Starting phenix.real_space_refine on Fri Aug 7 14:07:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w1e_65528/08_2026/9w1e_65528_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w1e_65528/08_2026/9w1e_65528.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9w1e_65528/08_2026/9w1e_65528.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w1e_65528/08_2026/9w1e_65528.map" model { file = "/net/cci-nas-00/data/ceres_data/9w1e_65528/08_2026/9w1e_65528_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w1e_65528/08_2026/9w1e_65528_trim.cif" } resolution = 2.74 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= 0.002 sd= 0.032 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: 7 Type Number sf(0) Gaussians Zn 6 6.06 5 P 24 5.49 5 Mg 6 5.21 5 S 86 5.16 5 C 13513 2.51 5 N 3936 2.21 5 O 3934 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21505 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4735 Classifications: {'peptide': 605} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 563} Chain breaks: 1 Chain: "B" Number of atoms: 4697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4697 Classifications: {'peptide': 600} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 558} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 2980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2980 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 355} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 3005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3005 Classifications: {'peptide': 388} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 359} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 2892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2892 Classifications: {'peptide': 372} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 347} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 2866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2866 Classifications: {'peptide': 369} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 344} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "X" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 132 Classifications: {'RNA': 6} Modifications used: {'rna2p_pur': 6} Link IDs: {'rna2p': 5} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.90, per 1000 atoms: 0.23 Number of scatterers: 21505 At special positions: 0 Unit cell: (97.86, 125.82, 175.216, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 6 29.99 S 86 16.00 P 24 15.00 Mg 6 11.99 O 3934 8.00 N 3936 7.00 C 13513 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: 1.74 Conformation dependent library (CDL) restraints added in 950.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 702 " pdb="ZN ZN A 702 " - pdb=" NE2 HIS A 260 " pdb="ZN ZN A 702 " - pdb=" NE2 HIS A 262 " pdb=" ZN B 702 " pdb="ZN ZN B 702 " - pdb=" NE2 HIS B 260 " pdb="ZN ZN B 702 " - pdb=" NE2 HIS B 262 " pdb="ZN ZN B 702 " - pdb=" NE2 HIS B 461 " pdb=" ZN C 702 " pdb="ZN ZN C 702 " - pdb=" NE2 HIS C 260 " pdb="ZN ZN C 702 " - pdb=" NE2 HIS C 262 " pdb="ZN ZN C 702 " - pdb=" NE2 HIS C 461 " pdb=" ZN D 702 " pdb="ZN ZN D 702 " - pdb=" NE2 HIS D 260 " pdb="ZN ZN D 702 " - pdb=" NE2 HIS D 262 " pdb="ZN ZN D 702 " - pdb=" NE2 HIS D 461 " pdb=" ZN E 702 " pdb="ZN ZN E 702 " - pdb=" NE2 HIS E 260 " pdb="ZN ZN E 702 " - pdb=" NE2 HIS E 262 " pdb="ZN ZN E 702 " - pdb=" NE2 HIS E 461 " pdb=" ZN F 702 " pdb="ZN ZN F 702 " - pdb=" NE2 HIS F 260 " pdb="ZN ZN F 702 " - pdb=" NE2 HIS F 262 " pdb="ZN ZN F 702 " - pdb=" NE2 HIS F 461 " 5388 Ramachandran restraints generated. 2694 Oldfield, 0 Emsley, 2694 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5108 Finding SS restraints... Secondary structure from input PDB file: 141 helices and 9 sheets defined 53.9% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 13 through 19 Processing helix chain 'A' and resid 20 through 21 No H-bonds generated for 'chain 'A' and resid 20 through 21' Processing helix chain 'A' and resid 22 through 26 removed outlier: 4.006A pdb=" N GLN A 25 " --> pdb=" O LEU A 22 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY A 26 " --> pdb=" O GLY A 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 22 through 26' Processing helix chain 'A' and resid 40 through 44 Processing helix chain 'A' and resid 46 through 54 removed outlier: 3.615A pdb=" N GLU A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 91 removed outlier: 3.522A pdb=" N HIS A 76 " --> pdb=" O SER A 72 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 95 No H-bonds generated for 'chain 'A' and resid 93 through 95' Processing helix chain 'A' and resid 105 through 119 Processing helix chain 'A' and resid 143 through 152 removed outlier: 3.648A pdb=" N ALA A 152 " --> pdb=" O GLU A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 178 Processing helix chain 'A' and resid 196 through 211 removed outlier: 4.036A pdb=" N GLN A 200 " --> pdb=" O MET A 196 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N HIS A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 230 Processing helix chain 'A' and resid 231 through 239 Processing helix chain 'A' and resid 247 through 254 Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.561A pdb=" N HIS A 274 " --> pdb=" O GLY A 270 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU A 279 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 305 through 313 removed outlier: 4.218A pdb=" N ARG A 309 " --> pdb=" O ILE A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 323 removed outlier: 3.877A pdb=" N LYS A 323 " --> pdb=" O ALA A 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 320 through 323' Processing helix chain 'A' and resid 324 through 342 Processing helix chain 'A' and resid 352 through 357 Processing helix chain 'A' and resid 362 through 381 removed outlier: 3.616A pdb=" N THR A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 400 Processing helix chain 'A' and resid 402 through 420 removed outlier: 3.589A pdb=" N GLU A 418 " --> pdb=" O ILE A 414 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TRP A 420 " --> pdb=" O ALA A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 435 removed outlier: 3.791A pdb=" N GLU A 435 " --> pdb=" O ALA A 432 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 432 through 435' Processing helix chain 'A' and resid 436 through 446 Processing helix chain 'A' and resid 448 through 455 Processing helix chain 'A' and resid 467 through 477 Processing helix chain 'A' and resid 488 through 491 removed outlier: 3.779A pdb=" N ARG A 491 " --> pdb=" O HIS A 488 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 488 through 491' Processing helix chain 'A' and resid 492 through 503 Processing helix chain 'A' and resid 509 through 517 Processing helix chain 'A' and resid 533 through 540 Processing helix chain 'A' and resid 556 through 568 removed outlier: 4.188A pdb=" N ALA A 565 " --> pdb=" O LEU A 561 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ARG A 566 " --> pdb=" O LEU A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 586 Processing helix chain 'A' and resid 590 through 602 Processing helix chain 'B' and resid 13 through 19 Processing helix chain 'B' and resid 39 through 54 removed outlier: 4.567A pdb=" N GLY B 43 " --> pdb=" O LYS B 39 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU B 45 " --> pdb=" O SER B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 90 removed outlier: 3.523A pdb=" N VAL B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 119 removed outlier: 3.940A pdb=" N GLN B 113 " --> pdb=" O SER B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 151 removed outlier: 3.778A pdb=" N ILE B 151 " --> pdb=" O VAL B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 173 removed outlier: 3.804A pdb=" N LEU B 172 " --> pdb=" O GLN B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 213 removed outlier: 3.855A pdb=" N GLN B 200 " --> pdb=" O MET B 196 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG B 210 " --> pdb=" O LEU B 206 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N HIS B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 230 Processing helix chain 'B' and resid 231 through 240 removed outlier: 3.714A pdb=" N HIS B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU B 240 " --> pdb=" O ARG B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 254 Processing helix chain 'B' and resid 270 through 279 removed outlier: 3.731A pdb=" N GLU B 279 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 286 Processing helix chain 'B' and resid 305 through 313 removed outlier: 4.171A pdb=" N ARG B 309 " --> pdb=" O ILE B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 323 removed outlier: 3.798A pdb=" N LYS B 323 " --> pdb=" O ALA B 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 320 through 323' Processing helix chain 'B' and resid 324 through 342 Processing helix chain 'B' and resid 352 through 357 Processing helix chain 'B' and resid 362 through 381 Processing helix chain 'B' and resid 404 through 420 removed outlier: 3.661A pdb=" N GLU B 418 " --> pdb=" O ILE B 414 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TRP B 420 " --> pdb=" O ALA B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 446 Processing helix chain 'B' and resid 448 through 455 Processing helix chain 'B' and resid 467 through 477 Processing helix chain 'B' and resid 492 through 503 Processing helix chain 'B' and resid 509 through 517 Processing helix chain 'B' and resid 532 through 539 Processing helix chain 'B' and resid 549 through 554 Processing helix chain 'B' and resid 556 through 568 removed outlier: 4.027A pdb=" N ALA B 565 " --> pdb=" O LEU B 561 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG B 566 " --> pdb=" O LEU B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 587 Processing helix chain 'B' and resid 590 through 602 Processing helix chain 'C' and resid 224 through 230 Processing helix chain 'C' and resid 231 through 239 Processing helix chain 'C' and resid 247 through 254 Processing helix chain 'C' and resid 270 through 279 removed outlier: 3.595A pdb=" N HIS C 274 " --> pdb=" O GLY C 270 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU C 279 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 Processing helix chain 'C' and resid 305 through 313 removed outlier: 4.370A pdb=" N ARG C 309 " --> pdb=" O ILE C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 323 removed outlier: 3.819A pdb=" N LYS C 323 " --> pdb=" O ALA C 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 320 through 323' Processing helix chain 'C' and resid 324 through 342 Processing helix chain 'C' and resid 362 through 381 Processing helix chain 'C' and resid 404 through 420 Processing helix chain 'C' and resid 433 through 436 removed outlier: 3.633A pdb=" N ASP C 436 " --> pdb=" O GLY C 433 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 433 through 436' Processing helix chain 'C' and resid 438 through 446 removed outlier: 3.754A pdb=" N ALA C 442 " --> pdb=" O THR C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 455 Processing helix chain 'C' and resid 467 through 477 Processing helix chain 'C' and resid 488 through 491 removed outlier: 3.658A pdb=" N ARG C 491 " --> pdb=" O HIS C 488 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 488 through 491' Processing helix chain 'C' and resid 492 through 503 Processing helix chain 'C' and resid 509 through 517 Processing helix chain 'C' and resid 532 through 539 Processing helix chain 'C' and resid 556 through 568 removed outlier: 4.105A pdb=" N ALA C 565 " --> pdb=" O LEU C 561 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ARG C 566 " --> pdb=" O LEU C 562 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 587 Processing helix chain 'C' and resid 590 through 602 Processing helix chain 'D' and resid 224 through 228 removed outlier: 3.798A pdb=" N ALA D 228 " --> pdb=" O PRO D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 239 Processing helix chain 'D' and resid 247 through 254 Processing helix chain 'D' and resid 270 through 279 removed outlier: 3.598A pdb=" N HIS D 274 " --> pdb=" O GLY D 270 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU D 279 " --> pdb=" O LYS D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 286 Processing helix chain 'D' and resid 305 through 314 removed outlier: 4.387A pdb=" N ARG D 309 " --> pdb=" O ILE D 305 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLY D 314 " --> pdb=" O TYR D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 323 removed outlier: 3.770A pdb=" N LYS D 323 " --> pdb=" O ALA D 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 320 through 323' Processing helix chain 'D' and resid 324 through 342 Processing helix chain 'D' and resid 352 through 357 Processing helix chain 'D' and resid 362 through 381 Processing helix chain 'D' and resid 402 through 420 Processing helix chain 'D' and resid 432 through 435 removed outlier: 3.627A pdb=" N GLU D 435 " --> pdb=" O ALA D 432 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 432 through 435' Processing helix chain 'D' and resid 437 through 445 Processing helix chain 'D' and resid 448 through 454 Processing helix chain 'D' and resid 467 through 478 Processing helix chain 'D' and resid 492 through 503 Processing helix chain 'D' and resid 509 through 517 Processing helix chain 'D' and resid 532 through 540 Processing helix chain 'D' and resid 556 through 568 removed outlier: 3.956A pdb=" N ALA D 565 " --> pdb=" O LEU D 561 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ARG D 566 " --> pdb=" O LEU D 562 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 587 Processing helix chain 'D' and resid 590 through 602 Processing helix chain 'E' and resid 234 through 238 Processing helix chain 'E' and resid 247 through 254 Processing helix chain 'E' and resid 270 through 279 removed outlier: 3.729A pdb=" N HIS E 274 " --> pdb=" O GLY E 270 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU E 279 " --> pdb=" O LYS E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 286 Processing helix chain 'E' and resid 305 through 313 removed outlier: 4.053A pdb=" N ARG E 309 " --> pdb=" O ILE E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 342 Processing helix chain 'E' and resid 362 through 380 Processing helix chain 'E' and resid 403 through 420 removed outlier: 3.631A pdb=" N ALA E 407 " --> pdb=" O ARG E 403 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 435 removed outlier: 3.942A pdb=" N GLU E 435 " --> pdb=" O ALA E 432 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 432 through 435' Processing helix chain 'E' and resid 438 through 446 removed outlier: 4.309A pdb=" N ALA E 442 " --> pdb=" O THR E 438 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 455 Processing helix chain 'E' and resid 467 through 477 Processing helix chain 'E' and resid 492 through 