F 226 PHE cc_start: 0.8190 (m-80) cc_final: 0.7990 (m-10) REVERT: F 368 ILE cc_start: 0.7787 (tp) cc_final: 0.7579 (tp) REVERT: F 371 LEU cc_start: 0.8705 (tp) cc_final: 0.8479 (tp) REVERT: F 382 LEU cc_start: 0.8421 (mt) cc_final: 0.8144 (mt) REVERT: F 404 HIS cc_start: 0.7112 (m170) cc_final: 0.6700 (m170) REVERT: F 422 LYS cc_start: 0.8399 (mttt) cc_final: 0.8187 (mttt) REVERT: F 456 PRO cc_start: 0.6577 (Cg_exo) cc_final: 0.6275 (Cg_endo) REVERT: F 470 ASN cc_start: 0.7176 (t0) cc_final: 0.6913 (t0) REVERT: F 520 GLU cc_start: 0.7994 (mp0) cc_final: 0.7681 (mp0) REVERT: F 524 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7367 (tm-30) REVERT: F 530 GLU cc_start: 0.7014 (mm-30) cc_final: 0.6511 (mm-30) outliers start: 35 outliers final: 26 residues processed: 599 average time/residue: 0.1890 time to fit residues: 173.0709 Evaluate side-chains 591 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 564 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 LYS Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 222 HIS Chi-restraints excluded: chain E residue 228 TRP Chi-restraints excluded: chain H residue 15 ASP Chi-restraints excluded: chain H residue 32 LYS Chi-restraints excluded: chain H residue 64 HIS Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 156 PHE Chi-restraints excluded: chain H residue 170 SER Chi-restraints excluded: chain H residue 258 LEU Chi-restraints excluded: chain H residue 273 ASN Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 468 LEU Chi-restraints excluded: chain F residue 136 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 260 optimal weight: 5.9990 chunk 248 optimal weight: 0.7980 chunk 81 optimal weight: 0.2980 chunk 179 optimal weight: 4.9990 chunk 186 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 148 optimal weight: 3.9990 chunk 65 optimal weight: 8.9990 chunk 164 optimal weight: 0.0270 chunk 17 optimal weight: 0.8980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 ASN C 230 ASN C 383 ASN ** C 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 431 HIS H 201 HIS ** H 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 143 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.188260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.153043 restraints weight = 36698.425| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 2.57 r_work: 0.3753 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25349 Z= 0.134 Angle : 0.603 9.792 34882 Z= 0.315 Chirality : 0.041 0.259 4015 Planarity : 0.004 0.054 4066 Dihedral : 18.703 179.001 4527 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.93 % Favored : 90.93 % Rotamer: Outliers : 2.32 % Allowed : 12.31 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.06 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.16), residues: 2843 helix: 1.08 (0.15), residues: 1298 sheet: -1.04 (0.30), residues: 301 loop : -1.72 (0.18), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 253 TYR 0.014 0.001 TYR A 229 PHE 0.021 0.001 PHE D 515 TRP 0.029 0.002 TRP E 228 HIS 0.012 0.001 HIS E 122 Details of bonding type rmsd covalent geometry : bond 0.00297 (25342) covalent geometry : angle 0.60085 (34876) hydrogen bonds : bond 0.03804 ( 1057) hydrogen bonds : angle 4.48101 ( 3028) metal coordination : bond 0.00586 ( 7) metal coordination : angle 4.11998 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5686 Ramachandran restraints generated. 2843 Oldfield, 0 Emsley, 2843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5686 Ramachandran restraints generated. 2843 Oldfield, 0 Emsley, 2843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 568 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 44 MET cc_start: 0.6889 (OUTLIER) cc_final: 0.6652 (tmm) REVERT: C 47 TYR cc_start: 0.8155 (t80) cc_final: 0.7708 (t80) REVERT: C 99 SER cc_start: 0.7673 (m) cc_final: 0.7403 (m) REVERT: C 115 ARG cc_start: 0.8316 (mtm-85) cc_final: 0.7677 (mtt90) REVERT: C 175 GLU cc_start: 0.7138 (tp30) cc_final: 0.6339 (tp30) REVERT: C 236 LYS cc_start: 0.7741 (mtmt) cc_final: 0.7453 (mtmt) REVERT: C 253 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7556 (pm20) REVERT: C 349 VAL cc_start: 0.7243 (p) cc_final: 0.6878 (m) REVERT: C 356 LEU cc_start: 0.7659 (mt) cc_final: 0.7413 (mt) REVERT: C 477 ARG cc_start: 0.8386 (mtt90) cc_final: 0.8045 (ttm170) REVERT: C 506 LYS cc_start: 0.8052 (ptmt) cc_final: 0.7718 (ptmt) REVERT: C 518 ASP cc_start: 0.6921 (p0) cc_final: 0.6380 (p0) REVERT: C 529 ILE cc_start: 0.7731 (tp) cc_final: 0.7360 (tt) REVERT: E 223 ASN cc_start: 0.6818 (m-40) cc_final: 0.6348 (m-40) REVERT: E 229 ASN cc_start: 0.5780 (p0) cc_final: 0.5198 (p0) REVERT: H 55 ARG cc_start: 0.6888 (mtm-85) cc_final: 0.6677 (mtm180) REVERT: H 80 ILE cc_start: 0.7581 (pt) cc_final: 0.7073 (pt) REVERT: H 156 PHE cc_start: 0.7387 (OUTLIER) cc_final: 0.7177 (m-80) REVERT: H 191 THR cc_start: 0.6973 (t) cc_final: 0.6532 (m) REVERT: H 210 ARG cc_start: 0.7225 (tmm-80) cc_final: 0.6903 (ttp-110) REVERT: H 215 ARG cc_start: 0.7972 (tpp80) cc_final: 0.7555 (tpp-160) REVERT: H 252 LYS cc_start: 0.8450 (mmmm) cc_final: 0.7902 (mmtp) REVERT: H 292 ARG cc_start: 0.8352 (mtp-110) cc_final: 0.7948 (mtp-110) REVERT: A 66 ILE cc_start: 0.7953 (tt) cc_final: 0.7501 (pt) REVERT: A 69 GLU cc_start: 0.7878 (tt0) cc_final: 0.7399 (tt0) REVERT: A 77 LEU cc_start: 0.8380 (tp) cc_final: 0.7776 (tp) REVERT: A 103 ASP cc_start: 0.7035 (t70) cc_final: 0.6662 (t70) REVERT: A 112 LEU cc_start: 0.7570 (tp) cc_final: 0.7162 (tt) REVERT: A 130 GLU cc_start: 0.6458 (mt-10) cc_final: 0.6244 (mt-10) REVERT: A 191 SER cc_start: 0.8415 (m) cc_final: 0.7909 (p) REVERT: A 227 LYS cc_start: 0.7559 (mmmt) cc_final: 0.6662 (mmmt) REVERT: A 240 LYS cc_start: 0.8174 (tttt) cc_final: 0.7755 (tttt) REVERT: A 270 LYS cc_start: 0.7981 (ptmm) cc_final: 0.7718 (mtpp) REVERT: A 410 GLN cc_start: 0.8010 (mt0) cc_final: 0.7724 (mt0) REVERT: A 416 ARG cc_start: 0.8170 (ttm110) cc_final: 0.7780 (tpp80) REVERT: A 451 GLN cc_start: 0.8083 (mp10) cc_final: 0.7854 (mp10) REVERT: A 507 LEU cc_start: 0.8221 (mt) cc_final: 0.7989 (mp) REVERT: B 14 PHE cc_start: 0.7435 (p90) cc_final: 0.6738 (p90) REVERT: B 40 LYS cc_start: 0.7743 (ptpp) cc_final: 0.7348 (ptpp) REVERT: B 72 GLU cc_start: 0.7587 (pp20) cc_final: 0.7326 (pp20) REVERT: B 199 ASN cc_start: 0.7206 (m-40) cc_final: 0.6947 (m-40) REVERT: D 44 MET cc_start: 0.3407 (ptp) cc_final: 0.2835 (ppp) REVERT: D 146 TYR cc_start: 0.7664 (t80) cc_final: 0.7441 (t80) REVERT: D 163 GLU cc_start: 0.7098 (tp30) cc_final: 0.6860 (tp30) REVERT: D 251 GLU cc_start: 0.6107 (tp30) cc_final: 0.5406 (tp30) REVERT: D 259 ASP cc_start: 0.7585 (m-30) cc_final: 0.7183 (m-30) REVERT: D 266 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7237 (tm-30) REVERT: D 317 ASN cc_start: 0.8009 (t0) cc_final: 0.7560 (t0) REVERT: D 330 SER cc_start: 0.7981 (m) cc_final: 0.7723 (t) REVERT: D 398 ILE cc_start: 0.6762 (mt) cc_final: 0.6109 (mt) REVERT: D 473 GLU cc_start: 0.6515 (tp30) cc_final: 0.6024 (tp30) REVERT: D 474 VAL cc_start: 0.8220 (t) cc_final: 0.7784 (p) REVERT: D 481 ASP cc_start: 0.5891 (t70) cc_final: 0.5584 (t70) REVERT: D 532 ARG cc_start: 0.7347 (mmm-85) cc_final: 0.7043 (mmm-85) REVERT: F 76 SER cc_start: 0.7633 (t) cc_final: 0.7367 (p) REVERT: F 82 SER cc_start: 0.7757 (t) cc_final: 0.7348 (m) REVERT: F 83 MET cc_start: 0.7727 (mmm) cc_final: 0.7501 (mmm) REVERT: F 110 THR cc_start: 0.7363 (p) cc_final: 0.7051 (t) REVERT: F 115 ARG cc_start: 0.8450 (mtt90) cc_final: 0.8194 (mtt-85) REVERT: F 124 ASP cc_start: 0.7409 (m-30) cc_final: 0.7102 (m-30) REVERT: F 135 GLN cc_start: 0.7952 (mm-40) cc_final: 0.7627 (mp10) REVERT: F 145 ASP cc_start: 0.7287 (t0) cc_final: 0.7056 (t0) REVERT: F 146 TYR cc_start: 0.7126 (t80) cc_final: 0.6854 (t80) REVERT: F 163 GLU cc_start: 0.6847 (tm-30) cc_final: 0.6543 (mm-30) REVERT: F 189 ASN cc_start: 0.8404 (p0) cc_final: 0.7985 (p0) REVERT: F 371 LEU cc_start: 0.8688 (tp) cc_final: 0.8467 (tp) REVERT: F 382 LEU cc_start: 0.8431 (mt) cc_final: 0.8180 (mt) REVERT: F 404 HIS cc_start: 0.7161 (m170) cc_final: 0.6718 (m170) REVERT: F 448 LYS cc_start: 0.7781 (ptmm) cc_final: 0.7462 (ttpp) REVERT: F 456 PRO cc_start: 0.6832 (Cg_exo) cc_final: 0.6507 (Cg_endo) REVERT: F 470 ASN cc_start: 0.7166 (t0) cc_final: 