503 Processing helix chain 'E' and resid 509 through 517 Processing helix chain 'E' and resid 532 through 540 Processing helix chain 'E' and resid 556 through 568 removed outlier: 4.009A pdb=" N ALA E 565 " --> pdb=" O LEU E 561 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ARG E 566 " --> pdb=" O LEU E 562 " (cutoff:3.500A) Processing helix chain 'E' and resid 572 through 587 Processing helix chain 'E' and resid 590 through 602 Processing helix chain 'F' and resid 236 through 240 Processing helix chain 'F' and resid 247 through 254 Processing helix chain 'F' and resid 270 through 279 removed outlier: 3.529A pdb=" N HIS F 274 " --> pdb=" O GLY F 270 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU F 279 " --> pdb=" O LYS F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 286 Processing helix chain 'F' and resid 306 through 313 Processing helix chain 'F' and resid 320 through 323 removed outlier: 3.680A pdb=" N LYS F 323 " --> pdb=" O ALA F 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 320 through 323' Processing helix chain 'F' and resid 324 through 342 Processing helix chain 'F' and resid 352 through 357 Processing helix chain 'F' and resid 362 through 381 Processing helix chain 'F' and resid 404 through 420 Processing helix chain 'F' and resid 437 through 446 Processing helix chain 'F' and resid 448 through 455 Processing helix chain 'F' and resid 467 through 477 Processing helix chain 'F' and resid 492 through 503 Processing helix chain 'F' and resid 509 through 517 Processing helix chain 'F' and resid 532 through 540 Processing helix chain 'F' and resid 556 through 568 removed outlier: 4.166A pdb=" N ALA F 565 " --> pdb=" O LEU F 561 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG F 566 " --> pdb=" O LEU F 562 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 587 Processing helix chain 'F' and resid 590 through 602 Processing sheet with id=AA1, first strand: chain 'A' and resid 156 through 162 removed outlier: 6.566A pdb=" N VAL A 124 " --> pdb=" O LEU A 161 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ARG A 97 " --> pdb=" O GLU A 123 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N PHE A 125 " --> pdb=" O ARG A 97 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ILE A 99 " --> pdb=" O PHE A 125 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N VAL A 127 " --> pdb=" O ILE A 99 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N LEU A 4 " --> pdb=" O HIS A 31 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N LEU A 33 " --> pdb=" O LEU A 4 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL A 30 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N SER A 62 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N VAL A 32 " --> pdb=" O SER A 62 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N VAL A 64 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N THR A 34 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N HIS A 189 " --> pdb=" O PHE A 59 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE A 61 " --> pdb=" O HIS A 189 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N VAL A 191 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ARG A 63 " --> pdb=" O VAL A 191 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 256 through 262 removed outlier: 4.478A pdb=" N VAL A 257 " --> pdb=" O TYR A 346 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N GLU A 348 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N LEU A 259 " --> pdb=" O GLU A 348 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ARG A 350 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N CYS A 261 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 11.736A pdb=" N VAL A 389 " --> pdb=" O VAL A 426 " (cutoff:3.500A) removed outlier: 10.269A pdb=" N GLY A 428 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU A 391 " --> pdb=" O GLY A 428 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ASP A 430 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU A 393 " --> pdb=" O ASP A 430 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N VAL A 458 " --> pdb=" O ARG A 482 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N GLY A 484 " --> pdb=" O VAL A 458 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL A 460 " --> pdb=" O GLY A 484 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LEU A 483 " --> pdb=" O GLU A 507 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 124 through 125 removed outlier: 8.919A pdb=" N PHE B 125 " --> pdb=" O ARG B 97 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ILE B 99 " --> pdb=" O PHE B 125 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE B 3 " --> pdb=" O TYR B 98 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N CYS B 100 " --> pdb=" O ILE B 3 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LEU B 5 " --> pdb=" O CYS B 100 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LEU B 4 " --> pdb=" O HIS B 31 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N LEU B 33 " --> pdb=" O LEU B 4 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N CYS B 6 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL B 30 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N SER B 62 " --> pdb=" O VAL B 30 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N VAL B 32 " --> pdb=" O SER B 62 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N VAL B 64 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N THR B 34 " --> pdb=" O VAL B 64 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG B 192 " --> pdb=" O GLU B 181 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 128 through 129 Processing sheet with id=AA5, first strand: chain 'B' and resid 256 through 262 removed outlier: 5.998A pdb=" N LYS B 256 " --> pdb=" O VAL B 344 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR B 346 " --> pdb=" O LYS B 256 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N HIS B 260 " --> pdb=" O GLU B 348 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N ARG B 350 " --> pdb=" O HIS B 260 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N HIS B 262 " --> pdb=" O ARG B 350 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL B 426 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU B 391 " --> pdb=" O VAL B 426 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLY B 428 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N VAL B 458 " --> pdb=" O ARG B 482 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N GLY B 484 " --> pdb=" O VAL B 458 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N VAL B 460 " --> pdb=" O GLY B 484 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LEU B 483 " --> pdb=" O GLU B 507 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 256 through 262 removed outlier: 6.074A pdb=" N LYS C 256 " --> pdb=" O VAL C 344 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TYR C 346 " --> pdb=" O LYS C 256 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N HIS C 260 " --> pdb=" O GLU C 348 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ARG C 350 " --> pdb=" O HIS C 260 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N HIS C 262 " --> pdb=" O ARG C 350 " (cutoff:3.500A) removed outlier: 11.533A pdb=" N VAL C 389 " --> pdb=" O VAL C 426 " (cutoff:3.500A) removed outlier: 10.337A pdb=" N GLY C 428 " --> pdb=" O VAL C 389 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LEU C 391 " --> pdb=" O GLY C 428 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ASP C 430 " --> pdb=" O LEU C 391 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU C 393 " --> pdb=" O ASP C 430 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL C 458 " --> pdb=" O ARG C 482 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N GLY C 484 " --> pdb=" O VAL C 458 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL C 460 " --> pdb=" O GLY C 484 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU C 483 " --> pdb=" O GLU C 507 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 256 through 262 removed outlier: 5.952A pdb=" N LYS D 256 " --> pdb=" O VAL D 344 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR D 346 " --> pdb=" O LYS D 256 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N HIS D 260 " --> pdb=" O GLU D 348 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ARG D 350 " --> pdb=" O HIS D 260 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N HIS D 262 " --> pdb=" O ARG D 350 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ALA D 345 " --> pdb=" O HIS D 388 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N ASN D 390 " --> pdb=" O ALA D 345 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ALA D 347 " --> pdb=" O ASN D 390 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N LEU D 392 " --> pdb=" O ALA D 347 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ILE D 349 " --> pdb=" O LEU D 392 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N THR D 394 " --> pdb=" O ILE D 349 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N CYS D 351 " --> pdb=" O THR D 394 " (cutoff:3.500A) removed outlier: 11.511A pdb=" N VAL D 389 " --> pdb=" O VAL D 426 " (cutoff:3.500A) removed outlier: 10.392A pdb=" N GLY D 428 " --> pdb=" O VAL D 389 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N LEU D 391 " --> pdb=" O GLY D 428 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ASP D 430 " --> pdb=" O LEU D 391 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LEU D 393 " --> pdb=" O ASP D 430 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VAL D 458 " --> pdb=" O ARG D 482 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N GLY D 484 " --> pdb=" O VAL D 458 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N VAL D 460 " --> pdb=" O GLY D 484 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU D 483 " --> pdb=" O GLU D 507 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 256 through 262 removed outlier: 5.962A pdb=" N LYS E 256 " --> pdb=" O VAL E 344 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR E 346 " --> pdb=" O LYS E 256 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N HIS E 260 " --> pdb=" O GLU E 348 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ARG E 350 " --> pdb=" O HIS E 260 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N HIS E 262 " --> pdb=" O ARG E 350 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ALA E 345 " --> pdb=" O HIS E 388 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N ASN E 390 " --> pdb=" O ALA E 345 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ALA E 347 " --> pdb=" O ASN E 390 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N LEU E 392 " --> pdb=" O ALA E 347 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE E 349 " --> pdb=" O LEU E 392 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N THR E 394 " --> pdb=" O ILE E 349 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N CYS E 351 " --> pdb=" O THR E 394 " (cutoff:3.500A) removed outlier: 11.893A pdb=" N VAL E 389 " --> pdb=" O VAL E 426 " (cutoff:3.500A) removed outlier: 10.285A pdb=" N GLY E 428 " --> pdb=" O VAL E 389 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LEU E 391 " --> pdb=" O GLY E 428 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ASP E 430 " --> pdb=" O LEU E 391 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU E 393 " --> pdb=" O ASP E 430 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N HIS E 461 " --> pdb=" O LEU E 431 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL E 458 " --> pdb=" O ARG E 482 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N GLY E 484 " --> pdb=" O VAL E 458 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL E 460 " --> pdb=" O GLY E 484 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU E 483 " --> pdb=" O GLU E 507 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 256 through 262 removed outlier: 6.128A pdb=" N LYS F 256 " --> pdb=" O VAL F 344 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TYR F 346 " --> pdb=" O LYS F 256 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N HIS F 260 " --> pdb=" O GLU F 348 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ARG F 350 " --> pdb=" O HIS F 260 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N HIS F 262 " --> pdb=" O ARG F 350 " (cutoff:3.500A) removed outlier: 11.578A pdb=" N VAL F 389 " --> pdb=" O VAL F 426 " (cutoff:3.500A) removed outlier: 10.287A pdb=" N GLY F 428 " --> pdb=" O VAL F 389 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LEU F 391 " --> pdb=" O GLY F 428 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ASP F 430 " --> pdb=" O LEU F 391 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N LEU F 393 " --> pdb=" O ASP F 430 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL F 458 " --> pdb=" O ARG F 482 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N GLY F 484 " --> pdb=" O VAL F 458 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL F 460 " --> pdb=" O GLY F 484 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU F 483 " --> pdb=" O GLU F 507 " (cutoff:3.500A) 966 hydrogen bonds defined for protein. 2718 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.14 Time building geometry restraints manager: 2.33 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: 7344 1.34 - 1.46: 3615 1.46 - 1.57: 10921 1.57 - 1.69: 39 1.69 - 1.81: 116 Bond restraints: 22035 Sorted by residual: bond pdb=" N9 A X 4 " pdb=" C4 A X 4 " ideal model delta sigma weight residual 1.374 1.366 0.008 6.00e-03 2.78e+04 1.97e+00 bond pdb=" N7 A X 5 " pdb=" C5 A X 5 " ideal model delta sigma weight residual 1.388 1.380 0.008 6.00e-03 2.78e+04 1.85e+00 bond pdb=" N9 A X 2 " pdb=" C4 A X 2 " ideal model delta sigma weight residual 1.374 1.366 0.008 6.00e-03 2.78e+04 1.61e+00 bond pdb=" CB TRP B 12 " pdb=" CG TRP B 12 " ideal model delta sigma weight residual 1.498 1.537 -0.039 3.10e-02 1.04e+03 1.56e+00 bond pdb=" C1' ATP C 701 " pdb=" O4' ATP C 701 " ideal model delta sigma weight residual 1.416 1.400 0.016 1.30e-02 5.92e+03 1.42e+00 ... (remaining 22030 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 29559 1.67 - 3.34: 456 3.34 - 5.00: 58 5.00 - 6.67: 27 6.67 - 8.34: 5 Bond angle restraints: 30105 Sorted by residual: angle pdb=" CA TRP B 12 " pdb=" CB TRP B 12 " pdb=" CG TRP B 12 " ideal model delta sigma weight residual 113.60 120.71 -7.11 1.90e+00 2.77e-01 1.40e+01 angle pdb=" C SER B 11 " pdb=" N TRP B 12 " pdb=" CA TRP B 12 " ideal model delta sigma weight residual 121.54 128.55 -7.01 1.91e+00 2.74e-01 1.35e+01 angle pdb=" O5' A X 4 " pdb=" C5' A X 4 " pdb=" C4' A X 4 " ideal model delta sigma weight residual 109.40 112.07 -2.67 8.00e-01 1.56e+00 1.12e+01 angle pdb=" O5' A X 2 " pdb=" C5' A X 2 " pdb=" C4' A X 2 " ideal model delta sigma weight residual 109.40 112.04 -2.64 8.00e-01 1.56e+00 1.09e+01 angle pdb=" C GLY A 463 " pdb=" N GLU A 464 " pdb=" CA GLU A 464 " ideal model delta sigma weight residual 122.42 117.42 5.00 1.55e+00 4.16e-01 1.04e+01 ... (remaining 30100 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 12430 17.90 - 35.80: 700 35.80 - 53.69: 165 53.69 - 71.59: 48 71.59 - 89.49: 11 Dihedral angle restraints: 13354 sinusoidal: 5492 harmonic: 7862 Sorted by residual: dihedral pdb=" CA ALA A 36 " pdb=" C ALA A 36 " pdb=" N SER A 37 " pdb=" CA SER A 37 " ideal model delta harmonic sigma weight residual 180.00 -155.35 -24.65 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA ALA B 441 " pdb=" C ALA B 441 " pdb=" N ALA B 442 " pdb=" CA ALA B 442 " ideal model delta harmonic sigma weight residual 180.00 158.49 21.51 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA PRO A 42 " pdb=" C PRO A 42 " pdb=" N GLY A 43 " pdb=" CA GLY A 43 " ideal model delta harmonic sigma weight residual 180.00 162.43 17.57 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 13351 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 2864 0.058 - 0.116: 449 0.116 - 0.174: 28 0.174 - 0.232: 1 0.232 - 0.290: 17 Chirality restraints: 3359 Sorted by residual: chirality pdb=" C2' ATP E 701 " pdb=" C1' ATP E 701 " pdb=" C3' ATP E 701 " pdb=" O2' ATP E 701 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" C3' ATP C 701 " pdb=" C2' ATP C 701 " pdb=" C4' ATP C 701 " pdb=" O3' ATP C 701 " both_signs ideal model delta sigma weight residual False -2.63 -2.92 0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" C3' ATP A 701 " pdb=" C2' ATP A 701 " pdb=" C4' ATP A 701 " pdb=" O3' ATP A 701 " both_signs ideal model delta sigma weight residual False -2.63 -2.92 0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 3356 not shown) Planarity restraints: 3909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP B 12 " 0.011 2.00e-02 2.50e+03 2.26e-02 5.12e+00 pdb=" C TRP B 12 " -0.039 2.00e-02 2.50e+03 pdb=" O TRP B 12 " 0.015 2.00e-02 2.50e+03 pdb=" N ALA B 13 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 441 " -0.010 2.00e-02 2.50e+03 1.91e-02 3.66e+00 pdb=" C ALA B 441 " 0.033 2.00e-02 2.50e+03 pdb=" O ALA B 441 " -0.012 2.00e-02 2.50e+03 pdb=" N ALA B 442 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 465 " 0.009 2.00e-02 2.50e+03 1.76e-02 3.08e+00 pdb=" C ASN B 465 " -0.030 2.00e-02 2.50e+03 pdb=" O ASN B 465 " 0.012 2.00e-02 2.50e+03 pdb=" N ASP B 466 " 0.010 2.00e-02 2.50e+03 ... (remaining 3906 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 172 2.53 - 3.12: 16673 3.12 - 3.71: 34160 3.71 - 4.31: 48429 4.31 - 4.90: 82165 Nonbonded interactions: 181599 Sorted by model distance: nonbonded pdb=" O2G ATP F 701 " pdb="MG MG F 703 " model vdw 1.935 2.170 nonbonded pdb=" OD1 ASP A 548 " pdb="ZN ZN A 702 " model vdw 1.964 2.230 nonbonded pdb=" OD1 ASP C 548 " pdb="ZN ZN C 702 " model vdw 1.991 2.230 nonbonded pdb=" OD1 ASP E 548 " pdb="ZN ZN E 702 " model vdw 2.002 2.230 nonbonded pdb=" OD1 ASP F 548 " pdb="ZN ZN F 702 " model vdw 2.008 2.230 ... (remaining 181594 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 235 or (resid 236 and (name N or name CA or name \ C or name O or name CB )) or resid 237 through 398 or resid 402 through 608 or \ resid 701 through 703)) selection = chain 'B' } ncs_group { reference = (chain 'C' and (resid 235 through 396 or (resid 397 and (name N or name CA or na \ me C or name O or name CB )) or resid 403 through 572 or (resid 573 and (name N \ or name CA or name C or name O or name CB )) or resid 574 through 703)) selection = (chain 'D' and (resid 235 through 397 or (resid 403 and (name N or name CA or na \ me C or name O or name CB )) or resid 404 through 572 or (resid 573 and (name N \ or name CA or name C or name O or name CB )) or resid 574 through 703)) selection = (chain 'E' and (resid 235 through 397 or (resid 403 and (name N or name CA or na \ me C or name O or name CB )) or resid 404 through 572 or (resid 573 and (name N \ or name CA or name C or name O or name CB )) or resid 574 through 703)) selection = (chain 'F' and (resid 235 through 397 or (resid 403 and (name N or name CA or na \ me C or name O or name CB )) or resid 404 through 703)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.680 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: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 23.370 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22052 Z= 0.193 Angle : 0.544 8.338 30105 Z= 0.287 Chirality : 0.046 0.290 3359 Planarity : 0.004 0.043 3909 Dihedral : 12.555 89.490 8246 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.64 % Favored : 95.25 % Rotamer: Outliers : 2.72 % Allowed : 6.80 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.16), residues: 2694 helix: 0.81 (0.14), residues: 1318 sheet: -0.62 (0.34), residues: 262 loop : -0.34 (0.19), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 573 TYR 0.012 0.001 TYR A 531 PHE 0.012 0.001 PHE E 476 TRP 0.026 0.002 TRP B 12 HIS 0.004 0.001 HIS F 461 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.19 (22035) covalent geometry : angle 0.54360 / 0.29 (30105) hydrogen bonds : bond 0.17576 / 11.94 ( 966) hydrogen bonds : angle 6.17145 / 4.33 ( 2718) metal coordination : bond 0.00909 / 0.55 ( 17) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5388 Ramachandran restraints generated. 2694 Oldfield, 0 Emsley, 2694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5388 Ramachandran restraints generated. 2694 Oldfield, 0 Emsley, 2694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 644 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.8824 (tppp) cc_final: 0.8379 (tptp) REVERT: A 60 SER cc_start: 0.8293 (t) cc_final: 0.8036 (p) REVERT: A 123 GLU cc_start: 0.7293 (tp30) cc_final: 0.6890 (tm-30) REVERT: A 130 GLU cc_start: 0.7581 (tp30) cc_final: 0.7224 (tm-30) REVERT: A 157 ARG cc_start: 0.7493 (mmm-85) cc_final: 0.7204 (mmt-90) REVERT: A 169 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7732 (mt0) REVERT: A 195 ASP cc_start: 0.6930 (p0) cc_final: 0.6706 (p0) REVERT: A 207 GLU cc_start: 0.7375 (tp30) cc_final: 0.7136 (tp30) REVERT: A 236 ARG cc_start: 0.8109 (mtm180) cc_final: 0.7458 (ttp-110) REVERT: A 240 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7941 (mp0) REVERT: A 285 SER cc_start: 0.9154 (m) cc_final: 0.8924 (t) REVERT: A 302 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7447 (mm-30) REVERT: A 312 ARG cc_start: 0.8845 (mmp80) cc_final: 0.8582 (mmp-170) REVERT: A 398 GLU cc_start: 0.6920 (OUTLIER) cc_final: 0.6564 (mp0) REVERT: A 425 ARG cc_start: 0.9182 (OUTLIER) cc_final: 0.8205 (ptm-80) REVERT: A 461 HIS cc_start: 0.8983 (OUTLIER) cc_final: 0.8279 (t-90) REVERT: A 466 ASP cc_start: 0.7481 (t0) cc_final: 0.7260 (t0) REVERT: B 28 ASP cc_start: 0.7658 (m-30) cc_final: 0.6943 (m-30) REVERT: B 29 GLU cc_start: 0.7386 (mt-10) cc_final: 0.7181 (mt-10) REVERT: B 48 LEU cc_start: 0.7327 (pp) cc_final: 0.6919 (pp) REVERT: B 53 MET cc_start: 0.7292 (ptp) cc_final: 0.6886 (ptp) REVERT: B 60 SER cc_start: 0.8015 (t) cc_final: 0.7633 (p) REVERT: B 81 GLU cc_start: 0.7347 (tt0) cc_final: 0.6710 (tt0) REVERT: B 93 GLN cc_start: 0.6092 (OUTLIER) cc_final: 0.5735 (pp30) REVERT: B 96 HIS cc_start: 0.6033 (OUTLIER) cc_final: 0.5407 (m-70) REVERT: B 123 GLU cc_start: 0.7408 (tp30) cc_final: 0.6523 (tp30) REVERT: B 130 GLU cc_start: 0.6728 (mp0) cc_final: 0.6330 (mp0) REVERT: B 164 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7685 (mm-30) REVERT: B 170 LEU cc_start: 0.8107 (mt) cc_final: 0.7868 (mp) REVERT: B 171 ARG cc_start: 0.8117 (ttm170) cc_final: 0.7724 (ttm110) REVERT: B 172 LEU cc_start: 0.8560 (mm) cc_final: 0.8353 (mm) REVERT: B 173 LEU cc_start: 0.8695 (mt) cc_final: 0.8435 (mp) REVERT: B 181 GLU cc_start: 0.7351 (mp0) cc_final: 0.6414 (mp0) REVERT: B 196 MET cc_start: 0.7516 (OUTLIER) cc_final: 0.6508 (mmm) REVERT: B 383 GLU cc_start: 0.7715 (tp30) cc_final: 0.7479 (tp30) REVERT: B 436 ASP cc_start: 0.7949 (t70) cc_final: 0.7614 (t70) REVERT: B 492 SER cc_start: 0.8463 (m) cc_final: 0.8239 (p) REVERT: B 507 GLU cc_start: 0.8787 (mt-10) cc_final: 0.8578 (mt-10) REVERT: B 522 ASP cc_start: 0.7834 (m-30) cc_final: 0.7594 (m-30) REVERT: C 271 GLU cc_start: 0.7212 (tp30) cc_final: 0.6846 (tp30) REVERT: C 279 GLU cc_start: 0.8322 (mm-30) cc_final: 0.7923 (mm-30) REVERT: C 302 GLU cc_start: 0.7496 (mp0) cc_final: 0.7248 (mp0) REVERT: C 315 ASP cc_start: 0.8137 (m-30) cc_final: 0.7841 (m-30) REVERT: C 329 ARG cc_start: 0.8452 (ttp80) cc_final: 0.8141 (ptm-80) REVERT: C 342 ASP cc_start: 0.8267 (t0) cc_final: 0.7974 (t0) REVERT: C 348 GLU cc_start: 0.8787 (mt-10) cc_final: 0.8480 (mt-10) REVERT: C 464 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7779 (mm-30) REVERT: D 258 GLU cc_start: 0.7789 (tm-30) cc_final: 0.7306 (tm-30) REVERT: D 302 GLU cc_start: 0.7393 (mp0) cc_final: 0.7143 (mp0) REVERT: D 312 ARG cc_start: 0.8420 (mmp80) cc_final: 0.8080 (mmp80) REVERT: D 383 GLU cc_start: 0.7894 (tp30) cc_final: 0.7593 (tp30) REVERT: D 409 HIS cc_start: 0.8587 (t-90) cc_final: 0.8383 (t-90) REVERT: D 421 LYS cc_start: 0.9214 (mtpp) cc_final: 0.8966 (mttp) REVERT: D 443 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.7776 (mpp) REVERT: D 461 HIS cc_start: 0.8678 (OUTLIER) cc_final: 0.8384 (m90) REVERT: D 498 VAL cc_start: 0.8764 (t) cc_final: 0.8540 (p) REVERT: E 243 ASP cc_start: 0.8155 (t0) cc_final: 0.7760 (t0) REVERT: E 418 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7692 (mt-10) REVERT: E 453 ARG cc_start: 0.8531 (mmm-85) cc_final: 0.8320 (mmm-85) REVERT: E 497 ARG cc_start: 0.7632 (ttp80) cc_final: 0.7188 (ttp-110) REVERT: E 598 TRP cc_start: 0.8419 (m100) cc_final: 0.8173 (m100) REVERT: F 290 ARG cc_start: 0.7722 (ttp-110) cc_final: 0.7471 (mtp85) REVERT: F 309 ARG cc_start: 0.8856 (mtp-110) cc_final: 0.8646 (ttp80) REVERT: F 390 ASN cc_start: 0.8898 (m110) cc_final: 0.8633 (m110) REVERT: F 437 ARG cc_start: 0.7236 (OUTLIER) cc_final: 0.6920 (tpm170) REVERT: F 492 SER cc_start: 0.8278 (t) cc_final: 0.8047 (p) REVERT: F 497 ARG cc_start: 0.7943 (ttp80) cc_final: 0.7301 (ttp80) REVERT: F 501 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7286 (mt-10) REVERT: F 572 THR cc_start: 0.8308 (m) cc_final: 0.8036 (t) REVERT: F 590 ASN cc_start: 0.8555 (p0) cc_final: 0.8353 (p0) outliers start: 60 outliers final: 18 residues processed: 676 average time/residue: 0.8953 time to fit residues: 666.8780 Evaluate side-chains 605 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 577 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 425 ARG Chi-restraints excluded: chain A residue 461 HIS Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 96 HIS Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain C residue 405 ARG Chi-restraints excluded: chain C residue 529 GLU Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 443 MET Chi-restraints excluded: chain D residue 461 HIS Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain E residue 384 ASP Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain F residue 246 GLN Chi-restraints excluded: chain F residue 284 GLU Chi-restraints excluded: chain F residue 350 ARG Chi-restraints excluded: chain F residue 437 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 20 GLN ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 GLN A 113 GLN ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 GLN A 372 ASN A 465 ASN ** A 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 549 ASN B 54 HIS B 96 HIS B 113 GLN B 126 HIS B 201 HIS B 282 ASN ** B 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 ASN B 525 GLN C 239 HIS C 252 GLN C 368 GLN C 375 GLN C 390 ASN C 409 HIS C 419 HIS C 513 ASN C 515 GLN C 549 ASN C 554 GLN D 278 GLN D 390 ASN D 513 ASN D 515 GLN D 554 GLN D 585 GLN E 246 GLN E 252 GLN E 355 ASN E 465 ASN E 485 HIS E 513 ASN E 515 GLN E 546 ASN E 549 ASN E 554 GLN E 560 ASN E 580 GLN ** F 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 282 ASN F 390 ASN F 465 ASN F 513 ASN F 515 GLN F 546 ASN F 554 GLN Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.108962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.096608 restraints weight = 33701.600| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.91 r_work: 0.3204 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 22052 Z= 0.185 Angle : 0.601 9.257 30105 Z= 0.306 Chirality : 0.043 0.241 3359 Planarity : 0.005 0.038 3909 Dihedral : 9.075 82.957 3306 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.60 % Favored : 95.36 % Rotamer: Outliers : 3.81 % Allowed : 13.15 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.17), residues: 2694 helix: 1.08 (0.15), residues: 1329 sheet: -0.63 (0.32), residues: 276 loop : -0.17 (0.20), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 160 TYR 0.011 0.001 TYR A 531 PHE 0.020 0.001 PHE B 59 TRP 0.023 0.002 TRP B 12 HIS 0.009 0.001 HIS A 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.19 (22035) covalent geometry : angle 0.60054 / 0.31 (30105) hydrogen bonds : bond 0.04890 / 3.33 ( 966) hydrogen bonds : angle 4.81235 / 3.40 ( 2718) metal coordination : bond 0.00398 / 0.28 ( 17) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5388 Ramachandran restraints generated. 2694 Oldfield, 0 Emsley, 2694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5388 Ramachandran restraints generated. 