0.6914 (t0) REVERT: F 520 GLU cc_start: 0.8017 (mp0) cc_final: 0.7695 (mp0) REVERT: F 524 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7349 (tm-30) REVERT: F 530 GLU cc_start: 0.7184 (mm-30) cc_final: 0.6635 (mm-30) outliers start: 54 outliers final: 36 residues processed: 580 average time/residue: 0.1869 time to fit residues: 164.9883 Evaluate side-chains 587 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 548 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 34 LYS Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 253 GLU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain E residue 222 HIS Chi-restraints excluded: chain H residue 15 ASP Chi-restraints excluded: chain H residue 32 LYS Chi-restraints excluded: chain H residue 59 GLU Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 156 PHE Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain H residue 271 ASP Chi-restraints excluded: chain H residue 273 ASN Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 432 SER Chi-restraints excluded: chain D residue 468 LEU Chi-restraints excluded: chain D residue 522 LEU Chi-restraints excluded: chain F residue 136 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 212 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 190 optimal weight: 7.9990 chunk 173 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 118 optimal weight: 30.0000 chunk 115 optimal weight: 9.9990 chunk 116 optimal weight: 9.9990 chunk 192 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 45 optimal weight: 0.0770 overall best weight: 1.7142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 26 GLN C 135 GLN ** C 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 431 HIS C 470 ASN E 65 ASN E 222 HIS H 27 HIS H 64 HIS H 201 HIS ** H 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 143 ASN A 184 HIS A 189 ASN A 470 ASN ** D 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 121 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.174700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.137545 restraints weight = 36077.570| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.54 r_work: 0.3630 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 25349 Z= 0.271 Angle : 0.719 11.393 34882 Z= 0.377 Chirality : 0.047 0.291 4015 Planarity : 0.005 0.065 4066 Dihedral : 18.846 179.548 4527 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.92 % Favored : 89.91 % Rotamer: Outliers : 3.13 % Allowed : 14.20 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.06 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.16), residues: 2843 helix: 0.87 (0.15), residues: 1310 sheet: -1.09 (0.29), residues: 306 loop : -1.81 (0.18), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 253 TYR 0.023 0.002 TYR C 483 PHE 0.041 0.002 PHE B 153 TRP 0.025 0.003 TRP E 228 HIS 0.012 0.002 HIS A 437 Details of bonding type rmsd covalent geometry : bond 0.00603 (25342) covalent geometry : angle 0.71456 (34876) hydrogen bonds : bond 0.04698 ( 1057) hydrogen bonds : angle 4.60711 ( 3028) metal coordination : bond 0.01007 ( 7) metal coordination : angle 6.03931 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5686 Ramachandran restraints generated. 2843 Oldfield, 0 Emsley, 2843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5686 Ramachandran restraints generated. 2843 Oldfield, 0 Emsley, 2843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 673 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 600 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 80 ASP cc_start: 0.7430 (t0) cc_final: 0.7224 (m-30) REVERT: C 99 SER cc_start: 0.7746 (m) cc_final: 0.7433 (m) REVERT: C 132 ARG cc_start: 0.7862 (ttt-90) cc_final: 0.7469 (ttt-90) REVERT: C 159 GLU cc_start: 0.7316 (pp20) cc_final: 0.7028 (pp20) REVERT: C 236 LYS cc_start: 0.7954 (mtmt) cc_final: 0.7623 (mtmt) REVERT: C 253 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7613 (pm20) REVERT: C 349 VAL cc_start: 0.7320 (p) cc_final: 0.6917 (m) REVERT: C 356 LEU cc_start: 0.7785 (mt) cc_final: 0.7543 (mt) REVERT: C 506 LYS cc_start: 0.8119 (ptmt) cc_final: 0.7750 (ptmt) REVERT: C 518 ASP cc_start: 0.6976 (p0) cc_final: 0.6387 (p0) REVERT: C 529 ILE cc_start: 0.8006 (tp) cc_final: 0.7669 (tt) REVERT: E 229 ASN cc_start: 0.5828 (p0) cc_final: 0.5305 (p0) REVERT: H 32 LYS cc_start: 0.7122 (mtpt) cc_final: 0.6876 (mtmt) REVERT: H 55 ARG cc_start: 0.6944 (mtm-85) cc_final: 0.6703 (mtm180) REVERT: H 161 VAL cc_start: 0.7983 (m) cc_final: 0.7732 (p) REVERT: H 191 THR cc_start: 0.7126 (t) cc_final: 0.6702 (m) REVERT: H 202 GLN cc_start: 0.7914 (mm-40) cc_final: 0.7621 (mm-40) REVERT: H 203 LYS cc_start: 0.8519 (tppt) cc_final: 0.8300 (tppt) REVERT: H 215 ARG cc_start: 0.7879 (tpp80) cc_final: 0.7588 (tpp-160) REVERT: H 253 ARG cc_start: 0.7768 (mtp85) cc_final: 0.7087 (mtp85) REVERT: H 292 ARG cc_start: 0.8304 (mtp-110) cc_final: 0.8005 (mtp-110) REVERT: A 60 GLN cc_start: 0.7775 (mp10) cc_final: 0.6882 (mp10) REVERT: A 62 ARG cc_start: 0.8023 (mmt180) cc_final: 0.7510 (mpt180) REVERT: A 77 LEU cc_start: 0.8470 (tp) cc_final: 0.8086 (tt) REVERT: A 103 ASP cc_start: 0.7234 (t70) cc_final: 0.6857 (t70) REVERT: A 112 LEU cc_start: 0.7657 (tp) cc_final: 0.7189 (tt) REVERT: A 145 ASP cc_start: 0.7417 (t0) cc_final: 0.7137 (t0) REVERT: A 191 SER cc_start: 0.8521 (m) cc_final: 0.7922 (p) REVERT: A 194 LEU cc_start: 0.8276 (tt) cc_final: 0.8054 (tp) REVERT: A 227 LYS cc_start: 0.7646 (mmmt) cc_final: 0.6805 (mmmt) REVERT: A 339 LYS cc_start: 0.7544 (mmtt) cc_final: 0.6688 (mtpt) REVERT: A 357 SER cc_start: 0.8282 (t) cc_final: 0.8040 (p) REVERT: A 416 ARG cc_start: 0.8287 (ttm110) cc_final: 0.7843 (tpp80) REVERT: A 451 GLN cc_start: 0.8389 (mp10) cc_final: 0.8165 (mp10) REVERT: A 507 LEU cc_start: 0.8288 (mt) cc_final: 0.8077 (mp) REVERT: B 40 LYS cc_start: 0.7789 (ptpp) cc_final: 0.7411 (ptpp) REVERT: B 72 GLU cc_start: 0.7503 (pp20) cc_final: 0.7287 (pp20) REVERT: B 110 LEU cc_start: 0.8358 (tp) cc_final: 0.8090 (tp) REVERT: B 183 ILE cc_start: 0.8467 (mt) cc_final: 0.8200 (mt) REVERT: B 199 ASN cc_start: 0.7320 (m-40) cc_final: 0.7053 (m-40) REVERT: D 197 MET cc_start: 0.7519 (mmm) cc_final: 0.6967 (tpt) REVERT: D 251 GLU cc_start: 0.6105 (tp30) cc_final: 0.5629 (tp30) REVERT: D 259 ASP cc_start: 0.7716 (m-30) cc_final: 0.7305 (m-30) REVERT: D 266 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7318 (tm-30) REVERT: D 270 LYS cc_start: 0.8138 (tppp) cc_final: 0.7220 (tppp) REVERT: D 330 SER cc_start: 0.8094 (m) cc_final: 0.7853 (p) REVERT: D 398 ILE cc_start: 0.7012 (mt) cc_final: 0.6412 (mt) REVERT: D 444 ILE cc_start: 0.8322 (tp) cc_final: 0.8060 (tp) REVERT: D 473 GLU cc_start: 0.6561 (tp30) cc_final: 0.6159 (tp30) REVERT: D 481 ASP cc_start: 0.6044 (t70) cc_final: 0.5817 (t70) REVERT: D 532 ARG cc_start: 0.7682 (mmm-85) cc_final: 0.7364 (mmm-85) REVERT: F 76 SER cc_start: 0.7525 (t) cc_final: 0.7000 (p) REVERT: F 82 SER cc_start: 0.7797 (t) cc_final: 0.7370 (m) REVERT: F 83 MET cc_start: 0.7682 (mmm) cc_final: 0.7440 (mmm) REVERT: F 99 SER cc_start: 0.7982 (m) cc_final: 0.7460 (p) REVERT: F 115 ARG cc_start: 0.8491 (mtt90) cc_final: 0.8211 (mtt-85) REVERT: F 135 GLN cc_start: 0.8121 (mm-40) cc_final: 0.7787 (mp10) REVERT: F 145 ASP cc_start: 0.7418 (t0) cc_final: 0.7114 (t0) REVERT: F 147 MET cc_start: 0.7270 (ppp) cc_final: 0.6950 (ppp) REVERT: F 163 GLU cc_start: 0.6944 (tm-30) cc_final: 0.6657 (mm-30) REVERT: F 189 ASN cc_start: 0.8396 (p0) cc_final: 0.7906 (p0) REVERT: F 226 PHE cc_start: 0.8254 (m-80) cc_final: 0.8043 (m-10) REVERT: F 374 ASP cc_start: 0.8681 (t0) cc_final: 0.7136 (m-30) REVERT: F 382 LEU cc_start: 0.8420 (mt) cc_final: 0.8181 (mt) REVERT: F 404 HIS cc_start: 0.7475 (m170) cc_final: 0.7008 (m170) REVERT: F 419 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8158 (ttmm) REVERT: F 454 LYS cc_start: 0.8045 (tptt) cc_final: 0.7827 (tptt) REVERT: F 481 ASP cc_start: 0.6767 (t0) cc_final: 0.6368 (t0) REVERT: F 520 GLU cc_start: 0.8136 (mp0) cc_final: 0.7685 (mp0) REVERT: F 524 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7646 (tm-30) REVERT: F 530 GLU cc_start: 0.7389 (mm-30) cc_final: 0.6901 (mm-30) REVERT: F 532 ARG cc_start: 0.7802 (mtp-110) cc_final: 0.7475 (mtp180) outliers start: 73 outliers final: 46 residues