2694 Oldfield, 0 Emsley, 2694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 584 time to evaluate : 0.826 Fit side-chains revert: symmetry clash REVERT: A 106 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.8008 (tppp) REVERT: A 169 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.8040 (mt0) REVERT: A 207 GLU cc_start: 0.7534 (tp30) cc_final: 0.7277 (tp30) REVERT: A 236 ARG cc_start: 0.8259 (mtm180) cc_final: 0.7617 (ttp-110) REVERT: A 240 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8078 (mp0) REVERT: A 285 SER cc_start: 0.9139 (m) cc_final: 0.8884 (t) REVERT: A 312 ARG cc_start: 0.8808 (mmp80) cc_final: 0.8447 (mmp-170) REVERT: A 398 GLU cc_start: 0.7011 (OUTLIER) cc_final: 0.6511 (mp0) REVERT: A 425 ARG cc_start: 0.9237 (OUTLIER) cc_final: 0.8049 (ptm-80) REVERT: A 461 HIS cc_start: 0.8730 (OUTLIER) cc_final: 0.8036 (t-90) REVERT: B 28 ASP cc_start: 0.8296 (m-30) cc_final: 0.7881 (m-30) REVERT: B 93 GLN cc_start: 0.6111 (OUTLIER) cc_final: 0.5800 (pp30) REVERT: B 96 HIS cc_start: 0.6737 (OUTLIER) cc_final: 0.5930 (m170) REVERT: B 123 GLU cc_start: 0.7512 (tp30) cc_final: 0.7303 (tm-30) REVERT: B 130 GLU cc_start: 0.7621 (mp0) cc_final: 0.7238 (mp0) REVERT: B 156 LEU cc_start: 0.9149 (mt) cc_final: 0.8931 (mt) REVERT: B 157 ARG cc_start: 0.7718 (mpt180) cc_final: 0.7038 (mpt180) REVERT: B 170 LEU cc_start: 0.8221 (mt) cc_final: 0.7970 (mp) REVERT: B 173 LEU cc_start: 0.8883 (mt) cc_final: 0.8659 (mp) REVERT: B 181 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.7873 (mp0) REVERT: B 199 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7380 (ttm170) REVERT: B 383 GLU cc_start: 0.7938 (tp30) cc_final: 0.7736 (tp30) REVERT: B 397 ARG cc_start: 0.6976 (mmm-85) cc_final: 0.6601 (mmm-85) REVERT: B 436 ASP cc_start: 0.7853 (t70) cc_final: 0.7390 (t70) REVERT: B 447 ASP cc_start: 0.8377 (t0) cc_final: 0.8051 (t0) REVERT: B 492 SER cc_start: 0.8657 (m) cc_final: 0.8341 (p) REVERT: B 522 ASP cc_start: 0.7974 (m-30) cc_final: 0.7735 (m-30) REVERT: B 591 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.7909 (mt0) REVERT: C 271 GLU cc_start: 0.7390 (tp30) cc_final: 0.6874 (tp30) REVERT: C 279 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8060 (mm-30) REVERT: C 302 GLU cc_start: 0.7855 (mp0) cc_final: 0.7648 (mp0) REVERT: C 329 ARG cc_start: 0.8419 (ttp80) cc_final: 0.8158 (ttt-90) REVERT: C 342 ASP cc_start: 0.8543 (t0) cc_final: 0.8214 (t0) REVERT: C 348 GLU cc_start: 0.8858 (mt-10) cc_final: 0.8534 (mt-10) REVERT: D 258 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7341 (tm-30) REVERT: D 383 GLU cc_start: 0.8089 (tp30) cc_final: 0.7733 (tp30) REVERT: D 406 ILE cc_start: 0.8482 (mt) cc_final: 0.8272 (mt) REVERT: D 421 LYS cc_start: 0.9263 (mtpp) cc_final: 0.9007 (mttp) REVERT: D 461 HIS cc_start: 0.8632 (OUTLIER) cc_final: 0.8369 (m90) REVERT: D 498 VAL cc_start: 0.8636 (t) cc_final: 0.8276 (p) REVERT: D 594 ARG cc_start: 0.8224 (ttm-80) cc_final: 0.7899 (mtt-85) REVERT: E 243 ASP cc_start: 0.8177 (t0) cc_final: 0.7771 (t0) REVERT: E 279 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8358 (mm-30) REVERT: E 308 GLU cc_start: 0.8222 (tp30) cc_final: 0.7764 (tp30) REVERT: E 333 ARG cc_start: 0.8512 (mmm-85) cc_final: 0.7989 (mmm-85) REVERT: E 403 ARG cc_start: 0.6917 (OUTLIER) cc_final: 0.6423 (tmm-80) REVERT: E 405 ARG cc_start: 0.7397 (OUTLIER) cc_final: 0.7070 (tmt170) REVERT: E 453 ARG cc_start: 0.8653 (mmm-85) cc_final: 0.8340 (mmm-85) REVERT: E 469 GLU cc_start: 0.7659 (tp30) cc_final: 0.7162 (tp30) REVERT: E 528 SER cc_start: 0.8649 (t) cc_final: 0.8403 (t) REVERT: E 591 GLN cc_start: 0.8476 (mm110) cc_final: 0.8239 (mm110) REVERT: E 598 TRP cc_start: 0.8474 (m100) cc_final: 0.8213 (m100) REVERT: F 290 ARG cc_start: 0.7788 (ttp-110) cc_final: 0.7533 (mtp85) REVERT: F 309 ARG cc_start: 0.8928 (mtp-110) cc_final: 0.8717 (ttp80) REVERT: F 437 ARG cc_start: 0.7186 (OUTLIER) cc_final: 0.6694 (tpm170) REVERT: F 495 LEU cc_start: 0.8213 (tp) cc_final: 0.7781 (tp) REVERT: F 497 ARG cc_start: 0.8150 (ttp80) cc_final: 0.7375 (ttp80) REVERT: F 501 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7608 (mt-10) REVERT: F 523 GLU cc_start: 0.8251 (mt-10) cc_final: 0.7999 (mt-10) REVERT: F 593 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8279 (mt-10) outliers start: 84 outliers final: 30 residues processed: 633 average time/residue: 0.8967 time to fit residues: 624.2277 Evaluate side-chains 617 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 573 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 425 ARG Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 461 HIS Chi-restraints excluded: chain A residue 529 GLU Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 96 HIS Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 199 ARG Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 517 LYS Chi-restraints excluded: chain B residue 591 GLN Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 405 ARG Chi-restraints excluded: chain C residue 529 GLU Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 443 MET Chi-restraints excluded: chain D residue 461 HIS Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 384 ASP Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 403 ARG Chi-restraints excluded: chain E residue 405 ARG Chi-restraints excluded: chain E residue 498 VAL Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 350 ARG Chi-restraints excluded: chain F residue 362 SER Chi-restraints excluded: chain F residue 437 ARG Chi-restraints excluded: chain F residue 477 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 29 optimal weight: 0.0040 chunk 267 optimal weight: 2.9990 chunk 260 optimal weight: 0.6980 chunk 238 optimal weight: 0.4980 chunk 119 optimal weight: 0.6980 chunk 268 optimal weight: 1.9990 chunk 227 optimal weight: 1.9990 chunk 175 optimal weight: 0.2980 chunk 79 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 31 HIS ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 GLN A 513 ASN B 65 GLN B 96 HIS B 246 GLN ** B 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 419 HIS B 465 ASN C 252 GLN C 368 GLN C 375 GLN C 409 HIS C 513 ASN C 515 GLN C 554 GLN D 465 ASN D 591 GLN E 316 ASN E 355 ASN E 515 GLN E 580 GLN F 282 ASN F 372 ASN F 376 GLN F 515 GLN F 546 ASN F 554 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.109737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.097242 restraints weight = 33737.709| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.93 r_work: 0.3219 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22052 Z= 0.132 Angle : 0.553 10.367 30105 Z= 0.280 Chirality : 0.041 0.223 3359 Planarity : 0.005 0.043 3909 Dihedral : 8.663 86.217 3291 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.64 % Favored : 95.29 % Rotamer: Outliers : 4.17 % Allowed : 15.15 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.17), residues: 2694 helix: 1.32 (0.15), residues: 1321 sheet: -0.66 (0.32), residues: 277 loop : -0.10 (0.19), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 139 TYR 0.013 0.001 TYR E 310 PHE 0.035 0.001 PHE B 59 TRP 0.018 0.001 TRP B 12 HIS 0.007 0.001 HIS E 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (22035) covalent geometry : angle 0.55279 / 0.28 (30105) hydrogen bonds : bond 0.04035 / 2.74 ( 966) hydrogen bonds : angle 4.47507 / 3.16 ( 2718) metal coordination : bond 0.00274 / 0.21 ( 17) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5388 Ramachandran restraints generated. 2694 Oldfield, 0 Emsley, 2694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5388 Ramachandran restraints generated. 2694 Oldfield, 0 Emsley, 2694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 584 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 ARG cc_start: 0.8203 (mtt90) cc_final: 0.7789 (mtm110) REVERT: A 69 ASP cc_start: 0.7644 (t70) cc_final: 0.7327 (t0) REVERT: A 70 LEU cc_start: 0.8447 (tp) cc_final: 0.8098 (tt) REVERT: A 195 ASP cc_start: 0.7790 (OUTLIER) cc_final: 0.7448 (p0) REVERT: A 199 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7955 (ttt180) REVERT: A 207 GLU cc_start: 0.7583 (tp30) cc_final: 0.7276 (tp30) REVERT: A 236 ARG cc_start: 0.8186 (mtm180) cc_final: 0.7847 (ttp-110) REVERT: A 240 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8130 (mp0) REVERT: A 285 SER cc_start: 0.9119 (m) cc_final: 0.8872 (t) REVERT: A 302 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7407 (mp0) REVERT: A 312 ARG cc_start: 0.8782 (mmp80) cc_final: 0.8448 (mmp-170) REVERT: A 398 GLU cc_start: 0.6874 (OUTLIER) cc_final: 0.6510 (mp0) REVERT: A 461 HIS cc_start: 0.8742 (OUTLIER) cc_final: 0.8010 (t-90) REVERT: B 28 ASP cc_start: 0.8297 (m-30) cc_final: 0.7897 (m-30) REVERT: B 32 VAL cc_start: 0.8762 (OUTLIER) cc_final: 0.8468 (m) REVERT: B 93 GLN cc_start: 0.5968 (OUTLIER) cc_final: 0.5671 (pp30) REVERT: B 96 HIS cc_start: 0.6679 (OUTLIER) cc_final: 0.6047 (m-70) REVERT: B 130 GLU cc_start: 0.7640 (mp0) cc_final: 0.7264 (mp0) REVERT: B 154 ASN cc_start: 0.8547 (m110) cc_final: 0.8230 (t0) REVERT: B 170 LEU cc_start: 0.8211 (mt) cc_final: 0.7957 (mp) REVERT: B 171 ARG cc_start: 0.8086 (ttp80) cc_final: 0.7691 (ttm110) REVERT: B 173 LEU cc_start: 0.8921 (mt) cc_final: 0.8678 (mp) REVERT: B 199 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.7201 (ttm170) REVERT: B 319 SER cc_start: 0.8459 (p) cc_final: 0.8095 (m) REVERT: B 378 MET cc_start: 0.8962 (mtp) cc_final: 0.8624 (mtp) REVERT: B 380 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7958 (mt-10) REVERT: B 383 GLU cc_start: 0.7886 (tp30) cc_final: 0.7680 (tp30) REVERT: B 436 ASP cc_start: 0.7815 (t70) cc_final: 0.7450 (t70) REVERT: B 447 ASP cc_start: 0.8283 (t0) cc_final: 0.7922 (t0) REVERT: B 492 SER cc_start: 0.8679 (m) cc_final: 0.8374 (p) REVERT: B 580 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7366 (mp-120) REVERT: B 591 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7918 (mt0) REVERT: C 243 ASP cc_start: 0.8094 (t70) cc_final: 0.7773 (t70) REVERT: C 271 GLU cc_start: 0.7414 (tp30) cc_final: 0.6868 (tp30) REVERT: C 279 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8001 (mm-30) REVERT: C 329 ARG cc_start: 0.8361 (ttp80) cc_final: 0.8113 (ttt-90) REVERT: C 342 ASP cc_start: 0.8536 (t0) cc_final: 0.8210 (t0) REVERT: C 397 ARG cc_start: 0.7651 (mmm160) cc_final: 0.7218 (tpt170) REVERT: D 258 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7354 (tm-30) REVERT: D 302 GLU cc_start: 0.7803 (mp0) cc_final: 0.7455 (mp0) REVERT: D 333 ARG cc_start: 0.8511 (mtp85) cc_final: 0.8153 (mtp85) REVERT: D 383 GLU cc_start: 0.8012 (tp30) cc_final: 0.7652 (tp30) REVERT: D 406 ILE cc_start: 0.8457 (mt) cc_final: 0.8238 (mt) REVERT: D 461 HIS cc_start: 0.8554 (OUTLIER) cc_final: 0.8244 (m90) REVERT: D 498 VAL cc_start: 0.8571 (t) cc_final: 0.8197 (p) REVERT: D 501 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7973 (mp0) REVERT: D 559 ASP cc_start: 0.8273 (m-30) cc_final: 0.8048 (m-30) REVERT: D 594 ARG cc_start: 0.8236 (ttm-80) cc_final: 0.7867 (ttm-80) REVERT: E 240 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.8036 (tp30) REVERT: E 243 ASP cc_start: 0.8175 (t0) cc_final: 0.7862 (t0) REVERT: E 279 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8402 (mm-30) REVERT: E 308 GLU cc_start: 0.8209 (tp30) cc_final: 0.7750 (tp30) REVERT: E 403 ARG cc_start: 0.6894 (OUTLIER) cc_final: 0.6388 (tmm-80) REVERT: E 405 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.7164 (tmt170) REVERT: E 453 ARG cc_start: 0.8692 (mmm-85) cc_final: 0.8370 (mmm-85) REVERT: E 469 GLU cc_start: 0.7593 (tp30) cc_final: 0.7108 (tp30) REVERT: E 473 GLN cc_start: 0.8451 (mm-40) cc_final: 0.8226 (mm-40) REVERT: E 591 GLN cc_start: 0.8446 (mm110) cc_final: 0.8209 (mm110) REVERT: E 598 TRP cc_start: 0.8477 (m100) cc_final: 0.8228 (m100) REVERT: F 290 ARG cc_start: 0.7798 (ttp-110) cc_final: 0.7555 (mtp85) REVERT: F 309 ARG cc_start: 0.8977 (mtp-110) cc_final: 0.8598 (ttp80) REVERT: F 333 ARG cc_start: 0.8125 (mtt-85) cc_final: 0.7820 (mtp85) REVERT: F 337 GLU cc_start: 0.8188 (tp30) cc_final: 0.7734 (mp0) REVERT: F 437 ARG cc_start: 0.7139 (OUTLIER) cc_final: 0.6707 (tpm170) REVERT: F 495 LEU cc_start: 0.8255 (tp) cc_final: 0.7792 (tp) REVERT: F 497 ARG cc_start: 0.8254 (ttp80) cc_final: 0.7437 (ttp80) REVERT: F 501 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7634 (mt-10) outliers start: 92 outliers final: 45 residues processed: 626 average time/residue: 0.8840 time to fit residues: 608.7277 Evaluate side-chains 639 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 577 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 199 ARG Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 461 HIS Chi-restraints excluded: chain A residue 529 GLU Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 96 HIS Chi-restraints excluded: chain B residue 138 ASN Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 199 ARG Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 525 GLN Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 591 GLN Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 405 ARG Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain D residue 376 GLN Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 438 THR Chi-restraints excluded: chain D residue 443 MET Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 461 HIS Chi-restraints excluded: chain D residue 501 GLU Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain D residue 573 ARG Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 403 ARG Chi-restraints excluded: chain E residue 405 ARG Chi-restraints excluded: chain E residue 498 VAL Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 350 ARG Chi-restraints excluded: chain F residue 362 SER Chi-restraints excluded: chain F residue 437 ARG Chi-restraints excluded: chain F residue 471 ILE Chi-restraints excluded: chain F residue 477 LYS Chi-restraints excluded: chain F residue 492 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 115 optimal weight: 0.9980 chunk 186 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 231 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 chunk 245 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 257 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 GLN ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 GLN B 282 ASN ** B 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 ASN B 473 GLN C 252 GLN C 409 HIS D 372 ASN D 409 HIS D 465 ASN D 488 HIS D 585 GLN E 316 ASN E 515 GLN E 560 ASN E 580 GLN F 546 ASN F 554 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.108689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.096279 restraints weight = 33703.896| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.92 r_work: 0.3209 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22052 Z= 0.178 Angle : 0.567 8.110 30105 Z= 0.286 Chirality : 0.042 0.253 3359 Planarity : 0.005 0.042 3909 Dihedral : 8.323 88.798 3278 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.83 % Favored : 95.10 % Rotamer: Outliers : 4.35 % Allowed : 15.92 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.17), residues: 2694 helix: 1.45 (0.15), residues: 1311 sheet: -0.67 (0.32), residues: 267 loop : -0.09 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 139 TYR 0.013 0.001 TYR B 98 PHE 0.029 0.001 PHE B 59 TRP 0.016 0.002 TRP F 364 HIS 0.007 0.001 HIS B 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.18 (22035) covalent geometry : angle 0.56679 / 0.29 (30105) hydrogen bonds : bond 0.04063 / 2.75 ( 966) hydrogen bonds : angle 4.39194 / 3.11 ( 2718) metal coordination : bond 0.00383 / 0.28 ( 17) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5388 Ramachandran restraints generated. 2694 Oldfield, 0 Emsley, 2694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5388 Ramachandran restraints generated. 