processed: 621 average time/residue: 0.1899 time to fit residues: 179.9577 Evaluate side-chains 626 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 578 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 253 GLU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 489 GLU Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain E residue 222 HIS Chi-restraints excluded: chain H residue 15 ASP Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 59 GLU Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 85 LYS Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 170 SER Chi-restraints excluded: chain H residue 257 SER Chi-restraints excluded: chain H residue 271 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 352 ASN Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 79 MET Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 395 ILE Chi-restraints excluded: chain D residue 431 HIS Chi-restraints excluded: chain D residue 432 SER Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 468 LEU Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain F residue 136 ASN Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 419 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 92 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 219 optimal weight: 2.9990 chunk 266 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 218 optimal weight: 1.9990 chunk 217 optimal weight: 8.9990 chunk 177 optimal weight: 0.0970 chunk 164 optimal weight: 0.4980 chunk 243 optimal weight: 5.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 223 ASN H 201 HIS ** H 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 269 ASN A 470 ASN D 410 GLN ** D 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 187 ASN ** F 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.176552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.139872 restraints weight = 36297.845| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 2.53 r_work: 0.3665 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 25349 Z= 0.185 Angle : 0.647 11.613 34882 Z= 0.340 Chirality : 0.043 0.287 4015 Planarity : 0.004 0.059 4066 Dihedral : 18.708 179.959 4527 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.97 % Favored : 90.85 % Rotamer: Outliers : 3.17 % Allowed : 16.22 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.06 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.16), residues: 2843 helix: 1.04 (0.15), residues: 1304 sheet: -1.08 (0.29), residues: 312 loop : -1.77 (0.18), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 253 TYR 0.015 0.001 TYR F 198 PHE 0.020 0.002 PHE B 153 TRP 0.019 0.002 TRP F 466 HIS 0.011 0.001 HIS C 514 Details of bonding type rmsd covalent geometry : bond 0.00414 (25342) covalent geometry : angle 0.64451 (34876) hydrogen bonds : bond 0.04019 ( 1057) hydrogen bonds : angle 4.42580 ( 3028) metal coordination : bond 0.00710 ( 7) metal coordination : angle 4.66105 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5686 Ramachandran restraints generated. 2843 Oldfield, 0 Emsley, 2843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5686 Ramachandran restraints generated. 2843 Oldfield, 0 Emsley, 2843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 583 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 99 SER cc_start: 0.7730 (m) cc_final: 0.7442 (m) REVERT: C 132 ARG cc_start: 0.7883 (ttt-90) cc_final: 0.7548 (ttt-90) REVERT: C 159 GLU cc_start: 0.7332 (pp20) cc_final: 0.7021 (pp20) REVERT: C 211 ILE cc_start: 0.6080 (OUTLIER) cc_final: 0.5824 (tt) REVERT: C 236 LYS cc_start: 0.7874 (mtmt) cc_final: 0.7589 (mtmt) REVERT: C 253 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7593 (pm20) REVERT: C 349 VAL cc_start: 0.7236 (p) cc_final: 0.6870 (m) REVERT: C 356 LEU cc_start: 0.7791 (mt) cc_final: 0.7521 (mt) REVERT: C 506 LYS cc_start: 0.8136 (ptmt) cc_final: 0.7908 (ptmt) REVERT: C 529 ILE cc_start: 0.7971 (tp) cc_final: 0.7603 (tt) REVERT: E 229 ASN cc_start: 0.5841 (p0) cc_final: 0.5475 (p0) REVERT: H 80 ILE cc_start: 0.7822 (pt) cc_final: 0.7344 (pt) REVERT: H 161 VAL cc_start: 0.7935 (m) cc_final: 0.7650 (p) REVERT: H 191 THR cc_start: 0.7125 (t) cc_final: 0.6715 (m) REVERT: H 202 GLN cc_start: 0.7825 (mm-40) cc_final: 0.7543 (mm-40) REVERT: H 210 ARG cc_start: 0.7538 (tmm-80) cc_final: 0.7206 (tmm-80) REVERT: H 212 PHE cc_start: 0.6998 (t80) cc_final: 0.6784 (t80) REVERT: H 215 ARG cc_start: 0.7920 (tpp80) cc_final: 0.7415 (tpp-160) REVERT: H 252 LYS cc_start: 0.8521 (mmmm) cc_final: 0.8047 (mmtp) REVERT: H 253 ARG cc_start: 0.7712 (mtp85) cc_final: 0.6785 (mtp85) REVERT: H 292 ARG cc_start: 0.8339 (mtp-110) cc_final: 0.7912 (mtp180) REVERT: A 60 GLN cc_start: 0.7734 (mp10) cc_final: 0.7516 (mp10) REVERT: A 72 LYS cc_start: 0.6886 (mmmt) cc_final: 0.6683 (mmmt) REVERT: A 77 LEU cc_start: 0.8484 (tp) cc_final: 0.8006 (tt) REVERT: A 103 ASP cc_start: 0.7179 (t70) cc_final: 0.6808 (t70) REVERT: A 145 ASP cc_start: 0.7329 (t0) cc_final: 0.7104 (t0) REVERT: A 191 SER cc_start: 0.8529 (m) cc_final: 0.7911 (p) REVERT: A 227 LYS cc_start: 0.7572 (mmmt) cc_final: 0.6755 (mmmt) REVERT: A 357 SER cc_start: 0.8301 (t) cc_final: 0.8066 (p) REVERT: A 399 ASP cc_start: 0.7512 (t0) cc_final: 0.7236 (t0) REVERT: A 410 GLN cc_start: 0.8103 (mt0) cc_final: 0.7872 (mt0) REVERT: A 416 ARG cc_start: 0.8270 (ttm110) cc_final: 0.7804 (tpp80) REVERT: A 417 LEU cc_start: 0.8180 (tp) cc_final: 0.7845 (tp) REVERT: A 451 GLN cc_start: 0.8338 (mp10) cc_final: 0.8090 (mp10) REVERT: B 40 LYS cc_start: 0.7777 (ptpp) cc_final: 0.7356 (ptpp) REVERT: B 110 LEU cc_start: 0.8356 (tp) cc_final: 0.8054 (tp) REVERT: B 183 ILE cc_start: 0.8444 (mt) cc_final: 0.8175 (mt) REVERT: B 199 ASN cc_start: 0.7269 (m-40) cc_final: 0.6959 (m-40) REVERT: D 27 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8306 (mm) REVERT: D 145 ASP cc_start: 0.7356 (t0) cc_final: 0.7086 (t0) REVERT: D 197 MET cc_start: 0.7548 (mmm) cc_final: 0.6888 (tpt) REVERT: D 251 GLU cc_start: 0.5972 (tp30) cc_final: 0.5368 (tp30) REVERT: D 259 ASP cc_start: 0.7666 (m-30) cc_final: 0.7276 (m-30) REVERT: D 266 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7275 (tm-30) REVERT: D 270 LYS cc_start: 0.8103 (tppp) cc_final: 0.7175 (tppp) REVERT: D 398 ILE cc_start: 0.6901 (mt) cc_final: 0.6437 (mt) REVERT: D 425 GLN cc_start: 0.8682 (pp30) cc_final: 0.8223 (pp30) REVERT: D 444 ILE cc_start: 0.8316 (tp) cc_final: 0.8058 (tp) REVERT: D 471 LEU cc_start: 0.8809 (mt) cc_final: 0.8607 (mp) REVERT: D 473 GLU cc_start: 0.6600 (tp30) cc_final: 0.6157 (tp30) REVERT: D 532 ARG cc_start: 0.7574 (mmm-85) cc_final: 0.7295 (mmm-85) REVERT: F 76 SER cc_start: 0.7511 (t) cc_final: 0.6985 (p) REVERT: F 79 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.7681 (ptp) REVERT: F 82 SER cc_start: 0.7781 (t) cc_final: 0.7348 (m) REVERT: F 83 MET cc_start: 0.7721 (mmm) cc_final: 0.7506 (mmm) REVERT: F 115 ARG cc_start: 0.8496 (mtt90) cc_final: 0.8211 (mtt-85) REVERT: F 135 GLN cc_start: 0.8206 (mm-40) cc_final: 0.7927 (mp10) REVERT: F 147 MET cc_start: 0.7295 (ppp) cc_final: 0.6988 (ppp) REVERT: F 163 GLU cc_start: 0.6964 (tm-30) cc_final: 0.6730 (mm-30) REVERT: F 189 ASN cc_start: 0.8371 (p0) cc_final: 0.7896 (p0) REVERT: F 226 PHE cc_start: 0.8190 (m-80) cc_final: 0.7967 (m-10) REVERT: F 382 LEU cc_start: 0.8419 (mt) cc_final: 0.8176 (mt) REVERT: F 400 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7036 (mm-30) REVERT: F 404 HIS cc_start: 0.7417 (m170) cc_final: 0.6905 (m170) REVERT: F 409 TRP cc_start: 0.7976 (OUTLIER) cc_final: 0.7299 (m-10) REVERT: F 419 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8083 (ttmm) REVERT: F 520 GLU cc_start: 0.8114 (mp0) cc_final: 0.7730 (mp0) REVERT: F 524 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7585 (tm-30) REVERT: F 530 GLU cc_start: 0.7353 (mm-30) cc_final: 0.6818 (mm-30) outliers start: 74 outliers final: 50 residues processed: 611 average time/residue: 0.1810 time to fit residues: 169.3813 Evaluate side-chains 628 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 572 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 253 GLU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 489 GLU Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 222 HIS Chi-restraints excluded: chain H residue 15 ASP Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 59 GLU Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 220 ASN Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain H residue 271 ASP Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 79 MET Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 395 ILE Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain D residue 432 SER Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 464 SER Chi-restraints excluded: chain D residue 468 LEU Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain F residue 79 MET Chi-restraints excluded: chain F residue 136 ASN Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 409 TRP Chi-restraints excluded: chain F residue 419 LYS Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 476 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 40 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 267 optimal weight: 6.9990 chunk 171 optimal weight: 0.8980 chunk 249 optimal weight: 1.9990 chunk 272 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 137 optimal weight: 0.9980 chunk 214 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 299 HIS ** C 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 142 ASN H 201 HIS ** H 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 70 ASN A 143 ASN ** A 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 470 ASN ** D 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 470 ASN F 187 ASN F 431 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.177024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.141602 restraints weight = 35846.863| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 2.46 r_work: 0.3671 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 25349 Z= 0.163 Angle : 0.633 12.407 34882 Z= 0.330 Chirality : 0.042 0.299 4015 Planarity : 0.004 0.057 4066 Dihedral : 18.654 179.584 4527 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.22 % Favored : 90.61 % Rotamer: Outliers : 3.39 % Allowed : 16.95 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.06 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.16), residues: 2843 helix: 1.15 (0.15), residues: 1305 sheet: -0.98 (0.30), residues: 301 loop : -1.72 (0.18), residues: 1237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 150 TYR 0.016 0.001 TYR A 144 PHE 0.020 0.002 PHE D 331 TRP 0.020 0.002 TRP E 228 HIS 0.010 0.001 HIS C 514 Details of bonding type rmsd covalent geometry : bond 0.00367 (25342) covalent geometry : angle 0.63013 (34876) hydrogen bonds : bond 0.03793 ( 1057) hydrogen bonds : angle 4.32376 ( 3028) metal coordination : bond 0.00668 ( 7) metal coordination : angle 4.28556 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5686 Ramachandran restraints generated. 2843 Oldfield, 0 Emsley, 2843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5686 Ramachandran restraints generated. 2843 Oldfield, 0 Emsley, 2843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 585 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 99 SER cc_start: 0.7772 (m) cc_final: 0.7506 (m) REVERT: C 132 ARG cc_start: 0.7871 (ttt-90) cc_final: 0.7561 (ttt-90) REVERT: C 159 GLU cc_start: 0.7334 (pp20) cc_final: 0.7010 (pp20) REVERT: C 211 ILE cc_start: 0.6176 (OUTLIER) cc_final: 0.5944 (tt) REVERT: C 236 LYS cc_start: 0.7797 (mtmt) cc_final: 0.7509 (mtmt) REVERT: C 253 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7635 (pm20) REVERT: C 349 VAL cc_start: 0.7194 (p) cc_final: 0.6833 (m) REVERT: C 506 LYS cc_start: 0.8157 (ptmt) cc_final: 0.7917 (ptmt) REVERT: C 524 GLU cc_start: 0.6518 (tt0) cc_final: 0.6135 (tm-30) REVERT: C 529 ILE cc_start: 0.7969 (tp) cc_final: 0.7617 (tt) REVERT: E 229 ASN cc_start: 0.6023 (p0) cc_final: 0.5653 (p0) REVERT: H 80 ILE cc_start: 0.7835 (pt) cc_final: 0.7326 (pt) REVERT: H 161 VAL cc_start: 0.7917 (m) cc_final: 0.7607 (p) REVERT: H 191 THR cc_start: 0.7137 (t) cc_final: 0.6760 (m) REVERT: H 202 GLN cc_start: 0.7851 (mm-40) cc_final: 0.7563 (mm-40) REVERT: H 210 ARG cc_start: 0.7539 (tmm-80) cc_final: 0.7285 (tmm-80) REVERT: H 215 ARG cc_start: 0.7973 (tpp80) cc_final: 0.7448 (tpp-160) REVERT: H 252 LYS cc_start: 0.8536 (mmmm) cc_final: 0.8152 (mmtp) REVERT: H 253 ARG cc_start: 0.7739 (mtp85) cc_final: 0.6825 (mtp85) REVERT: H 292 ARG cc_start: 0.8285 (mtp-110) cc_final: 0.7858 (mtp180) REVERT: A 77 LEU cc_start: 0.8503 (tp) cc_final: 0.8049 (tt) REVERT: A 145 ASP cc_start: 0.7323 (t0) cc_final: 0.7106 (t0) REVERT: A 191 SER cc_start: 0.8511 (m) cc_final: 0.7877 (p) REVERT: A 227 LYS cc_start: 0.7618 (mmmt) cc_final: 0.6778 (mmmt) REVERT: A 357 SER cc_start: 0.8291 (t) cc_final: 0.8023 (p) REVERT: A 399 ASP cc_start: 0.7484 (t0) cc_final: 0.7234 (t0) REVERT: A 410 GLN cc_start: 0.8101 (mt0) cc_final: 0.7846 (mt0) REVERT: A 416 ARG cc_start: 0.8266 (ttm110) cc_final: 0.7759 (tpp80) REVERT: A 417 LEU cc_start: 0.8155 (tp) cc_final: 0.7789 (tp) REVERT: A 451 GLN cc_start: 0.8318 (mp10) cc_final: 0.8071 (mp10) REVERT: A 534 TRP cc_start: 0.6748 (t60) cc_final: 0.5610 (t60) REVERT: B 40 LYS cc_start: 0.7796 (ptpp) cc_final: 0.7380 (ptpp) REVERT: B 110 LEU cc_start: 0.8346 (tp) cc_final: 0.8052 (tp) REVERT: B 183 ILE cc_start: 0.8454 (mt) cc_final: 0.8164 (mt) REVERT: B 199 ASN cc_start: 0.7231 (m-40) cc_final: 0.6921 (m-40) REVERT: B 204 LYS cc_start: 0.7912 (ttmm) cc_final: 0.7608 (mtpp) REVERT: D 27 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8297 (mm) REVERT: D 145 ASP cc_start: 0.7350 (t0) cc_final: 0.7034 (t0) REVERT: D 164 ASP cc_start: 0.8321 (OUTLIER) cc_final: 0.7834 (m-30) REVERT: D 197 MET cc_start: 0.7358 (OUTLIER) cc_final: 0.6737 (tpt) REVERT: D 251 GLU cc_start: 0.6208 (tp30) cc_final: 0.5721 (tp30) REVERT: D 259 ASP cc_start: 0.7590 (m-30) cc_final: 0.7256 (m-30) REVERT: D 266 GLU cc_start: 0.7964 (tm-30) cc_final: 0.7336 (tm-30) REVERT: D 270 LYS cc_start: 0.8092 (tppp) cc_final: 0.7155 (tppp) REVERT: D 363 GLN cc_start: 0.8164 (tp40) cc_final: 0.7785 (tm-30) REVERT: D 398 ILE cc_start: 0.6929 (mt) cc_final: 0.6726 (mt) REVERT: D 444 ILE cc_start: 0.8297 (tp) cc_final: 0.8057 (tp) REVERT: D 473 GLU cc_start: 0.6446 (tp30) cc_final: 0.6059 (tp30) REVERT: D 532 ARG cc_start: 0.7561 (mmm-85) cc_final: 0.7348 (mmm-85) REVERT: F 76 SER cc_start: 0.7487 (t) cc_final: 0.6961 (p) REVERT: F 79 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.7661 (ptp) REVERT: F 82 SER cc_start: 0.7801 (t) cc_final: 0.7367 (m) REVERT: F 83 MET cc_start: 0.7664 (mmm) cc_final: 0.7418 (mmm) REVERT: F 89 ILE cc_start: 0.8438 (OUTLIER) cc_final: 0.8094 (mt) REVERT: F 99 SER cc_start: 0.7954 (m) cc_final: 0.7454 (p) REVERT: F 115 ARG cc_start: 0.8489 (mtt90) cc_final: 0.8065 (mtt-85) REVERT: F 135 GLN cc_start: 0.8212 (mm-40) cc_final: 0.7981 (mp10) REVERT: F 147 MET cc_start: 0.7255 (ppp) cc_final: 0.6908 (ppp) REVERT: F 189 ASN cc_start: 0.8344 (p0) cc_final: 0.7885 (p0) REVERT: F 382 LEU cc_start: 0.8398 (mt) cc_final: 0.8171 (mt) REVERT: F 409 TRP cc_start: 0.7989 (OUTLIER) cc_final: 0.7297 (m-10) REVERT: F 419 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8165 (ttpp) REVERT: F 448 LYS cc_start: 0.7748 (ptmm) cc_final: 0.7423 (ttpp) REVERT: F 520 GLU cc_start: 0.8031 (mp0) cc_final: 0.7681 (mp0) REVERT: F 524 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7586 (tm-30) REVERT: F 526 LYS cc_start: 0.8133 (mtpp) cc_final: 0.7896 (mtpp) REVERT: F 530 GLU cc_start: 0.7167 (mm-30) cc_final: 0.6699 (mm-30) outliers start: 79 outliers final: 55 residues processed: 613 average time/residue: 0.1904 time to fit residues: 178.1353 Evaluate side-chains 635 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 571 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 34 LYS Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 253 GLU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 222 HIS Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 59 GLU Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 85 LYS Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 220 ASN Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain H residue 257 SER Chi-restraints excluded: chain H residue 271 ASP Chi-restraints excluded: chain H residue 272 ILE Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 395 ILE Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain D residue 431 HIS Chi-restraints excluded: chain D residue 432 SER Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 464 SER Chi-restraints excluded: chain D residue 468 LEU Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain D residue 487 LEU Chi-restraints excluded: chain F residue 79 MET Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 136 ASN Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 409 TRP Chi-restraints excluded: chain F residue 419 LYS Chi-restraints excluded: chain F residue 428 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 262 optimal weight: 8.9990 chunk 237 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 chunk 264 optimal weight: 1.9990 chunk 206 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 79 optimal weight: 0.0040 chunk 54 optimal weight: 8.9990 chunk 67 optimal weight: 7.9990 chunk 97 optimal weight: 0.9990 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 276 ASN ** C 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 GLN H 64 HIS H 201 HIS ** H 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 410 GLN F 187 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.175865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.138801 restraints weight = 35942.020| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 2.52 r_work: 0.3666 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 25349 Z= 0.178 Angle : 0.655 12.889 34882 Z= 0.340 Chirality : 0.043 0.295 4015 Planarity : 0.004 0.057 4066 Dihedral : 18.640 179.167 4527 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.32 % Favored : 90.54 % Rotamer: Outliers : 3.26 % Allowed : 17.80 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.06 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.16), residues: 2843 helix: 1.15 (0.15), residues: 1308 sheet: -0.91 (0.30), residues: 306 loop : -1.70 (0.18), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 150 TYR 0.011 0.001 TYR A 490 PHE 0.021 0.002 PHE H 212 TRP 0.021 0.002 TRP E 228 HIS 0.009 0.001 HIS A 437 Details of bonding type rmsd covalent geometry : bond 0.00402 (25342) covalent geometry : angle 0.65261 (34876) hydrogen bonds : bond 0.03846 ( 1057) hydrogen bonds : angle 4.31343 ( 3028) metal coordination : bond 0.00739 ( 7) metal coordination : angle 4.30444 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5686 Ramachandran restraints generated. 2843 Oldfield, 0 Emsley, 2843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5686 Ramachandran restraints generated. 2843 Oldfield, 0 Emsley, 2843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 582 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 75 GLU cc_start: 0.7752 (tp30) cc_final: 0.7162 (tm-30) REVERT: C 159 GLU cc_start: 0.7343 (pp20) cc_final: 0.7041 (pp20) REVERT: C 236 LYS cc_start: 0.7810 (mtmt) cc_final: 0.7494 (mtmt) REVERT: C 253 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7660 (pm20) REVERT: C 349 VAL cc_start: 0.7185 (p) cc_final: 0.6826 (m) REVERT: C 506 LYS cc_start: 0.8173 (ptmt) cc_final: 0.7929 (ptmt) REVERT: C 529 ILE cc_start: 0.7983 (tp) cc_final: 0.7621 (tt) REVERT: E 229 ASN cc_start: 0.5960 (p0) cc_final: 0.5558 (p0) REVERT: H 47 THR cc_start: 0.7015 (OUTLIER) cc_final: 0.6693 (p) REVERT: H 161 VAL cc_start: 0.7908 (m) cc_final: 0.7606 (p) REVERT: H 191 THR cc_start: 0.7188 (t) cc_final: 0.6843 (m) REVERT: H 202 GLN cc_start: 0.7822 (mm-40) cc_final: 0.7506 (mm-40) REVERT: H 210 ARG cc_start: 0.7552 (tmm-80) cc_final: 0.7336 (tmm-80) REVERT: H 211 PHE cc_start: 0.7629 (m-10) cc_final: 0.6879 (m-10) REVERT: H 215 ARG cc_start: 0.7799 (tpp80) cc_final: 0.7429 (tpp-160) REVERT: H 252 LYS cc_start: 0.8526 (mmmm) cc_final: 0.8028 (mmtp) REVERT: H 253 ARG cc_start: 0.7773 (mtp85) cc_final: 0.7116 (mtp85) REVERT: H 269 ASN cc_start: 0.8131 (t0) cc_final: 0.7797 (t0) REVERT: H 292 ARG cc_start: 0.8304 (mtp-110) cc_final: 0.7889 (mtp180) REVERT: A 77 LEU cc_start: 0.8516 (tp) cc_final: 0.8068 (tt) REVERT: A 136 ASN cc_start: 0.7700 (p0) cc_final: 0.7446 (p0) REVERT: A 191 SER cc_start: 0.8482 (m) cc_final: 0.7835 (p) REVERT: A 227 LYS cc_start: 0.7479 (mmmt) cc_final: 0.6682 (mmmt) REVERT: A 229 TYR cc_start: 0.6794 (m-80) cc_final: 0.6591 (m-80) REVERT: A 410 GLN cc_start: 0.8012 (mt0) cc_final: 0.7757 (mt0) REVERT: A 416 ARG cc_start: 0.8284 (ttm110) cc_final: 0.7676 (tpp80) REVERT: A 534 TRP cc_start: 0.6840 (t60) cc_final: 0.5380 (t60) REVERT: A 536 ASP cc_start: 0.7943 (t0) cc_final: 0.7739 (t0) REVERT: B 40 LYS cc_start: 0.7798 (ptpp) cc_final: 0.7386 (ptpp) REVERT: B 110 LEU cc_start: 0.8331 (tp) cc_final: 0.8043 (tp) REVERT: B 183 ILE cc_start: 0.8458 (mt) cc_final: 0.8165 (mt) REVERT: B 199 ASN cc_start: 0.7224 (m-40) cc_final: 0.6916 (m-40) REVERT: B 216 ARG cc_start: 0.5963 (mtm-85) cc_final: 0.5551 (mtm-85) REVERT: D 27 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8289 (mm) REVERT: D 101 ILE cc_start: 0.8726 (OUTLIER) cc_final: 0.8447 (tt) REVERT: D 145 ASP cc_start: 0.7508 (t0) cc_final: 0.7209 (t0) REVERT: D 164 ASP cc_start: 0.8340 (OUTLIER) cc_final: 0.7852 (m-30) REVERT: D 197 MET cc_start: 0.7310 (OUTLIER) cc_final: 0.6825 (tpp) REVERT: D 251 GLU cc_start: 0.6304 (tp30) cc_final: 0.5476 (tp30) REVERT: D 259 ASP cc_start: 0.7609 (m-30) cc_final: 0.7265 (m-30) REVERT: D 266 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7289 (tm-30) REVERT: D 267 ILE cc_start: 0.8103 (tt) cc_final: 0.7822 (pt) REVERT: D 270 LYS cc_start: 0.8091 (tppp) cc_final: 0.7167 (tppp) REVERT: D 363 GLN cc_start: 0.8168 (tp40) cc_final: 0.7790 (tm-30) REVERT: D 398 ILE cc_start: 0.6985 (mt) cc_final: 0.6781 (mt) REVERT: D 444 ILE cc_start: 0.8290 (tp) cc_final: 0.8028 (tp) REVERT: D 467 VAL cc_start: 0.8569 (m) cc_final: 0.8335 (t) REVERT: D 473 GLU cc_start: 0.6417 (tp30) cc_final: 0.6057 (tp30) REVERT: D 532 ARG cc_start: 0.7594 (mmm-85) cc_final: 0.7293 (mmm-85) REVERT: F 76 SER cc_start: 0.7488 (t) cc_final: 0.6970 (p) REVERT: F 79 MET cc_start: 0.8247 (OUTLIER) cc_final: 0.7620 (ptp) REVERT: F 82 SER cc_start: 0.7806 (t) cc_final: 0.7376 (m) REVERT: F 83 MET cc_start: 0.7637 (mmm) cc_final: 0.7398 (mmm) REVERT: F 89 ILE cc_start: 0.8468 (OUTLIER) cc_final: 0.8109 (mt) REVERT: F 99 SER cc_start: 0.7921 (m) cc_final: 0.7468 (p) REVERT: F 115 ARG cc_start: 0.8507 (mtt90) cc_final: 0.8177 (mtt-85) REVERT: F 135 GLN cc_start: 0.8180 (mm-40) cc_final: 0.7955 (mp10) REVERT: F 147 MET cc_start: 0.7310 (ppp) cc_final: 0.6929 (ppp) REVERT: F 163 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6855 (mm-30) REVERT: F 189 ASN cc_start: 0.8312 (p0) cc_final: 0.7856 (p0) REVERT: F 246 PHE cc_start: 0.7135 (t80) cc_final: 0.6681 (t80) REVERT: F 382 LEU cc_start: 0.8412 (mt) cc_final: 0.8192 (mt) REVERT: F 409 TRP cc_start: 0.8019 (OUTLIER) cc_final: 0.7375 (m-10) REVERT: F 419 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8123 (ttpp) REVERT: F 520 GLU cc_start: 0.8022 (mp0) cc_final: 0.7676 (mp0) REVERT: F 524 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7563 (tm-30) REVERT: F 526 LYS cc_start: 0.8201 (mtpp) cc_final: 0.7940 (mtpp) REVERT: F 530 GLU cc_start: 0.7246 (mm-30) cc_final: 0.6745 (mm-30) outliers start: 76 outliers final: 54 residues processed: 613 average time/residue: 0.1882 time to fit residues: 175.0999 Evaluate side-chains 638 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 573 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 34 LYS Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 253 GLU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 222 HIS Chi-restraints excluded: chain E residue 227 GLN Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 59 GLU Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 85 LYS Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 145 LEU Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain H residue 271 ASP Chi-restraints excluded: chain H residue 272 ILE Chi-restraints excluded: chain H residue 275 LEU Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 395 ILE Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain D residue 431 HIS Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 468 LEU Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain D residue 487 LEU Chi-restraints excluded: chain F residue 79 MET Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 