2694 Oldfield, 0 Emsley, 2694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 562 time to evaluate : 0.727 Fit side-chains revert: symmetry clash REVERT: A 58 ARG cc_start: 0.8157 (mtt90) cc_final: 0.7784 (mtm110) REVERT: A 69 ASP cc_start: 0.7695 (t70) cc_final: 0.7357 (t0) REVERT: A 70 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8118 (tt) REVERT: A 196 MET cc_start: 0.8680 (OUTLIER) cc_final: 0.8392 (ttp) REVERT: A 207 GLU cc_start: 0.7618 (tp30) cc_final: 0.7317 (tp30) REVERT: A 285 SER cc_start: 0.9139 (m) cc_final: 0.8888 (t) REVERT: A 312 ARG cc_start: 0.8805 (mmp80) cc_final: 0.8439 (mmp-170) REVERT: A 398 GLU cc_start: 0.6882 (OUTLIER) cc_final: 0.6504 (mp0) REVERT: A 461 HIS cc_start: 0.8742 (OUTLIER) cc_final: 0.8001 (t-90) REVERT: B 28 ASP cc_start: 0.8275 (m-30) cc_final: 0.7903 (m-30) REVERT: B 32 VAL cc_start: 0.8731 (OUTLIER) cc_final: 0.8454 (m) REVERT: B 93 GLN cc_start: 0.6151 (OUTLIER) cc_final: 0.5862 (pp30) REVERT: B 96 HIS cc_start: 0.6646 (OUTLIER) cc_final: 0.6011 (m-70) REVERT: B 130 GLU cc_start: 0.7715 (mp0) cc_final: 0.7281 (mp0) REVERT: B 154 ASN cc_start: 0.8585 (m110) cc_final: 0.8257 (t0) REVERT: B 170 LEU cc_start: 0.8180 (mt) cc_final: 0.7935 (mp) REVERT: B 173 LEU cc_start: 0.8946 (mt) cc_final: 0.8719 (mp) REVERT: B 199 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7415 (ttm110) REVERT: B 319 SER cc_start: 0.8446 (p) cc_final: 0.8080 (m) REVERT: B 378 MET cc_start: 0.8981 (mtp) cc_final: 0.8626 (mtp) REVERT: B 380 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7912 (mt-10) REVERT: B 383 GLU cc_start: 0.7839 (tp30) cc_final: 0.7623 (tp30) REVERT: B 436 ASP cc_start: 0.7828 (t70) cc_final: 0.7459 (t70) REVERT: B 447 ASP cc_start: 0.8312 (t0) cc_final: 0.7951 (t0) REVERT: B 492 SER cc_start: 0.8672 (m) cc_final: 0.8360 (p) REVERT: B 591 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7949 (mt0) REVERT: C 243 ASP cc_start: 0.8031 (t70) cc_final: 0.7661 (t70) REVERT: C 271 GLU cc_start: 0.7369 (tp30) cc_final: 0.6879 (tp30) REVERT: C 279 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8026 (mm-30) REVERT: C 329 ARG cc_start: 0.8414 (ttp80) cc_final: 0.8191 (ttt-90) REVERT: C 342 ASP cc_start: 0.8553 (t0) cc_final: 0.8269 (t0) REVERT: C 397 ARG cc_start: 0.7559 (OUTLIER) cc_final: 0.7096 (tpt170) REVERT: D 243 ASP cc_start: 0.8495 (t70) cc_final: 0.8283 (t70) REVERT: D 258 GLU cc_start: 0.7906 (tm-30) cc_final: 0.7354 (tm-30) REVERT: D 302 GLU cc_start: 0.7812 (mp0) cc_final: 0.7460 (mp0) REVERT: D 333 ARG cc_start: 0.8517 (mtp85) cc_final: 0.8120 (mtp85) REVERT: D 383 GLU cc_start: 0.7977 (tp30) cc_final: 0.7621 (tp30) REVERT: D 406 ILE cc_start: 0.8476 (mt) cc_final: 0.8251 (mt) REVERT: D 443 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.8454 (mtt) REVERT: D 461 HIS cc_start: 0.8593 (OUTLIER) cc_final: 0.8344 (m90) REVERT: D 498 VAL cc_start: 0.8620 (t) cc_final: 0.8265 (p) REVERT: D 501 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.8031 (mp0) REVERT: D 594 ARG cc_start: 0.8213 (ttm-80) cc_final: 0.7754 (ttm-80) REVERT: E 243 ASP cc_start: 0.8239 (t0) cc_final: 0.7920 (t0) REVERT: E 279 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8426 (mm-30) REVERT: E 308 GLU cc_start: 0.8203 (tp30) cc_final: 0.7761 (tp30) REVERT: E 375 GLN cc_start: 0.8797 (tp40) cc_final: 0.8554 (tp40) REVERT: E 403 ARG cc_start: 0.6907 (OUTLIER) cc_final: 0.6398 (tmm-80) REVERT: E 405 ARG cc_start: 0.7434 (OUTLIER) cc_final: 0.7146 (tmt170) REVERT: E 453 ARG cc_start: 0.8661 (mmm-85) cc_final: 0.8381 (mmm-85) REVERT: E 469 GLU cc_start: 0.7685 (tp30) cc_final: 0.7166 (tp30) REVERT: E 591 GLN cc_start: 0.8487 (mm110) cc_final: 0.8256 (mm110) REVERT: E 598 TRP cc_start: 0.8498 (m100) cc_final: 0.8255 (m100) REVERT: F 282 ASN cc_start: 0.8576 (p0) cc_final: 0.8277 (p0) REVERT: F 290 ARG cc_start: 0.7788 (ttp-110) cc_final: 0.7553 (mtp85) REVERT: F 309 ARG cc_start: 0.8927 (mtp-110) cc_final: 0.8554 (ttp80) REVERT: F 333 ARG cc_start: 0.8099 (mtt-85) cc_final: 0.7791 (mtp85) REVERT: F 337 GLU cc_start: 0.8159 (tp30) cc_final: 0.7724 (mp0) REVERT: F 437 ARG cc_start: 0.7144 (OUTLIER) cc_final: 0.6708 (tpm170) REVERT: F 491 ARG cc_start: 0.8102 (mtm-85) cc_final: 0.7890 (mtm-85) REVERT: F 495 LEU cc_start: 0.8261 (tp) cc_final: 0.7800 (tp) REVERT: F 497 ARG cc_start: 0.8179 (ttp80) cc_final: 0.7287 (ttp80) REVERT: F 501 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7581 (mt-10) outliers start: 96 outliers final: 42 residues processed: 613 average time/residue: 0.8506 time to fit residues: 573.9431 Evaluate side-chains 622 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 563 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 461 HIS Chi-restraints excluded: chain A residue 529 GLU Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 96 HIS Chi-restraints excluded: chain B residue 138 ASN Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 199 ARG Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 517 LYS Chi-restraints excluded: chain B residue 525 GLN Chi-restraints excluded: chain B residue 591 GLN Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 397 ARG Chi-restraints excluded: chain C residue 405 ARG Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain D residue 221 GLU Chi-restraints excluded: chain D residue 303 GLU Chi-restraints excluded: chain D residue 376 GLN Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 438 THR Chi-restraints excluded: chain D residue 443 MET Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 461 HIS Chi-restraints excluded: chain D residue 501 GLU Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 384 ASP Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 403 ARG Chi-restraints excluded: chain E residue 405 ARG Chi-restraints excluded: chain E residue 490 SER Chi-restraints excluded: chain E residue 498 VAL Chi-restraints excluded: chain E residue 504 ILE Chi-restraints excluded: chain F residue 284 GLU Chi-restraints excluded: chain F residue 350 ARG Chi-restraints excluded: chain F residue 362 SER Chi-restraints excluded: chain F residue 437 ARG Chi-restraints excluded: chain F residue 471 ILE Chi-restraints excluded: chain F residue 477 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 25 optimal weight: 1.9990 chunk 246 optimal weight: 0.9980 chunk 225 optimal weight: 0.0970 chunk 105 optimal weight: 0.5980 chunk 84 optimal weight: 0.6980 chunk 219 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 242 optimal weight: 1.9990 chunk 215 optimal weight: 0.5980 chunk 218 optimal weight: 2.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 54 HIS A 185 GLN B 185 GLN B 372 ASN ** B 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 ASN B 473 GLN B 580 GLN C 252 GLN C 409 HIS D 409 HIS D 585 GLN E 316 ASN E 473 GLN E 515 GLN E 580 GLN F 388 HIS F 546 ASN F 554 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.110043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.097573 restraints weight = 33548.686| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.92 r_work: 0.3216 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22052 Z= 0.139 Angle : 0.552 8.955 30105 Z= 0.279 Chirality : 0.041 0.220 3359 Planarity : 0.004 0.046 3909 Dihedral : 8.212 85.877 3275 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.68 % Favored : 95.25 % Rotamer: Outliers : 4.22 % Allowed : 17.64 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.17), residues: 2694 helix: 1.54 (0.15), residues: 1312 sheet: -0.66 (0.32), residues: 265 loop : -0.09 (0.19), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 139 TYR 0.015 0.001 TYR F 356 PHE 0.030 0.001 PHE B 59 TRP 0.016 0.001 TRP F 364 HIS 0.006 0.001 HIS B 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (22035) covalent geometry : angle 0.55169 / 0.28 (30105) hydrogen bonds : bond 0.03737 / 2.52 ( 966) hydrogen bonds : angle 4.30688 / 3.05 ( 2718) metal coordination : bond 0.00270 / 0.21 ( 17) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5388 Ramachandran restraints generated. 2694 Oldfield, 0 Emsley, 2694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5388 Ramachandran restraints generated. 2694 Oldfield, 0 Emsley, 2694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 566 time to evaluate : 0.856 Fit side-chains revert: symmetry clash REVERT: A 58 ARG cc_start: 0.8156 (mtt90) cc_final: 0.7775 (mtm110) REVERT: A 123 GLU cc_start: 0.7535 (tm-30) cc_final: 0.7252 (tm-30) REVERT: A 171 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.7920 (mtp-110) REVERT: A 207 GLU cc_start: 0.7711 (tp30) cc_final: 0.7404 (tp30) REVERT: A 245 VAL cc_start: 0.9242 (t) cc_final: 0.9018 (p) REVERT: A 285 SER cc_start: 0.9112 (m) cc_final: 0.8856 (t) REVERT: A 302 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7372 (mp0) REVERT: A 312 ARG cc_start: 0.8792 (mmp80) cc_final: 0.8428 (mmp-170) REVERT: A 398 GLU cc_start: 0.6888 (OUTLIER) cc_final: 0.6507 (mp0) REVERT: A 430 ASP cc_start: 0.8199 (t0) cc_final: 0.7941 (t0) REVERT: A 461 HIS cc_start: 0.8763 (OUTLIER) cc_final: 0.7973 (t-90) REVERT: B 28 ASP cc_start: 0.8312 (m-30) cc_final: 0.7916 (m-30) REVERT: B 32 VAL cc_start: 0.8727 (OUTLIER) cc_final: 0.8462 (m) REVERT: B 93 GLN cc_start: 0.6032 (OUTLIER) cc_final: 0.5764 (pp30) REVERT: B 96 HIS cc_start: 0.6629 (OUTLIER) cc_final: 0.6032 (m-70) REVERT: B 130 GLU cc_start: 0.7692 (mp0) cc_final: 0.7206 (mp0) REVERT: B 144 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8211 (mm) REVERT: B 154 ASN cc_start: 0.8502 (m110) cc_final: 0.7386 (t0) REVERT: B 157 ARG cc_start: 0.7681 (mpt180) cc_final: 0.7097 (mpt180) REVERT: B 170 LEU cc_start: 0.8183 (mt) cc_final: 0.7926 (mp) REVERT: B 171 ARG cc_start: 0.7899 (ttp80) cc_final: 0.7523 (ttm110) REVERT: B 173 LEU cc_start: 0.8955 (mt) cc_final: 0.8707 (mp) REVERT: B 199 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7393 (ttm110) REVERT: B 319 SER cc_start: 0.8496 (p) cc_final: 0.8138 (m) REVERT: B 378 MET cc_start: 0.8982 (mtp) cc_final: 0.8609 (mtp) REVERT: B 380 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7951 (mt-10) REVERT: B 383 GLU cc_start: 0.7814 (tp30) cc_final: 0.7594 (tp30) REVERT: B 436 ASP cc_start: 0.7783 (t70) cc_final: 0.7349 (t70) REVERT: B 447 ASP cc_start: 0.8229 (t0) cc_final: 0.7882 (t0) REVERT: B 492 SER cc_start: 0.8714 (m) cc_final: 0.8408 (p) REVERT: B 591 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7908 (mt0) REVERT: C 243 ASP cc_start: 0.8069 (t70) cc_final: 0.7677 (t70) REVERT: C 271 GLU cc_start: 0.7441 (tp30) cc_final: 0.6926 (tp30) REVERT: C 279 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8004 (mm-30) REVERT: C 329 ARG cc_start: 0.8355 (ttp80) cc_final: 0.8117 (ttt-90) REVERT: C 397 ARG cc_start: 0.7469 (OUTLIER) cc_final: 0.7104 (tpt170) REVERT: D 243 ASP cc_start: 0.8492 (t70) cc_final: 0.8115 (t70) REVERT: D 258 GLU cc_start: 0.7932 (tm-30) cc_final: 0.7377 (tm-30) REVERT: D 302 GLU cc_start: 0.7769 (mp0) cc_final: 0.7423 (mp0) REVERT: D 312 ARG cc_start: 0.8289 (mmp80) cc_final: 0.7924 (mmp80) REVERT: D 333 ARG cc_start: 0.8487 (mtp85) cc_final: 0.8104 (mtp85) REVERT: D 383 GLU cc_start: 0.7958 (tp30) cc_final: 0.7598 (tp30) REVERT: D 438 THR cc_start: 0.8536 (OUTLIER) cc_final: 0.8251 (p) REVERT: D 443 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.8444 (mtt) REVERT: D 461 HIS cc_start: 0.8525 (OUTLIER) cc_final: 0.8216 (m90) REVERT: D 498 VAL cc_start: 0.8565 (t) cc_final: 0.8224 (p) REVERT: D 501 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7991 (mp0) REVERT: D 559 ASP cc_start: 0.8275 (m-30) cc_final: 0.8069 (m-30) REVERT: D 594 ARG cc_start: 0.8207 (ttm-80) cc_final: 0.7718 (ttm-80) REVERT: E 243 ASP cc_start: 0.8153 (t0) cc_final: 0.7842 (t0) REVERT: E 279 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8419 (mm-30) REVERT: E 308 GLU cc_start: 0.8222 (tp30) cc_final: 0.7754 (tp30) REVERT: E 375 GLN cc_start: 0.8752 (tp40) cc_final: 0.8528 (tp40) REVERT: E 403 ARG cc_start: 0.6841 (OUTLIER) cc_final: 0.6348 (tmm-80) REVERT: E 405 ARG cc_start: 0.7428 (OUTLIER) cc_final: 0.7123 (tmt170) REVERT: E 469 GLU cc_start: 0.7590 (tp30) cc_final: 0.7064 (tp30) REVERT: E 591 GLN cc_start: 0.8408 (mm110) cc_final: 0.8161 (mm110) REVERT: E 598 TRP cc_start: 0.8485 (m100) cc_final: 0.8234 (m100) REVERT: F 282 ASN cc_start: 0.8556 (p0) cc_final: 0.8251 (p0) REVERT: F 290 ARG cc_start: 0.7824 (ttp-110) cc_final: 0.7597 (mtp85) REVERT: F 309 ARG cc_start: 0.8971 (mtp-110) cc_final: 0.8607 (ttp80) REVERT: F 329 ARG cc_start: 0.8297 (ttt90) cc_final: 0.8043 (ttt90) REVERT: F 337 GLU cc_start: 0.8170 (tp30) cc_final: 0.7723 (mp0) REVERT: F 437 ARG cc_start: 0.7152 (OUTLIER) cc_final: 0.6759 (tpm170) REVERT: F 491 ARG cc_start: 0.8175 (mtm-85) cc_final: 0.7945 (mtm-85) REVERT: F 495 LEU cc_start: 0.8274 (tp) cc_final: 0.7796 (tp) REVERT: F 497 ARG cc_start: 0.8237 (ttp80) cc_final: 0.7320 (ttp80) REVERT: F 501 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7573 (mt-10) REVERT: F 534 ARG cc_start: 0.8410 (mmm-85) cc_final: 0.8167 (mmm-85) outliers start: 93 outliers final: 51 residues processed: 614 average time/residue: 0.8756 time to fit residues: 592.3829 Evaluate side-chains 632 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 563 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 461 HIS Chi-restraints excluded: chain A residue 529 GLU Chi-restraints excluded: chain A residue 591 GLN Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 96 HIS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 138 ASN Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 199 ARG Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 517 LYS Chi-restraints excluded: chain B residue 525 GLN Chi-restraints excluded: chain B residue 591 GLN Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain C residue 278 GLN Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 397 ARG Chi-restraints excluded: chain C residue 405 ARG Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain C residue 437 ARG Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain D residue 221 GLU Chi-restraints excluded: chain D residue 303 GLU Chi-restraints excluded: chain D residue 422 ASN Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 438 THR Chi-restraints excluded: chain D residue 443 MET Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 461 HIS Chi-restraints excluded: chain D residue 501 GLU Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 384 ASP Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 403 ARG Chi-restraints excluded: chain E residue 405 ARG Chi-restraints excluded: chain E residue 473 GLN Chi-restraints excluded: chain E residue 490 SER Chi-restraints excluded: chain E residue 498 VAL Chi-restraints excluded: chain E residue 504 ILE Chi-restraints excluded: chain F residue 284 GLU Chi-restraints excluded: chain F residue 362 SER Chi-restraints excluded: chain F residue 437 ARG Chi-restraints excluded: chain F residue 454 VAL Chi-restraints excluded: chain F residue 471 ILE Chi-restraints excluded: chain F residue 477 LYS Chi-restraints excluded: chain F residue 498 VAL Chi-restraints excluded: chain F residue 543 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 127 optimal weight: 0.6980 chunk 227 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 237 optimal weight: 0.9980 chunk 162 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 161 optimal weight: 0.9990 chunk 66 optimal weight: 0.2980 chunk 89 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 GLN B 185 GLN B 282 ASN B 372 ASN ** B 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 ASN B 473 GLN C 252 GLN C 409 HIS D 409 HIS D 488 HIS D 585 GLN E 316 ASN E 473 GLN E 515 GLN E 580 GLN F 372 ASN F 546 ASN F 554 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.108867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.096477 restraints weight = 33712.215| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.93 r_work: 0.3212 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22052 Z= 0.162 Angle : 0.559 9.848 30105 Z= 0.283 Chirality : 0.041 0.224 3359 Planarity : 0.005 0.061 3909 Dihedral : 8.093 83.136 3271 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.83 % Favored : 95.10 % Rotamer: Outliers : 4.44 % Allowed : 17.96 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.17), residues: 2694 helix: 1.56 (0.15), residues: 1312 sheet: -0.68 (0.32), residues: 265 loop : -0.07 (0.19), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 139 TYR 0.011 0.001 TYR B 98 PHE 0.029 0.001 PHE B 59 TRP 0.016 0.001 TRP F 364 HIS 0.006 0.001 HIS B 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.16 (22035) covalent geometry : angle 0.55923 / 0.28 (30105) hydrogen bonds : bond 0.03823 / 2.57 ( 966) hydrogen bonds : angle 4.26172 / 3.02 ( 2718) metal coordination : bond 0.00341 / 0.26 ( 17) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5388 Ramachandran restraints generated. 