136 ASN Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 163 GLU Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 409 TRP Chi-restraints excluded: chain F residue 419 LYS Chi-restraints excluded: chain F residue 428 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 42 optimal weight: 0.5980 chunk 138 optimal weight: 0.8980 chunk 146 optimal weight: 0.0770 chunk 202 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 chunk 215 optimal weight: 0.0770 chunk 213 optimal weight: 0.0000 chunk 217 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 196 optimal weight: 0.1980 overall best weight: 0.1900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 135 GLN ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 ASN ** C 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 GLN H 201 HIS ** H 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 143 ASN ** A 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 ASN D 410 GLN D 411 GLN F 187 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.179727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.143318 restraints weight = 36091.491| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 2.53 r_work: 0.3724 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25349 Z= 0.119 Angle : 0.623 13.865 34882 Z= 0.322 Chirality : 0.041 0.311 4015 Planarity : 0.004 0.048 4066 Dihedral : 18.494 178.752 4527 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.72 % Favored : 91.14 % Rotamer: Outliers : 2.66 % Allowed : 18.70 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.06 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.17), residues: 2843 helix: 1.37 (0.15), residues: 1306 sheet: -0.84 (0.30), residues: 310 loop : -1.64 (0.18), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 62 TYR 0.014 0.001 TYR A 198 PHE 0.017 0.001 PHE D 331 TRP 0.027 0.001 TRP E 228 HIS 0.015 0.001 HIS C 514 Details of bonding type rmsd covalent geometry : bond 0.00260 (25342) covalent geometry : angle 0.62227 (34876) hydrogen bonds : bond 0.03385 ( 1057) hydrogen bonds : angle 4.17337 ( 3028) metal coordination : bond 0.00386 ( 7) metal coordination : angle 2.77411 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5686 Ramachandran restraints generated. 2843 Oldfield, 0 Emsley, 2843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5686 Ramachandran restraints generated. 2843 Oldfield, 0 Emsley, 2843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 573 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 ASP cc_start: 0.8264 (m-30) cc_final: 0.8042 (m-30) REVERT: C 106 GLN cc_start: 0.7034 (mt0) cc_final: 0.6533 (mt0) REVERT: C 133 LYS cc_start: 0.7860 (mmtp) cc_final: 0.7654 (mmmm) REVERT: C 159 GLU cc_start: 0.7338 (pp20) cc_final: 0.7000 (pp20) REVERT: C 211 ILE cc_start: 0.6003 (OUTLIER) cc_final: 0.5798 (tt) REVERT: C 236 LYS cc_start: 0.7699 (mtmt) cc_final: 0.7430 (mtmt) REVERT: C 253 GLU cc_start: 0.7993 (pt0) cc_final: 0.7610 (pm20) REVERT: C 257 ASN cc_start: 0.7804 (t0) cc_final: 0.7452 (t0) REVERT: C 349 VAL cc_start: 0.7034 (p) cc_final: 0.6695 (m) REVERT: C 351 LYS cc_start: 0.6714 (pptt) cc_final: 0.6502 (pttt) REVERT: C 506 LYS cc_start: 0.8140 (ptmt) cc_final: 0.7903 (ptmt) REVERT: C 529 ILE cc_start: 0.7863 (tp) cc_final: 0.7539 (tt) REVERT: E 229 ASN cc_start: 0.6100 (p0) cc_final: 0.5537 (p0) REVERT: H 47 THR cc_start: 0.7000 (OUTLIER) cc_final: 0.6679 (p) REVERT: H 62 LYS cc_start: 0.8155 (tttt) cc_final: 0.7771 (tttt) REVERT: H 130 LYS cc_start: 0.8228 (ttmm) cc_final: 0.7708 (ttpp) REVERT: H 161 VAL cc_start: 0.7750 (m) cc_final: 0.7441 (p) REVERT: H 191 THR cc_start: 0.7062 (t) cc_final: 0.6722 (m) REVERT: H 202 GLN cc_start: 0.7762 (mm-40) cc_final: 0.7505 (mm-40) REVERT: H 215 ARG cc_start: 0.7793 (tpp80) cc_final: 0.7398 (tpp-160) REVERT: H 252 LYS cc_start: 0.8526 (mmmm) cc_final: 0.8093 (mmtp) REVERT: H 269 ASN cc_start: 0.8092 (t0) cc_final: 0.7759 (t0) REVERT: A 77 LEU cc_start: 0.8479 (tp) cc_final: 0.7872 (tp) REVERT: A 130 GLU cc_start: 0.6552 (mt-10) cc_final: 0.6283 (mt-10) REVERT: A 191 SER cc_start: 0.8441 (m) cc_final: 0.7811 (p) REVERT: A 229 TYR cc_start: 0.6636 (m-80) cc_final: 0.6345 (m-80) REVERT: A 361 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7399 (mp) REVERT: A 378 ARG cc_start: 0.7801 (mmt90) cc_final: 0.7477 (mmt90) REVERT: A 399 ASP cc_start: 0.7411 (t0) cc_final: 0.7205 (t0) REVERT: A 410 GLN cc_start: 0.7967 (mt0) cc_final: 0.7632 (mt0) REVERT: A 417 LEU cc_start: 0.8161 (tp) cc_final: 0.7807 (tp) REVERT: A 436 CYS cc_start: 0.8709 (t) cc_final: 0.8319 (p) REVERT: A 534 TRP cc_start: 0.6735 (t60) cc_final: 0.5545 (t60) REVERT: B 40 LYS cc_start: 0.7773 (ptpp) cc_final: 0.7344 (ptpp) REVERT: B 110 LEU cc_start: 0.8294 (tp) cc_final: 0.8075 (tp) REVERT: B 183 ILE cc_start: 0.8409 (mt) cc_final: 0.8114 (mt) REVERT: B 199 ASN cc_start: 0.7091 (m-40) cc_final: 0.6803 (m-40) REVERT: D 27 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8215 (mm) REVERT: D 145 ASP cc_start: 0.7422 (t0) cc_final: 0.6994 (t0) REVERT: D 163 GLU cc_start: 0.7203 (tp30) cc_final: 0.6955 (tp30) REVERT: D 164 ASP cc_start: 0.8274 (OUTLIER) cc_final: 0.7554 (m-30) REVERT: D 197 MET cc_start: 0.7283 (OUTLIER) cc_final: 0.6865 (tpp) REVERT: D 259 ASP cc_start: 0.7527 (m-30) cc_final: 0.7177 (m-30) REVERT: D 266 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7289 (tm-30) REVERT: D 267 ILE cc_start: 0.8014 (tt) cc_final: 0.7539 (pt) REVERT: D 270 LYS cc_start: 0.8056 (tppp) cc_final: 0.7113 (tppp) REVERT: D 271 GLU cc_start: 0.7692 (tt0) cc_final: 0.7485 (tt0) REVERT: D 363 GLN cc_start: 0.8065 (tp40) cc_final: 0.7693 (tm-30) REVERT: D 411 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.8324 (tt0) REVERT: D 444 ILE cc_start: 0.8281 (tp) cc_final: 0.7975 (tp) REVERT: D 467 VAL cc_start: 0.8532 (m) cc_final: 0.8299 (t) REVERT: D 473 GLU cc_start: 0.6385 (tp30) cc_final: 0.6072 (tp30) REVERT: D 510 THR cc_start: 0.7127 (p) cc_final: 0.6618 (t) REVERT: D 532 ARG cc_start: 0.7469 (mmm-85) cc_final: 0.7269 (mmm-85) REVERT: F 76 SER cc_start: 0.7650 (t) cc_final: 0.7164 (p) REVERT: F 82 SER cc_start: 0.7877 (t) cc_final: 0.7427 (m) REVERT: F 83 MET cc_start: 0.7543 (mmm) cc_final: 0.7310 (mmm) REVERT: F 89 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.7997 (mt) REVERT: F 99 SER cc_start: 0.7828 (m) cc_final: 0.7355 (p) REVERT: F 115 ARG cc_start: 0.8438 (mtt90) cc_final: 0.8099 (mtt-85) REVERT: F 163 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6897 (mm-30) REVERT: F 187 ASN cc_start: 0.7359 (t0) cc_final: 0.7137 (t0) REVERT: F 189 ASN cc_start: 0.8307 (p0) cc_final: 0.7827 (p0) REVERT: F 246 PHE cc_start: 0.7047 (t80) cc_final: 0.6660 (t80) REVERT: F 382 LEU cc_start: 0.8363 (mt) cc_final: 0.8136 (mt) REVERT: F 409 TRP cc_start: 0.7904 (OUTLIER) cc_final: 0.7309 (m-10) REVERT: F 419 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8063 (ttpp) REVERT: F 520 GLU cc_start: 0.7954 (mp0) cc_final: 0.7557 (mp0) REVERT: F 524 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7554 (tm-30) REVERT: F 526 LYS cc_start: 0.8168 (mtpp) cc_final: 0.7929 (mtpp) REVERT: F 530 GLU cc_start: 0.7174 (mm-30) cc_final: 0.6650 (mm-30) outliers start: 62 outliers final: 39 residues processed: 595 average time/residue: 0.1832 time to fit residues: 165.2854 Evaluate side-chains 611 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 561 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain E residue 222 HIS Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 59 GLU Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 85 LYS Chi-restraints excluded: chain H residue 145 LEU Chi-restraints excluded: chain H residue 220 ASN Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain H residue 271 ASP Chi-restraints excluded: chain H residue 272 ILE Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 411 GLN Chi-restraints excluded: chain D residue 431 HIS Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 468 LEU Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain D residue 487 LEU Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 136 ASN Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 163 GLU Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 409 TRP Chi-restraints excluded: chain F residue 419 LYS Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 454 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 52 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 164 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 68 optimal weight: 9.9990 chunk 180 optimal weight: 0.9980 chunk 94 optimal weight: 0.3980 chunk 182 optimal weight: 10.0000 chunk 228 optimal weight: 0.6980 chunk 156 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 ASN ** C 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 434 GLN ** A 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 411 GLN ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.175942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.138941 restraints weight = 36214.638| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 2.57 r_work: 0.3666 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 25349 Z= 0.178 Angle : 0.659 13.955 34882 Z= 0.342 Chirality : 0.043 0.297 4015 Planarity : 0.004 0.056 4066 Dihedral : 18.516 178.437 4527 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.00 % Favored : 90.85 % Rotamer: Outliers : 2.40 % Allowed : 19.31 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.06 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.16), residues: 2843 helix: 1.31 (0.15), residues: 1308 sheet: -0.75 (0.30), residues: 304 loop : -1.69 (0.18), residues: 1231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 342 TYR 0.016 0.001 TYR F 137 PHE 0.021 0.002 PHE B 153 TRP 0.017 0.002 TRP C 223 HIS 0.012 0.001 HIS C 514 Details of bonding type rmsd covalent geometry : bond 0.00400 (25342) covalent geometry : angle 0.65765 (34876) hydrogen bonds : bond 0.03810 ( 1057) hydrogen bonds : angle 4.23305 ( 3028) metal coordination : bond 0.00790 ( 7) metal coordination : angle 3.81338 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5686 Ramachandran restraints generated. 2843 Oldfield, 0 Emsley, 2843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5686 Ramachandran restraints generated. 2843 Oldfield, 0 Emsley, 2843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 575 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 133 LYS cc_start: 0.7882 (mmtp) cc_final: 0.7662 (mmmm) REVERT: C 159 GLU cc_start: 0.7353 (pp20) cc_final: 0.6809 (pp20) REVERT: C 197 MET cc_start: 0.7640 (ttp) cc_final: 0.7427 (ttp) REVERT: C 211 ILE cc_start: 0.6140 (OUTLIER) cc_final: 0.5908 (tt) REVERT: C 236 LYS cc_start: 0.7740 (mtmt) cc_final: 0.7510 (mtmt) REVERT: C 253 GLU cc_start: 0.8076 (pt0) cc_final: 0.7698 (pm20) REVERT: C 257 ASN cc_start: 0.7850 (t0) cc_final: 0.7517 (t0) REVERT: C 349 VAL cc_start: 0.7041 (p) cc_final: 0.6710 (m) REVERT: C 506 LYS cc_start: 0.8170 (ptmt) cc_final: 0.7944 (ptmt) REVERT: C 527 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7287 (tt) REVERT: C 529 ILE cc_start: 0.7941 (tp) cc_final: 0.7615 (tt) REVERT: E 229 ASN cc_start: 0.6026 (p0) cc_final: 0.5437 (p0) REVERT: H 47 THR cc_start: 0.6972 (OUTLIER) cc_final: 0.6672 (p) REVERT: H 80 ILE cc_start: 0.7763 (pt) cc_final: 0.7210 (pt) REVERT: H 130 LYS cc_start: 0.8239 (ttmm) cc_final: 0.7888 (ttpt) REVERT: H 161 VAL cc_start: 0.7920 (m) cc_final: 0.7629 (p) REVERT: H 191 THR cc_start: 0.7118 (t) cc_final: 0.6789 (m) REVERT: H 215 ARG cc_start: 0.7846 (tpp80) cc_final: 0.7270 (tpp-160) REVERT: H 252 LYS cc_start: 0.8584 (mmmm) cc_final: 0.8198 (mmtp) REVERT: H 269 ASN cc_start: 0.8161 (t0) cc_final: 0.7779 (t0) REVERT: A 77 LEU cc_start: 0.8519 (tp) cc_final: 0.8072 (tt) REVERT: A 103 ASP cc_start: 0.6902 (t70) cc_final: 0.6475 (t70) REVERT: A 191 SER cc_start: 0.8401 (m) cc_final: 0.7775 (p) REVERT: A 227 LYS cc_start: 0.7429 (mmmt) cc_final: 0.6665 (mmmt) REVERT: A 229 TYR cc_start: 0.6833 (m-80) cc_final: 0.6564 (m-80) REVERT: A 361 LEU cc_start: 0.7889 (mm) cc_final: 0.7569 (mp) REVERT: A 410 GLN cc_start: 0.8004 (mt0) cc_final: 0.7712 (mt0) REVERT: A 416 ARG cc_start: 0.8480 (tpp80) cc_final: 0.8112 (tpp80) REVERT: A 417 LEU cc_start: 0.8140 (tp) cc_final: 0.7810 (tp) REVERT: A 436 CYS cc_start: 0.8718 (t) cc_final: 0.8371 (p) REVERT: A 534 TRP cc_start: 0.6852 (t60) cc_final: 0.5428 (t60) REVERT: B 74 PHE cc_start: 0.6947 (t80) cc_final: 0.6649 (t80) REVERT: B 110 LEU cc_start: 0.8316 (tp) cc_final: 0.7954 (tp) REVERT: B 183 ILE cc_start: 0.8460 (mt) cc_final: 0.8164 (mt) REVERT: B 225 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7761 (tp) REVERT: D 27 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8265 (mm) REVERT: D 145 ASP cc_start: 0.7453 (t0) cc_final: 0.7162 (t0) REVERT: D 259 ASP cc_start: 0.7624 (m-30) cc_final: 0.7282 (m-30) REVERT: D 266 GLU cc_start: 0.7958 (tm-30) cc_final: 0.7629 (mm-30) REVERT: D 267 ILE cc_start: 0.8040 (tt) cc_final: 0.7746 (pt) REVERT: D 270 LYS cc_start: 0.8111 (tppp) cc_final: 0.7194 (tppp) REVERT: D 271 GLU cc_start: 0.7696 (tt0) cc_final: 0.7473 (tt0) REVERT: D 328 MET cc_start: 0.7042 (mmm) cc_final: 0.6820 (mtm) REVERT: D 363 GLN cc_start: 0.8112 (tp40) cc_final: 0.7749 (tm-30) REVERT: D 411 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.8550 (tt0) REVERT: D 444 ILE cc_start: 0.8322 (tp) cc_final: 0.8046 (tp) REVERT: D 473 GLU cc_start: 0.6489 (tp30) cc_final: 0.6170 (tp30) REVERT: F 76 SER cc_start: 0.7497 (t) cc_final: 0.6962 (p) REVERT: F 82 SER cc_start: 0.7920 (t) cc_final: 0.7490 (m) REVERT: F 83 MET cc_start: 0.7571 (mmm) cc_final: 0.7331 (mmm) REVERT: F 89 ILE cc_start: 0.8446 (OUTLIER) cc_final: 0.8105 (mt) REVERT: F 99 SER cc_start: 0.7935 (m) cc_final: 0.7423 (p) REVERT: F 115 ARG cc_start: 0.8533 (mtt90) cc_final: 0.8273 (mtt-85) REVERT: F 147 MET cc_start: 0.7335 (ppp) cc_final: 0.6983 (ppp) REVERT: F 163 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6933 (mm-30) REVERT: F 189 ASN cc_start: 0.8265 (p0) cc_final: 0.7763 (p0) REVERT: F 382 LEU cc_start: 0.8400 (mt) cc_final: 0.8179 (mt) REVERT: F 409 TRP cc_start: 0.8004 (OUTLIER) cc_final: 0.7369 (m-10) REVERT: F 419 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8086 (ttpp) REVERT: F 520 GLU cc_start: 0.8039 (mp0) cc_final: 0.7640 (mp0) REVERT: F 524 GLU cc_start: 0.8052 (tm-30) cc_final: 0.7608 (tm-30) REVERT: F 530 GLU cc_start: 0.7277 (mm-30) cc_final: 0.6748 (mm-30) outliers start: 56 outliers final: 40 residues processed: 598 average time/residue: 0.1898 time to fit residues: 172.1625 Evaluate side-chains 617 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 567 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 222 HIS Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 145 LEU Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain H residue 271 ASP Chi-restraints excluded: chain H residue 272 ILE Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain D residue 411 GLN Chi-restraints excluded: chain D residue 431 HIS Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 468 LEU Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain D residue 487 LEU Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 136 ASN Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 163 GLU Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 409 TRP Chi-restraints excluded: chain F residue 419 LYS Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 454 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 192 optimal weight: 0.9990 chunk 162 optimal weight: 1.9990 chunk 45 optimal weight: 0.2980 chunk 239 optimal weight: 0.5980 chunk 20 optimal weight: 0.2980 chunk 72 optimal weight: 0.9990 chunk 286 optimal weight: 0.9980 chunk 26 optimal weight: 8.9990 chunk 55 optimal weight: 9.9990 chunk 164 optimal weight: 0.9980 chunk 198 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 201 HIS ** H 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 411 GLN ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 187 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.177391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.140652 restraints weight = 36077.423| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 2.54 r_work: 0.3691 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25349 Z= 0.141 Angle : 0.643 14.169 34882 Z= 0.332 Chirality : 0.042 0.303 4015 Planarity : 0.004 0.053 4066 Dihedral : 18.434 178.147 4527 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.79 % Favored : 91.07 % Rotamer: Outliers : 2.40 % Allowed : 19.43 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.06 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.16), residues: 2843 helix: 1.37 (0.15), residues: 1308 sheet: -0.66 (0.31), residues: 304 loop : -1.68 (0.18), residues: 1231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 342 TYR 0.015 0.001 TYR A 198 PHE 0.016 0.001 PHE H 262 TRP 0.044 0.002 TRP F 534 HIS 0.015 0.001 HIS H 201 Details of bonding type rmsd covalent geometry : bond 0.00320 (25342) covalent geometry : angle 0.64175 (34876) hydrogen bonds : bond 0.03545 ( 1057) hydrogen bonds : angle 4.18476 ( 3028) metal coordination : bond 0.00562 ( 7) metal coordination : angle 3.18612 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5686 Ramachandran restraints generated. 2843 Oldfield, 0 Emsley, 2843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5686 Ramachandran restraints generated. 2843 Oldfield, 0 Emsley, 2843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 559 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 159 GLU cc_start: 0.7330 (pp20) cc_final: 0.6819 (pp20) REVERT: C 197 MET cc_start: 0.7553 (ttp) cc_final: 0.7276 (ttp) REVERT: C 211 ILE cc_start: 0.6066 (OUTLIER) cc_final: 0.5852 (tt) REVERT: C 236 LYS cc_start: 0.7768 (mtmt) cc_final: 0.7501 (mtmt) REVERT: C 253 GLU cc_start: 0.8050 (pt0) cc_final: 0.7674 (pm20) REVERT: C 257 ASN cc_start: 0.7732 (t0) cc_final: 0.7408 (t0) REVERT: C 349 VAL cc_start: 0.7006 (p) cc_final: 0.6684 (m) REVERT: C 506 LYS cc_start: 0.8167 (ptmt) cc_final: 0.7939 (ptmt) REVERT: C 527 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7255 (tt) REVERT: C 529 ILE cc_start: 0.7927 (tp) cc_final: 0.7586 (tt) REVERT: E 229 ASN cc_start: 0.6123 (p0) cc_final: 0.5615 (p0) REVERT: H 47 THR cc_start: 0.6951 (OUTLIER) cc_final: 0.6665 (p) REVERT: H 130 LYS cc_start: 0.8240 (ttmm) cc_final: 0.7924 (ttpt) REVERT: H 161 VAL cc_start: 0.7824 (m) cc_final: 0.7526 (p) REVERT: H 191 THR cc_start: 0.7095 (t) cc_final: 0.6749 (m) REVERT: H 252 LYS cc_start: 0.8571 (mmmm) cc_final: 0.8198 (mmtp) REVERT: H 253 ARG cc_start: 0.7712 (mtp85) cc_final: 0.7044 (mtp85) REVERT: H 269 ASN cc_start: 0.8135 (t0) cc_final: 0.7731 (t0) REVERT: A 77 LEU cc_start: 0.8489 (tp) cc_final: 0.7926 (tp) REVERT: A 103 ASP cc_start: 0.6824 (t70) cc_final: 0.6411 (t70) REVERT: A 191 SER cc_start: 0.8410 (m) cc_final: 0.7774 (p) REVERT: A 229 TYR cc_start: 0.6769 (m-80) cc_final: 0.6527 (m-80) REVERT: A 339 LYS cc_start: 0.7527 (mmtt) cc_final: 0.6735 (mttt) REVERT: A 410 GLN cc_start: 0.7988 (mt0) cc_final: 0.7639 (mt0) REVERT: A 416 ARG cc_start: 0.8459 (tpp80) cc_final: 0.8080 (tpp80) REVERT: A 417 LEU cc_start: 0.8184 (tp) cc_final: 0.7863 (tp) REVERT: A 436 CYS cc_start: 0.8694 (t) cc_final: 0.8279 (p) REVERT: A 534 TRP cc_start: 0.6791 (t60) cc_final: 0.5377 (t60) REVERT: B 114 LEU cc_start: 0.8274 (mp) cc_final: 0.8044 (mt) REVERT: B 183 ILE cc_start: 0.8457 (mt) cc_final: 0.8157 (mt) REVERT: B 225 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7634 (tt) REVERT: D 27 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8253 (mm) REVERT: D 145 ASP cc_start: 0.7393 (t0) cc_final: 0.7089 (t0) REVERT: D 164 ASP cc_start: 0.8254 (t70) cc_final: 0.7606 (m-30) REVERT: D 197 MET cc_start: 0.7209 (OUTLIER) cc_final: 0.6848 (tpp) REVERT: D 259 ASP cc_start: 0.7565 (m-30) cc_final: 0.7229 (m-30) REVERT: D 266 GLU cc_start: 0.7943 (tm-30) cc_final: 0.7610 (mm-30) REVERT: D 267 ILE cc_start: 0.8018 (tt) cc_final: 0.7740 (pt) REVERT: D 270 LYS cc_start: 0.8100 (tppp) cc_final: 0.7182 (tppp) REVERT: D 271 GLU cc_start: 0.7654 (tt0) cc_final: 0.7431 (tt0) REVERT: D 363 GLN cc_start: 0.8044 (tp40) cc_final: 0.7781 (tm-30) REVERT: D 398 ILE cc_start: 0.6895 (mt) cc_final: 0.6494 (mm) REVERT: D 411 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.8449 (tt0) REVERT: D 444 ILE cc_start: 0.8306 (tp) cc_final: 0.8007 (tp) REVERT: D 467 VAL cc_start: 0.8551 (m) cc_final: 0.8337 (t) REVERT: D 473 GLU cc_start: 0.6414 (tp30) cc_final: 0.6114 (tp30) REVERT: D 531 LYS cc_start: 0.8104 (ttpp) cc_final: 0.7864 (ttpp) REVERT: D 532 ARG cc_start: 0.7559 (mmm-85) cc_final: 0.6848 (mmm-85) REVERT: F 76 SER cc_start: 0.7462 (t) cc_final: 0.6936 (p) REVERT: F 79 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.7545 (ptp) REVERT: F 82 SER cc_start: 0.7865 (t) cc_final: 0.7392 (m) REVERT: F 83 MET cc_start: 0.7519 (mmm) cc_final: 0.7275 (mmm) REVERT: F 89 ILE cc_start: 0.8427 (OUTLIER) cc_final: 0.8080 (mt) REVERT: F 99 SER cc_start: 0.7886 (m) cc_final: 0.7375 (p) REVERT: F 115 ARG cc_start: 0.8450 (mtt90) cc_final: 0.8132 (mtt-85) REVERT: F 163 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.6948 (mm-30) REVERT: F 187 ASN cc_start: 0.7286 (t0) cc_final: 0.7070 (t0) REVERT: F 189 ASN cc_start: 0.8235 (p0) cc_final: 0.7736 (p0) REVERT: F 270 LYS cc_start: 0.8870 (mtmt) cc_final: 0.8397 (mtmt) REVERT: F 307 LYS cc_start: 0.7935 (mmtt) cc_final: 0.7561 (mmtt) REVERT: F 409 TRP cc_start: 0.8055 (OUTLIER) cc_final: 0.7456 (m-10) REVERT: F 419 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8030 (ttpp) REVERT: F 520 GLU cc_start: 0.7981 (mp0) cc_final: 0.7593 (mp0) REVERT: F 524 GLU cc_start: 0.8020 (tm-30) cc_final: 0.7589 (tm-30) REVERT: F 530 GLU cc_start: 0.7167 (mm-30) cc_final: 0.6652 (mm-30) outliers start: 56 outliers final: 39 residues processed: 580 average time/residue: 0.1910 time to fit residues: 168.7966 Evaluate side-chains 608 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 557 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 222 HIS Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 145 LEU Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain H residue 271 ASP Chi-restraints excluded: chain H residue 272 ILE Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 135 GLN Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain D residue 411 GLN Chi-restraints excluded: chain D residue 431 HIS Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 468 LEU Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain D residue 487 LEU Chi-restraints excluded: chain F residue 79 MET Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 136 ASN Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 163 GLU Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 409 TRP Chi-restraints excluded: chain F residue 419 LYS Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 454 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 161 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 123 optimal weight: 0.9990 chunk 290 optimal weight: 1.9990 chunk 148 optimal weight: 0.9980 chunk 256 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 288 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 246 optimal weight: 0.0070 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 201 HIS ** H 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 ASN D 411 GLN ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.176602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.140050 restraints weight = 36031.857| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 2.52 r_work: 0.3670 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25349 Z= 0.151 Angle : 0.645 14.155 34882 Z= 0.332 Chirality : 0.042 0.301 4015 Planarity : 0.004 0.053 4066 Dihedral : 18.410 178.012 4527 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.00 % Favored : 90.89 % Rotamer: Outliers : 2.62 % Allowed : 19.48 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.06 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.16), residues: 2843 helix: 1.34 (0.15), residues: 1317 sheet: -0.70 (0.31), residues: 307 loop : -1.71 (0.18), residues: 1219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 342 TYR 0.019 0.001 TYR A 198 PHE 0.020 0.001 PHE H 262 TRP 0.024 0.002 TRP F 534 HIS 0.013 0.001 HIS H 201 Details of bonding type rmsd covalent geometry : bond 0.00342 (25342) covalent geometry : angle 0.64355 (34876) hydrogen bonds : bond 0.03579 ( 1057) hydrogen bonds : angle 4.16154 ( 3028) metal coordination : bond 0.00658 ( 7) metal coordination : angle 3.36276 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7225.40 seconds wall clock time: 124 minutes 22.74 seconds (7462.74 seconds total)