2694 Oldfield, 0 Emsley, 2694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5388 Ramachandran restraints generated. 2694 Oldfield, 0 Emsley, 2694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 561 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 ARG cc_start: 0.8164 (mtt90) cc_final: 0.7783 (mtm110) REVERT: A 106 LYS cc_start: 0.8186 (tptt) cc_final: 0.7956 (tppp) REVERT: A 123 GLU cc_start: 0.7559 (tm-30) cc_final: 0.7314 (tm-30) REVERT: A 171 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.7947 (mtp-110) REVERT: A 195 ASP cc_start: 0.8257 (p0) cc_final: 0.8007 (p0) REVERT: A 207 GLU cc_start: 0.7703 (tp30) cc_final: 0.7389 (tp30) REVERT: A 245 VAL cc_start: 0.9254 (t) cc_final: 0.9047 (p) REVERT: A 285 SER cc_start: 0.9132 (m) cc_final: 0.8876 (t) REVERT: A 312 ARG cc_start: 0.8781 (mmp80) cc_final: 0.8421 (mmp-170) REVERT: A 398 GLU cc_start: 0.6966 (OUTLIER) cc_final: 0.6572 (mp0) REVERT: A 430 ASP cc_start: 0.8203 (t0) cc_final: 0.7934 (t0) REVERT: A 461 HIS cc_start: 0.8764 (OUTLIER) cc_final: 0.7945 (t-90) REVERT: B 28 ASP cc_start: 0.8292 (m-30) cc_final: 0.7908 (m-30) REVERT: B 32 VAL cc_start: 0.8676 (OUTLIER) cc_final: 0.8424 (m) REVERT: B 93 GLN cc_start: 0.6150 (OUTLIER) cc_final: 0.5900 (pp30) REVERT: B 96 HIS cc_start: 0.6549 (OUTLIER) cc_final: 0.5911 (m-70) REVERT: B 130 GLU cc_start: 0.7740 (mp0) cc_final: 0.7229 (mp0) REVERT: B 144 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8278 (mm) REVERT: B 154 ASN cc_start: 0.8567 (m110) cc_final: 0.7442 (t0) REVERT: B 157 ARG cc_start: 0.7686 (mpt180) cc_final: 0.7050 (mpt180) REVERT: B 170 LEU cc_start: 0.8152 (mt) cc_final: 0.7897 (mp) REVERT: B 171 ARG cc_start: 0.7882 (ttp80) cc_final: 0.7492 (ttm110) REVERT: B 173 LEU cc_start: 0.8967 (mt) cc_final: 0.8731 (mp) REVERT: B 199 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7406 (ttm110) REVERT: B 319 SER cc_start: 0.8468 (p) cc_final: 0.8110 (m) REVERT: B 378 MET cc_start: 0.8996 (mtp) cc_final: 0.8632 (mtp) REVERT: B 380 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7903 (mt-10) REVERT: B 383 GLU cc_start: 0.7818 (tp30) cc_final: 0.7593 (tp30) REVERT: B 436 ASP cc_start: 0.7811 (t70) cc_final: 0.7248 (t70) REVERT: B 447 ASP cc_start: 0.8263 (t0) cc_final: 0.7965 (t0) REVERT: B 492 SER cc_start: 0.8702 (m) cc_final: 0.8382 (p) REVERT: B 591 GLN cc_start: 0.8165 (OUTLIER) cc_final: 0.7933 (mt0) REVERT: C 243 ASP cc_start: 0.8048 (t70) cc_final: 0.7655 (t70) REVERT: C 271 GLU cc_start: 0.7428 (tp30) cc_final: 0.6931 (tp30) REVERT: C 279 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8013 (mm-30) REVERT: C 329 ARG cc_start: 0.8348 (ttp80) cc_final: 0.8128 (ttt-90) REVERT: C 397 ARG cc_start: 0.7499 (OUTLIER) cc_final: 0.7168 (tpt170) REVERT: D 243 ASP cc_start: 0.8450 (t70) cc_final: 0.8091 (t70) REVERT: D 258 GLU cc_start: 0.7929 (tm-30) cc_final: 0.7376 (tm-30) REVERT: D 302 GLU cc_start: 0.7833 (mp0) cc_final: 0.7467 (mp0) REVERT: D 312 ARG cc_start: 0.8269 (mmp80) cc_final: 0.8058 (mmp-170) REVERT: D 333 ARG cc_start: 0.8504 (mtp85) cc_final: 0.8114 (mtp85) REVERT: D 383 GLU cc_start: 0.7932 (tp30) cc_final: 0.7578 (tp30) REVERT: D 438 THR cc_start: 0.8538 (m) cc_final: 0.8259 (p) REVERT: D 443 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.8475 (mtt) REVERT: D 461 HIS cc_start: 0.8542 (OUTLIER) cc_final: 0.8290 (m90) REVERT: D 498 VAL cc_start: 0.8578 (t) cc_final: 0.8227 (p) REVERT: D 501 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.8057 (mp0) REVERT: D 559 ASP cc_start: 0.8309 (m-30) cc_final: 0.8084 (m-30) REVERT: D 594 ARG cc_start: 0.8210 (ttm-80) cc_final: 0.7956 (ttm-80) REVERT: E 243 ASP cc_start: 0.8172 (t0) cc_final: 0.7866 (t0) REVERT: E 279 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8417 (mm-30) REVERT: E 308 GLU cc_start: 0.8201 (tp30) cc_final: 0.7755 (tp30) REVERT: E 403 ARG cc_start: 0.6884 (OUTLIER) cc_final: 0.6389 (tmm-80) REVERT: E 405 ARG cc_start: 0.7415 (OUTLIER) cc_final: 0.7148 (tmt170) REVERT: E 469 GLU cc_start: 0.7477 (tp30) cc_final: 0.6946 (tp30) REVERT: E 473 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.8062 (mm110) REVERT: E 496 LEU cc_start: 0.8399 (tm) cc_final: 0.8165 (tm) REVERT: E 591 GLN cc_start: 0.8495 (mm110) cc_final: 0.8271 (mm110) REVERT: E 598 TRP cc_start: 0.8502 (m100) cc_final: 0.8260 (m100) REVERT: F 282 ASN cc_start: 0.8465 (p0) cc_final: 0.8213 (p0) REVERT: F 290 ARG cc_start: 0.7800 (ttp-110) cc_final: 0.7566 (mtp85) REVERT: F 309 ARG cc_start: 0.8945 (mtp180) cc_final: 0.8675 (ttp80) REVERT: F 329 ARG cc_start: 0.8265 (ttt90) cc_final: 0.8019 (ttt90) REVERT: F 337 GLU cc_start: 0.8165 (tp30) cc_final: 0.7727 (mp0) REVERT: F 405 ARG cc_start: 0.7154 (mtp85) cc_final: 0.6931 (mtp85) REVERT: F 434 PHE cc_start: 0.7776 (OUTLIER) cc_final: 0.7539 (t80) REVERT: F 437 ARG cc_start: 0.7039 (OUTLIER) cc_final: 0.6667 (tpm170) REVERT: F 491 ARG cc_start: 0.8142 (mtm-85) cc_final: 0.7930 (mtm-85) REVERT: F 495 LEU cc_start: 0.8276 (tp) cc_final: 0.7814 (tp) REVERT: F 497 ARG cc_start: 0.8159 (ttp80) cc_final: 0.7227 (ttp80) REVERT: F 501 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7596 (mt-10) REVERT: F 534 ARG cc_start: 0.8462 (mmm-85) cc_final: 0.8187 (mmm-85) REVERT: F 544 THR cc_start: 0.8700 (p) cc_final: 0.8497 (p) outliers start: 98 outliers final: 50 residues processed: 614 average time/residue: 0.8017 time to fit residues: 543.1964 Evaluate side-chains 628 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 559 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 461 HIS Chi-restraints excluded: chain A residue 529 GLU Chi-restraints excluded: chain A residue 591 GLN Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 96 HIS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 138 ASN Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 199 ARG Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 517 LYS Chi-restraints excluded: chain B residue 525 GLN Chi-restraints excluded: chain B residue 591 GLN Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 397 ARG Chi-restraints excluded: chain C residue 405 ARG Chi-restraints excluded: chain C residue 437 ARG Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain D residue 221 GLU Chi-restraints excluded: chain D residue 303 GLU Chi-restraints excluded: chain D residue 422 ASN Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 443 MET Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 461 HIS Chi-restraints excluded: chain D residue 501 GLU Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain E residue 324 ASP Chi-restraints excluded: chain E residue 384 ASP Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 403 ARG Chi-restraints excluded: chain E residue 405 ARG Chi-restraints excluded: chain E residue 473 GLN Chi-restraints excluded: chain E residue 490 SER Chi-restraints excluded: chain E residue 498 VAL Chi-restraints excluded: chain E residue 504 ILE Chi-restraints excluded: chain E residue 571 ILE Chi-restraints excluded: chain F residue 284 GLU Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 362 SER Chi-restraints excluded: chain F residue 434 PHE Chi-restraints excluded: chain F residue 437 ARG Chi-restraints excluded: chain F residue 454 VAL Chi-restraints excluded: chain F residue 471 ILE Chi-restraints excluded: chain F residue 477 LYS Chi-restraints excluded: chain F residue 492 SER Chi-restraints excluded: chain F residue 498 VAL Chi-restraints excluded: chain F residue 543 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 253 optimal weight: 3.9990 chunk 127 optimal weight: 0.3980 chunk 94 optimal weight: 2.9990 chunk 224 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 169 optimal weight: 1.9990 chunk 190 optimal weight: 0.0010 chunk 108 optimal weight: 1.9990 chunk 140 optimal weight: 0.9980 chunk 117 optimal weight: 0.9980 chunk 263 optimal weight: 4.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 GLN B 185 GLN B 246 GLN B 282 ASN B 372 ASN B 465 ASN B 473 GLN C 252 GLN C 409 HIS D 409 HIS D 488 HIS D 585 GLN E 316 ASN E 473 GLN E 515 GLN E 560 ASN E 580 GLN F 554 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.109217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.096700 restraints weight = 33702.688| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.93 r_work: 0.3214 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 22052 Z= 0.154 Angle : 0.574 12.842 30105 Z= 0.289 Chirality : 0.042 0.230 3359 Planarity : 0.005 0.046 3909 Dihedral : 8.018 83.294 3271 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.57 % Favored : 95.36 % Rotamer: Outliers : 4.26 % Allowed : 18.64 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.17), residues: 2694 helix: 1.59 (0.15), residues: 1313 sheet: -0.68 (0.32), residues: 265 loop : -0.07 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 139 TYR 0.017 0.001 TYR F 356 PHE 0.033 0.001 PHE B 59 TRP 0.016 0.001 TRP F 364 HIS 0.006 0.001 HIS B 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.15 (22035) covalent geometry : angle 0.57390 / 0.29 (30105) hydrogen bonds : bond 0.03750 / 2.53 ( 966) hydrogen bonds : angle 4.23169 / 3.00 ( 2718) metal coordination : bond 0.00317 / 0.24 ( 17) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5388 Ramachandran restraints generated. 2694 Oldfield, 0 Emsley, 2694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5388 Ramachandran restraints generated. 2694 Oldfield, 0 Emsley, 2694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 562 time to evaluate : 0.819 Fit side-chains revert: symmetry clash REVERT: A 58 ARG cc_start: 0.8187 (mtt90) cc_final: 0.7891 (mtm110) REVERT: A 59 PHE cc_start: 0.7506 (m-80) cc_final: 0.7133 (m-80) REVERT: A 74 GLN cc_start: 0.7974 (mp10) cc_final: 0.7732 (mp10) REVERT: A 106 LYS cc_start: 0.8218 (tptt) cc_final: 0.7992 (tppp) REVERT: A 122 CYS cc_start: 0.8585 (t) cc_final: 0.8347 (t) REVERT: A 123 GLU cc_start: 0.7608 (tm-30) cc_final: 0.7333 (tm-30) REVERT: A 171 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.7955 (mtp-110) REVERT: A 195 ASP cc_start: 0.8255 (OUTLIER) cc_final: 0.8001 (p0) REVERT: A 245 VAL cc_start: 0.9256 (t) cc_final: 0.9048 (p) REVERT: A 285 SER cc_start: 0.9106 (m) cc_final: 0.8847 (t) REVERT: A 312 ARG cc_start: 0.8781 (mmp80) cc_final: 0.8423 (mmp-170) REVERT: A 418 GLU cc_start: 0.8194 (pt0) cc_final: 0.7944 (pp20) REVERT: A 430 ASP cc_start: 0.8208 (t0) cc_final: 0.7954 (t0) REVERT: A 473 GLN cc_start: 0.8517 (mt0) cc_final: 0.8312 (mt0) REVERT: B 28 ASP cc_start: 0.8322 (m-30) cc_final: 0.7939 (m-30) REVERT: B 32 VAL cc_start: 0.8672 (OUTLIER) cc_final: 0.8433 (m) REVERT: B 93 GLN cc_start: 0.6071 (OUTLIER) cc_final: 0.5853 (pp30) REVERT: B 96 HIS cc_start: 0.6587 (OUTLIER) cc_final: 0.5953 (m-70) REVERT: B 130 GLU cc_start: 0.7745 (mp0) cc_final: 0.7272 (mp0) REVERT: B 144 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8343 (mm) REVERT: B 146 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7506 (pt0) REVERT: B 154 ASN cc_start: 0.8496 (m110) cc_final: 0.7388 (t0) REVERT: B 157 ARG cc_start: 0.7673 (mpt180) cc_final: 0.7056 (mpt180) REVERT: B 164 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7404 (mm-30) REVERT: B 170 LEU cc_start: 0.8167 (mt) cc_final: 0.7903 (mp) REVERT: B 171 ARG cc_start: 0.7909 (ttp80) cc_final: 0.7519 (ttm110) REVERT: B 173 LEU cc_start: 0.8959 (mt) cc_final: 0.8709 (mp) REVERT: B 199 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7408 (ttm110) REVERT: B 319 SER cc_start: 0.8506 (p) cc_final: 0.8154 (m) REVERT: B 378 MET cc_start: 0.9010 (mtp) cc_final: 0.8647 (mtp) REVERT: B 397 ARG cc_start: 0.6950 (mmm-85) cc_final: 0.6661 (mmm-85) REVERT: B 436 ASP cc_start: 0.7770 (t70) cc_final: 0.7192 (t70) REVERT: B 447 ASP cc_start: 0.8185 (t0) cc_final: 0.7913 (t0) REVERT: B 492 SER cc_start: 0.8720 (m) cc_final: 0.8407 (p) REVERT: B 591 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7936 (mt0) REVERT: C 243 ASP cc_start: 0.8060 (t70) cc_final: 0.7665 (t70) REVERT: C 271 GLU cc_start: 0.7455 (tp30) cc_final: 0.6947 (tp30) REVERT: C 279 GLU cc_start: 0.8488 (mm-30) cc_final: 0.8003 (mm-30) REVERT: C 329 ARG cc_start: 0.8346 (ttp80) cc_final: 0.8130 (ttt-90) REVERT: C 397 ARG cc_start: 0.7404 (OUTLIER) cc_final: 0.7112 (tpt170) REVERT: D 243 ASP cc_start: 0.8470 (t70) cc_final: 0.8181 (t70) REVERT: D 258 GLU cc_start: 0.7944 (tm-30) cc_final: 0.7385 (tm-30) REVERT: D 302 GLU cc_start: 0.7823 (mp0) cc_final: 0.7465 (mp0) REVERT: D 312 ARG cc_start: 0.8256 (mmp80) cc_final: 0.8042 (mmp-170) REVERT: D 324 ASP cc_start: 0.8389 (t0) cc_final: 0.8179 (t70) REVERT: D 333 ARG cc_start: 0.8506 (mtp85) cc_final: 0.8123 (mtp85) REVERT: D 379 GLU cc_start: 0.8277 (mt-10) cc_final: 0.8075 (mt-10) REVERT: D 383 GLU cc_start: 0.7929 (tp30) cc_final: 0.7571 (tp30) REVERT: D 421 LYS cc_start: 0.9113 (mtpp) cc_final: 0.8866 (mttm) REVERT: D 438 THR cc_start: 0.8513 (OUTLIER) cc_final: 0.8221 (p) REVERT: D 443 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.8495 (mtt) REVERT: D 461 HIS cc_start: 0.8516 (OUTLIER) cc_final: 0.8244 (m90) REVERT: D 498 VAL cc_start: 0.8553 (t) cc_final: 0.8212 (p) REVERT: D 501 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.8008 (mp0) REVERT: D 594 ARG cc_start: 0.8199 (ttm-80) cc_final: 0.7899 (ttm-80) REVERT: E 243 ASP cc_start: 0.8142 (t0) cc_final: 0.7854 (t0) REVERT: E 279 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8420 (mm-30) REVERT: E 308 GLU cc_start: 0.8234 (tp30) cc_final: 0.7764 (tp30) REVERT: E 312 ARG cc_start: 0.8257 (mmp80) cc_final: 0.8024 (mmp80) REVERT: E 403 ARG cc_start: 0.6845 (OUTLIER) cc_final: 0.6421 (tmm-80) REVERT: E 405 ARG cc_start: 0.7446 (OUTLIER) cc_final: 0.7211 (tmt170) REVERT: E 469 GLU cc_start: 0.7445 (tp30) cc_final: 0.6963 (tp30) REVERT: E 591 GLN cc_start: 0.8390 (mm110) cc_final: 0.8162 (mm110) REVERT: E 598 TRP cc_start: 0.8486 (m100) cc_final: 0.8247 (m100) REVERT: F 282 ASN cc_start: 0.8494 (p0) cc_final: 0.8208 (p0) REVERT: F 290 ARG cc_start: 0.7802 (ttp-110) cc_final: 0.7562 (mtp85) REVERT: F 309 ARG cc_start: 0.8987 (mtp180) cc_final: 0.8696 (ttp80) REVERT: F 329 ARG cc_start: 0.8292 (ttt90) cc_final: 0.8036 (ttt90) REVERT: F 337 GLU cc_start: 0.8185 (tp30) cc_final: 0.7749 (mp0) REVERT: F 437 ARG cc_start: 0.7048 (OUTLIER) cc_final: 0.6652 (tpm170) REVERT: F 440 ARG cc_start: 0.7950 (mmm-85) cc_final: 0.7521 (ttm170) REVERT: F 491 ARG cc_start: 0.8161 (mtm-85) cc_final: 0.7946 (mtm-85) REVERT: F 492 SER cc_start: 0.8198 (OUTLIER) cc_final: 0.7969 (m) REVERT: F 495 LEU cc_start: 0.8280 (tp) cc_final: 0.7808 (tp) REVERT: F 497 ARG cc_start: 0.8207 (ttp80) cc_final: 0.7272 (ttp80) REVERT: F 501 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7618 (mt-10) outliers start: 94 outliers final: 52 residues processed: 610 average time/residue: 0.7983 time to fit residues: 536.1208 Evaluate side-chains 630 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 561 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 529 GLU Chi-restraints excluded: chain A residue 591 GLN Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 96 HIS Chi-restraints excluded: chain B residue 138 ASN Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 199 ARG Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 517 LYS Chi-restraints excluded: chain B residue 525 GLN Chi-restraints excluded: chain B residue 591 GLN Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 397 ARG Chi-restraints excluded: chain C residue 405 ARG Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain D residue 221 GLU Chi-restraints excluded: chain D residue 303 GLU Chi-restraints excluded: chain D residue 376 GLN Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 438 THR Chi-restraints excluded: chain D residue 443 MET Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 461 HIS Chi-restraints excluded: chain D residue 501 GLU Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain E residue 324 ASP Chi-restraints excluded: chain E residue 360 SER Chi-restraints excluded: chain E residue 384 ASP Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 403 ARG Chi-restraints excluded: chain E residue 405 ARG Chi-restraints excluded: chain E residue 490 SER Chi-restraints excluded: chain E residue 498 VAL Chi-restraints excluded: chain E residue 504 ILE Chi-restraints excluded: chain E residue 571 ILE Chi-restraints excluded: chain F residue 284 GLU Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 362 SER Chi-restraints excluded: chain F residue 437 ARG Chi-restraints excluded: chain F residue 454 VAL Chi-restraints excluded: chain F residue 471 ILE Chi-restraints excluded: chain F residue 477 LYS Chi-restraints excluded: chain F residue 492 SER Chi-restraints excluded: chain F residue 498 VAL Chi-restraints excluded: chain F residue 543 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 144 optimal weight: 0.9980 chunk 130 optimal weight: 0.6980 chunk 138 optimal weight: 0.8980 chunk 161 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 210 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 230 optimal weight: 1.9990 chunk 214 optimal weight: 0.9990 chunk 163 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 GLN B 282 ASN B 372 ASN B 465 ASN C 252 GLN C 409 HIS D 409 HIS D 488 HIS D 585 GLN E 316 ASN E 515 GLN ** E 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 580 GLN F 554 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.108403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.096123 restraints weight = 33625.947| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.91 r_work: 0.3205 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 22052 Z= 0.183 Angle : 0.586 12.412 30105 Z= 0.297 Chirality : 0.043 0.233 3359 Planarity : 0.005 0.063 3909 Dihedral : 7.912 83.592 3266 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.71 % Favored : 95.21 % Rotamer: Outliers : 3.85 % Allowed : 19.46 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.17), residues: 2694 helix: 1.57 (0.15), residues: 1312 sheet: -0.63 (0.33), residues: 265 loop : -0.08 (0.19), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 139 TYR 0.013 0.001 TYR F 511 PHE 0.035 0.001 PHE B 59 TRP 0.017 0.002 TRP F 364 HIS 0.006 0.001 HIS A 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.18 (22035) covalent geometry : angle 0.58645 / 0.30 (30105) hydrogen bonds : bond 0.03912 / 2.64 ( 966) hydrogen bonds : angle 4.25971 / 3.01 ( 2718) metal coordination : bond 0.00389 / 0.29 ( 17) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5388 Ramachandran restraints generated. 2694 Oldfield, 0 Emsley, 2694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5388 Ramachandran restraints generated. 2694 Oldfield, 0 Emsley, 2694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 569 time to evaluate : 0.812 Fit side-chains revert: symmetry clash REVERT: A 58 ARG cc_start: 0.8156 (mtt90) cc_final: 0.7788 (mtm110) REVERT: A 74 GLN cc_start: 0.7977 (mp10) cc_final: 0.7723 (mp10) REVERT: A 106 LYS cc_start: 0.8202 (tptt) cc_final: 0.7949 (tppp) REVERT: A 122 CYS cc_start: 0.8569 (t) cc_final: 0.8312 (t) REVERT: A 123 GLU cc_start: 0.7628 (tm-30) cc_final: 0.7413 (tm-30) REVERT: A 139 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.7364 (mtm-85) REVERT: A 171 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.7982 (mtp-110) REVERT: A 195 ASP cc_start: 0.8277 (OUTLIER) cc_final: 0.7995 (p0) REVERT: A 245 VAL cc_start: 0.9270 (t) cc_final: 0.9066 (p) REVERT: A 285 SER cc_start: 0.9107 (m) cc_final: 0.8846 (t) REVERT: A 312 ARG cc_start: 0.8791 (mmp80) cc_final: 0.8425 (mmp-170) REVERT: A 418 GLU cc_start: 0.8216 (pt0) cc_final: 0.7973 (pp20) REVERT: A 430 ASP cc_start: 0.8203 (t0) cc_final: 0.7943 (t0) REVERT: B 28 ASP cc_start: 0.8270 (m-30) cc_final: 0.7904 (m-30) REVERT: B 32 VAL cc_start: 0.8635 (OUTLIER) cc_final: 0.8403 (m) REVERT: B 93 GLN cc_start: 0.6154 (OUTLIER) cc_final: 0.5844 (pp30) REVERT: B 96 HIS cc_start: 0.6534 (OUTLIER) cc_final: 0.5855 (m-70) REVERT: B 144 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8370 (mm) REVERT: B 146 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7452 (pt0) REVERT: B 154 ASN cc_start: 0.8571 (m110) cc_final: 0.8296 (t0) REVERT: B 170 LEU cc_start: 0.8154 (mt) cc_final: 0.7891 (mp) REVERT: B 171 ARG cc_start: 0.7903 (ttp80) cc_final: 0.7526 (ttm110) REVERT: B 173 LEU cc_start: 0.8973 (mt) cc_final: 0.8739 (mp) REVERT: B 199 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7398 (ttm110) REVERT: B 319 SER cc_start: 0.8483 (p) cc_final: 0.8129 (m) REVERT: B 378 MET cc_start: 0.8987 (mtp) cc_final: 0.8627 (mtp) REVERT: B 436 ASP cc_start: 0.7823 (t70) cc_final: 0.7273 (t70) REVERT: B 447 ASP cc_start: 0.8223 (t0) cc_final: 0.7949 (t0) REVERT: B 492 SER cc_start: 0.8703 (m) cc_final: 0.8383 (p) REVERT: B 591 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7933 (mt0) REVERT: C 243 ASP cc_start: 0.8039 (t70) cc_final: 0.7647 (t70) REVERT: C 271 GLU cc_start: 0.7448 (tp30) cc_final: 0.6940 (tp30) REVERT: C 279 GLU cc_start: 0.8477 (mm-30) cc_final: 0.8000 (mm-30) REVERT: C 329 ARG cc_start: 0.8450 (ttp80) cc_final: 0.8223 (ttt-90) REVERT: C 593 GLU cc_start: 0.8233 (mt-10) cc_final: 0.8001 (pt0) REVERT: D 243 ASP cc_start: 0.8460 (t70) cc_final: 0.8072 (t70) REVERT: D 258 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7379 (tm-30) REVERT: D 302 GLU cc_start: 0.7840 (mp0) cc_final: 0.7461 (mp0) REVERT: D 312 ARG cc_start: 0.8257 (mmp80) cc_final: 0.8038 (mmp-170) REVERT: D 324 ASP cc_start: 0.8420 (t0) cc_final: 0.8211 (t70) REVERT: D 333 ARG cc_start: 0.8503 (mtp85) cc_final: 0.8131 (mtp85) REVERT: D 383 GLU cc_start: 0.7920 (tp30) cc_final: 0.7543 (tp30) REVERT: D 421 LYS cc_start: 0.9117 (mtpp) cc_final: 0.8871 (mttm) REVERT: D 438 THR cc_start: 0.8532 (OUTLIER) cc_final: 0.8231 (p) REVERT: D 443 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.8503 (mtt) REVERT: D 461 HIS cc_start: 0.8560 (OUTLIER) cc_final: 0.8297 (m90) REVERT: D 498 VAL cc_start: 0.8589 (t) cc_final: 0.8242 (p) REVERT: D 501 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.8042 (mp0) REVERT: D 559 ASP cc_start: 0.8295 (m-30) cc_final: 0.8085 (m-30) REVERT: E 243 ASP cc_start: 0.8194 (t0) cc_final: 0.7895 (t0) REVERT: E 279 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8426 (mm-30) REVERT: E 375 GLN cc_start: 0.8777 (tp40) cc_final: 0.8480 (tp40) REVERT: E 403 ARG cc_start: 0.6864 (OUTLIER) cc_final: 0.6454 (tmm-80) REVERT: E 405 ARG cc_start: 0.7403 (OUTLIER) cc_final: 0.7192 (tmt170) REVERT: E 469 GLU cc_start: 0.7580 (tp30) cc_final: 0.7113 (tp30) REVERT: E 598 TRP cc_start: 0.8506 (m100) cc_final: 0.8271 (m100) REVERT: F 282 ASN cc_start: 0.8472 (p0) cc_final: 0.8190 (p0) REVERT: F 290 ARG cc_start: 0.7822 (ttp-110) cc_final: 0.7584 (mtp85) REVERT: F 309 ARG cc_start: 0.8964 (mtp180) cc_final: 0.8753 (ttp80) REVERT: F 329 ARG cc_start: 0.8263 (ttt90) cc_final: 0.8019 (ttt90) REVERT: F 337 GLU cc_start: 0.8162 (tp30) cc_final: 0.7728 (mp0) REVERT: F 437 ARG cc_start: 0.7018 (OUTLIER) cc_final: 0.6587 (tpm170) REVERT: F 491 ARG cc_start: 0.8151 (mtm-85) cc_final: 0.7945 (mtm-85) REVERT: F 492 SER cc_start: 0.8175 (OUTLIER) cc_final: 0.7948 (m) REVERT: F 495 LEU cc_start: 0.8298 (tp) cc_final: 0.7839 (tp) REVERT: F 497 ARG cc_start: 0.8154 (ttp80) cc_final: 0.7189 (ttp80) REVERT: F 501 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7580 (mt-10) REVERT: F 515 GLN cc_start: 0.8889 (mt0) cc_final: 0.8018 (mt0) outliers start: 85 outliers final: 51 residues processed: 611 average time/residue: 0.8055 time to fit residues: 541.1867 Evaluate side-chains 630 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 562 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 529 GLU Chi-restraints excluded: chain A residue 591 GLN Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 96 HIS Chi-restraints excluded: chain B residue 138 ASN Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 199 ARG Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 517 LYS Chi-restraints excluded: chain B residue 525 GLN Chi-restraints excluded: chain B residue 591 GLN Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 405 ARG Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain D residue 221 GLU Chi-restraints excluded: chain D residue 303 GLU Chi-restraints excluded: chain D residue 376 GLN Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 438 THR Chi-restraints excluded: chain D residue 443 MET Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 461 HIS Chi-restraints excluded: chain D residue 501 GLU Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain E residue 324 ASP Chi-restraints excluded: chain E residue 360 SER Chi-restraints excluded: chain E residue 383 GLU Chi-restraints excluded: chain E residue 384 ASP Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 403 ARG Chi-restraints excluded: chain E residue 405 ARG Chi-restraints excluded: chain E residue 490 SER Chi-restraints excluded: chain E residue 498 VAL Chi-restraints excluded: chain E residue 504 ILE Chi-restraints excluded: chain F residue 284 GLU Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 362 SER Chi-restraints excluded: chain F residue 437 ARG Chi-restraints excluded: chain F residue 454 VAL Chi-restraints excluded: chain F residue 471 ILE Chi-restraints excluded: chain F residue 477 LYS Chi-restraints excluded: chain F residue 492 SER Chi-restraints excluded: chain F residue 498 VAL Chi-restraints excluded: chain F residue 543 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 134 optimal weight: 1.9990 chunk 171 optimal weight: 0.6980 chunk 185 optimal weight: 0.4980 chunk 137 optimal weight: 0.6980 chunk 113 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 207 optimal weight: 0.7980 chunk 249 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 138 optimal weight: 0.9990 chunk 99 optimal weight: 7.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 GLN B 282 ASN B 372 ASN B 465 ASN C 252 GLN C 409 HIS D 409 HIS D 488 HIS D 585 GLN E 316 ASN E 515 GLN E 580 GLN F 554 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.108858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.096522 restraints weight = 33597.153| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.92 r_work: 0.3216 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 22052 Z= 0.164 Angle : 0.608 17.830 30105 Z= 0.307 Chirality : 0.042 0.232 3359 Planarity : 0.005 0.052 3909 Dihedral : 7.874 83.641 3266 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.57 % Favored : 95.36 % Rotamer: Outliers : 3.81 % Allowed : 20.00 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.17), residues: 2694 helix: 1.56 (0.14), residues: 1313 sheet: -0.61 (0.33), residues: 265 loop : -0.09 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 139 TYR 0.019 0.001 TYR F 356 PHE 0.034 0.001 PHE B 59 TRP 0.017 0.001 TRP F 364 HIS 0.005 0.001 HIS E 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.16 (22035) covalent geometry : angle 0.60759 / 0.31 (30105) hydrogen bonds : bond 0.03841 / 2.58 ( 966) hydrogen bonds : angle 4.25284 / 3.01 ( 2718) metal coordination : bond 0.00336 / 0.26 ( 17) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5388 Ramachandran restraints generated. 2694 Oldfield, 0 Emsley, 2694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5388 Ramachandran restraints generated. 2694 Oldfield, 0 Emsley, 2694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 564 time to evaluate : 0.836 Fit side-chains revert: symmetry clash REVERT: A 58 ARG cc_start: 0.8165 (mtt90) cc_final: 0.7883 (mtm110) REVERT: A 59 PHE cc_start: 0.7532 (m-80) cc_final: 0.7158 (m-80) REVERT: A 74 GLN cc_start: 0.7972 (mp10) cc_final: 0.7756 (mp10) REVERT: A 106 LYS cc_start: 0.8192 (tptt) cc_final: 0.7942 (tppp) REVERT: A 123 GLU cc_start: 0.7668 (tm-30) cc_final: 0.7454 (tm-30) REVERT: A 139 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.7358 (mtm-85) REVERT: A 171 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.7933 (mtp-110) REVERT: A 195 ASP cc_start: 0.8308 (p0) cc_final: 0.8001 (p0) REVERT: A 245 VAL cc_start: 0.9267 (t) cc_final: 0.9060 (p) REVERT: A 285 SER cc_start: 0.9108 (m) cc_final: 0.8849 (t) REVERT: A 312 ARG cc_start: 0.8787 (mmp80) cc_final: 0.8428 (mmp-170) REVERT: A 418 GLU cc_start: 0.8188 (pt0) cc_final: 0.7971 (pp20) REVERT: A 430 ASP cc_start: 0.8181 (t0) cc_final: 0.7931 (t0) REVERT: B 28 ASP cc_start: 0.8297 (m-30) cc_final: 0.7934 (m-30) REVERT: B 32 VAL cc_start: 0.8635 (OUTLIER) cc_final: 0.8398 (m) REVERT: B 93 GLN cc_start: 0.6113 (OUTLIER) cc_final: 0.5792 (pp30) REVERT: B 96 HIS cc_start: 0.6500 (OUTLIER) cc_final: 0.5825 (m-70) REVERT: B 144 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8404 (mm) REVERT: B 146 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7437 (pt0) REVERT: B 154 ASN cc_start: 0.8562 (m110) cc_final: 0.7340 (t0) REVERT: B 157 ARG cc_start: 0.7791 (mpt180) cc_final: 0.7042 (mpt180) REVERT: B 170 LEU cc_start: 0.8147 (mt) cc_final: 0.7882 (mp) REVERT: B 171 ARG cc_start: 0.7892 (ttp80) cc_final: 0.7521 (ttm110) REVERT: B 173 LEU cc_start: 0.8970 (mt) cc_final: 0.8730 (mp) REVERT: B 319 SER cc_start: 0.8468 (p) cc_final: 0.8119 (m) REVERT: B 378 MET cc_start: 0.8989 (mtp) cc_final: 0.8631 (mtp) REVERT: B 436 ASP cc_start: 0.7799 (t70) cc_final: 0.7338 (t70) REVERT: B 447 ASP cc_start: 0.8207 (t0) cc_final: 0.7944 (t0) REVERT: B 492 SER cc_start: 0.8700 (m) cc_final: 0.8381 (p) REVERT: B 591 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7961 (mt0) REVERT: C 243 ASP cc_start: 0.8043 (t70) cc_final: 0.7656 (t70) REVERT: C 271 GLU cc_start: 0.7441 (tp30) cc_final: 0.6935 (tp30) REVERT: C 279 GLU cc_start: 0.8489 (mm-30) cc_final: 0.8013 (mm-30) REVERT: C 329 ARG cc_start: 0.8415 (ttp80) cc_final: 0.8213 (ttt-90) REVERT: C 368 GLN cc_start: 0.8274 (mt0) cc_final: 0.8055 (mt0) REVERT: C 593 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7974 (pt0) REVERT: D 243 ASP cc_start: 0.8455 (t70) cc_final: 0.8070 (t70) REVERT: D 258 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7376 (tm-30) REVERT: D 302 GLU cc_start: 0.7816 (mp0) cc_final: 0.7446 (mp0) REVERT: D 312 ARG cc_start: 0.8249 (mmp80) cc_final: 0.8036 (mmp-170) REVERT: D 324 ASP cc_start: 0.8395 (t0) cc_final: 0.8183 (t70) REVERT: D 383 GLU cc_start: 0.7913 (tp30) cc_final: 0.7540 (tp30) REVERT: D 421 LYS cc_start: 0.9111 (mtpp) cc_final: 0.8864 (mttm) REVERT: D 438 THR cc_start: 0.8519 (OUTLIER) cc_final: 0.8211 (p) REVERT: D 461 HIS cc_start: 0.8539 (OUTLIER) cc_final: 0.8284 (m90) REVERT: D 498 VAL cc_start: 0.8576 (t) cc_final: 0.8222 (p) REVERT: D 501 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.8027 (mp0) REVERT: D 559 ASP cc_start: 0.8288 (m-30) cc_final: 0.8069 (m-30) REVERT: E 243 ASP cc_start: 0.8107 (t0) cc_final: 0.7815 (t0) REVERT: E 279 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8386 (mm-30) REVERT: E 375 GLN cc_start: 0.8765 (tp40) cc_final: 0.8494 (tp40) REVERT: E 403 ARG cc_start: 0.6854 (OUTLIER) cc_final: 0.6449 (tmm-80) REVERT: E 405 ARG cc_start: 0.7405 (OUTLIER) cc_final: 0.7174 (tmt170) REVERT: E 469 GLU cc_start: 0.7554 (tp30) cc_final: 0.7082 (tp30) REVERT: E 598 TRP cc_start: 0.8506 (m100) cc_final: 0.8267 (m100) REVERT: F 282 ASN cc_start: 0.8443 (p0) cc_final: 0.8150 (p0) REVERT: F 290 ARG cc_start: 0.7808 (ttp-110) cc_final: 0.7571 (mtp85) REVERT: F 309 ARG cc_start: 0.8919 (mtp180) cc_final: 0.8638 (mtp85) REVERT: F 329 ARG cc_start: 0.8262 (ttt90) cc_final: 0.8019 (ttt90) REVERT: F 337 GLU cc_start: 0.8155 (tp30) cc_final: 0.7710 (mp0) REVERT: F 434 PHE cc_start: 0.7671 (OUTLIER) cc_final: 0.7353 (t80) REVERT: F 437 ARG cc_start: 0.6991 (OUTLIER) cc_final: 0.6644 (tpm170) REVERT: F 491 ARG cc_start: 0.8135 (mtm-85) cc_final: 0.7924 (mtm-85) REVERT: F 492 SER cc_start: 0.8159 (OUTLIER) cc_final: 0.7936 (m) REVERT: F 495 LEU cc_start: 0.8299 (tp) cc_final: 0.7826 (tp) REVERT: F 497 ARG cc_start: 0.8147 (ttp80) cc_final: 0.7172 (ttp80) REVERT: F 501 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7568 (mt-10) REVERT: F 544 THR cc_start: 0.8711 (p) cc_final: 0.8488 (p) outliers start: 84 outliers final: 56 residues processed: 608 average time/residue: 0.8512 time to fit residues: 570.0936 Evaluate side-chains 618 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 547 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 529 GLU Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 591 GLN Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 46 GLN Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 96 HIS Chi-restraints excluded: chain B residue 138 ASN Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 517 LYS Chi-restraints excluded: chain B residue 525 GLN Chi-restraints excluded: chain B residue 591 GLN Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 405 ARG Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain D residue 221 GLU Chi-restraints excluded: chain D residue 303 GLU Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 438 THR Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 461 HIS Chi-restraints excluded: chain D residue 501 GLU Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain E residue 324 ASP Chi-restraints excluded: chain E residue 360 SER Chi-restraints excluded: chain E residue 383 GLU Chi-restraints excluded: chain E residue 384 ASP Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 403 ARG Chi-restraints excluded: chain E residue 405 ARG Chi-restraints excluded: chain E residue 490 SER Chi-restraints excluded: chain E residue 498 VAL Chi-restraints excluded: chain E residue 504 ILE Chi-restraints excluded: chain F residue 284 GLU Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 362 SER Chi-restraints excluded: chain F residue 434 PHE Chi-restraints excluded: chain F residue 437 ARG Chi-restraints excluded: chain F residue 454 VAL Chi-restraints excluded: chain F residue 471 ILE Chi-restraints excluded: chain F residue 477 LYS Chi-restraints excluded: chain F residue 492 SER Chi-restraints excluded: chain F residue 498 VAL Chi-restraints excluded: chain F residue 543 VAL Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain F residue 580 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 264 optimal weight: 0.0980 chunk 112 optimal weight: 0.7980 chunk 191 optimal weight: 0.4980 chunk 15 optimal weight: 0.7980 chunk 183 optimal weight: 1.9990 chunk 221 optimal weight: 0.6980 chunk 239 optimal weight: 0.0980 chunk 66 optimal weight: 0.2980 chunk 141 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 150 optimal weight: 0.6980 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 GLN A 473 GLN B 20 GLN B 89 GLN B 282 ASN B 372 ASN B 465 ASN C 409 HIS C 515 GLN D 409 HIS D 488 HIS D 515 GLN D 554 GLN E 316 ASN E 515 GLN E 546 ASN E 580 GLN F 409 HIS F 554 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.110868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.098525 restraints weight = 33736.092| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.92 r_work: 0.3234 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22052 Z= 0.124 Angle : 0.596 13.040 30105 Z= 0.303 Chirality : 0.041 0.240 3359 Planarity : 0.005 0.063 3909 Dihedral : 7.674 83.948 3263 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.53 % Favored : 95.40 % Rotamer: Outliers : 3.31 % Allowed : 21.13 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.17), residues: 2694 helix: 1.67 (0.15), residues: 1311 sheet: -0.59 (0.33), residues: 266 loop : -0.03 (0.19), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 333 TYR 0.016 0.001 TYR F 511 PHE 0.034 0.001 PHE B 59 TRP 0.018 0.001 TRP B 12 HIS 0.005 0.001 HIS E 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 (22035) covalent geometry : angle 0.59606 / 0.30 (30105) hydrogen bonds : bond 0.03487 / 2.36 ( 966) hydrogen bonds : angle 4.18639 / 2.96 ( 2718) metal coordination : bond 0.00194 / 0.16 ( 17) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5388 Ramachandran restraints generated. 2694 Oldfield, 0 Emsley, 2694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5388 Ramachandran restraints generated. 2694 Oldfield, 0 Emsley, 2694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 554 time to evaluate : 0.759 Fit side-chains revert: symmetry clash REVERT: A 58 ARG cc_start: 0.8169 (mtt90) cc_final: 0.7842 (mtm110) REVERT: A 74 GLN cc_start: 0.7964 (mp10) cc_final: 0.7737 (mm-40) REVERT: A 106 LYS cc_start: 0.8210 (tptt) cc_final: 0.7971 (tppp) REVERT: A 123 GLU cc_start: 0.7641 (tm-30) cc_final: 0.7436 (tm-30) REVERT: A 139 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.7316 (mtm-85) REVERT: A 171 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.7973 (mtp-110) REVERT: A 195 ASP cc_start: 0.8372 (p0) cc_final: 0.8039 (p0) REVERT: A 245 VAL cc_start: 0.9255 (t) cc_final: 0.9041 (p) REVERT: A 285 SER cc_start: 0.9107 (m) cc_final: 0.8853 (t) REVERT: A 312 ARG cc_start: 0.8760 (mmp80) cc_final: 0.8411 (mmp-170) REVERT: A 418 GLU cc_start: 0.8195 (pt0) cc_final: 0.7965 (pp20) REVERT: B 28 ASP cc_start: 0.8325 (m-30) cc_final: 0.7953 (m-30) REVERT: B 32 VAL cc_start: 0.8649 (OUTLIER) cc_final: 0.8410 (m) REVERT: B 37 SER cc_start: 0.8527 (t) cc_final: 0.8170 (p) REVERT: B 93 GLN cc_start: 0.6115 (OUTLIER) cc_final: 0.5802 (pp30) REVERT: B 96 HIS cc_start: 0.6487 (OUTLIER) cc_final: 0.5832 (m-70) REVERT: B 144 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8510 (mm) REVERT: B 146 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7501 (pm20) REVERT: B 154 ASN cc_start: 0.8454 (m110) cc_final: 0.7221 (t0) REVERT: B 157 ARG cc_start: 0.7803 (mpt180) cc_final: 0.7090 (mpt180) REVERT: B 171 ARG cc_start: 0.7848 (ttp80) cc_final: 0.7545 (ttm110) REVERT: B 173 LEU cc_start: 0.8957 (mt) cc_final: 0.8713 (mp) REVERT: B 319 SER cc_start: 0.8491 (p) cc_final: 0.8096 (m) REVERT: B 378 MET cc_start: 0.9001 (mtp) cc_final: 0.8651 (mtp) REVERT: B 436 ASP cc_start: 0.7753 (t70) cc_final: 0.7415 (t70) REVERT: B 447 ASP cc_start: 0.8132 (t0) cc_final: 0.7893 (t0) REVERT: B 492 SER cc_start: 0.8713 (m) cc_final: 0.8404 (p) REVERT: B 591 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7948 (mt0) REVERT: C 243 ASP cc_start: 0.8062 (t70) cc_final: 0.7667 (t70) REVERT: C 271 GLU cc_start: 0.7424 (tp30) cc_final: 0.6910 (tp30) REVERT: C 279 GLU cc_start: 0.8471 (mm-30) cc_final: 0.7971 (mm-30) REVERT: C 329 ARG cc_start: 0.8331 (ttp80) cc_final: 0.8125 (ttt-90) REVERT: C 368 GLN cc_start: 0.8260 (mt0) cc_final: 0.8052 (mt0) REVERT: D 243 ASP cc_start: 0.8463 (t70) cc_final: 0.8074 (t70) REVERT: D 258 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7398 (tm-30) REVERT: D 302 GLU cc_start: 0.7807 (mp0) cc_final: 0.7435 (mp0) REVERT: D 324 ASP cc_start: 0.8369 (t0) cc_final: 0.8165 (t70) REVERT: D 383 GLU cc_start: 0.7922 (tp30) cc_final: 0.7564 (tp30) REVERT: D 421 LYS cc_start: 0.9081 (mtpp) cc_final: 0.8840 (mttm) REVERT: D 498 VAL cc_start: 0.8505 (t) cc_final: 0.8172 (p) REVERT: D 501 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7980 (mp0) REVERT: D 559 ASP cc_start: 0.8298 (m-30) cc_final: 0.8091 (m-30) REVERT: E 243 ASP cc_start: 0.8016 (t0) cc_final: 0.7737 (t0) REVERT: E 279 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8435 (mm-30) REVERT: E 316 ASN cc_start: 0.8523 (OUTLIER) cc_final: 0.8265 (m-40) REVERT: E 403 ARG cc_start: 0.6835 (OUTLIER) cc_final: 0.6411 (tmm-80) REVERT: E 405 ARG cc_start: 0.7394 (mmt180) cc_final: 0.7187 (tmt170) REVERT: E 469 GLU cc_start: 0.7493 (tp30) cc_final: 0.7091 (tp30) REVERT: E 598 TRP cc_start: 0.8471 (m100) cc_final: 0.8223 (m100) REVERT: F 275 LYS cc_start: 0.8617 (mtpp) cc_final: 0.8301 (ttmt) REVERT: F 282 ASN cc_start: 0.8448 (p0) cc_final: 0.8143 (p0) REVERT: F 290 ARG cc_start: 0.7817 (ttp-110) cc_final: 0.7595 (mtp85) REVERT: F 309 ARG cc_start: 0.8898 (mtp180) cc_final: 0.8622 (ttp80) REVERT: F 329 ARG cc_start: 0.8263 (ttt90) cc_final: 0.8009 (ttt90) REVERT: F 337 GLU cc_start: 0.8157 (tp30) cc_final: 0.7722 (mp0) REVERT: F 437 ARG cc_start: 0.7039 (OUTLIER) cc_final: 0.6679 (tpm170) REVERT: F 491 ARG cc_start: 0.8201 (mtm-85) cc_final: 0.8000 (mtm-85) REVERT: F 492 SER cc_start: 0.8179 (OUTLIER) cc_final: 0.7964 (m) REVERT: F 495 LEU cc_start: 0.8272 (tp) cc_final: 0.7796 (tp) REVERT: F 497 ARG cc_start: 0.8182 (ttp80) cc_final: 0.7205 (ttp80) REVERT: F 501 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7567 (mt-10) REVERT: F 515 GLN cc_start: 0.8834 (mt0) cc_final: 0.7945 (mt0) outliers start: 73 outliers final: 48 residues processed: 595 average time/residue: 0.8987 time to fit residues: 587.8465 Evaluate side-chains 602 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 542 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 529 GLU Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 46 GLN Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 96 HIS Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 517 LYS Chi-restraints excluded: chain B residue 525 GLN Chi-restraints excluded: chain B residue 591 GLN Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 405 ARG Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain D residue 221 GLU Chi-restraints excluded: chain D residue 303 GLU Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 501 GLU Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain E residue 316 ASN Chi-restraints excluded: chain E residue 324 ASP Chi-restraints excluded: chain E residue 360 SER Chi-restraints excluded: chain E residue 384 ASP Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 403 ARG Chi-restraints excluded: chain E residue 490 SER Chi-restraints excluded: chain E residue 498 VAL Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 362 SER Chi-restraints excluded: chain F residue 437 ARG Chi-restraints excluded: chain F residue 454 VAL Chi-restraints excluded: chain F residue 471 ILE Chi-restraints excluded: chain F residue 477 LYS Chi-restraints excluded: chain F residue 492 SER Chi-restraints excluded: chain F residue 498 VAL Chi-restraints excluded: chain F residue 543 VAL Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain F residue 580 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 231 optimal weight: 0.2980 chunk 219 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 120 optimal weight: 0.0570 chunk 267 optimal weight: 0.9980 chunk 240 optimal weight: 0.9990 chunk 249 optimal weight: 0.0030 chunk 67 optimal weight: 0.9990 chunk 55 optimal weight: 0.4980 chunk 125 optimal weight: 0.1980 overall best weight: 0.2108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 138 ASN A 185 GLN A 211 HIS ** A 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 ASN ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 ASN B 372 ASN B 465 ASN C 409 HIS D 409 HIS D 515 GLN E 515 GLN ** E 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 409 HIS F 554 GLN F 591 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.110359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.097948 restraints weight = 33772.897| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.94 r_work: 0.3233 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.136 22052 Z= 0.180 Angle : 0.833 59.189 30105 Z= 0.444 Chirality : 0.043 0.686 3359 Planarity : 0.006 0.169 3909 Dihedral : 7.611 83.967 3259 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.57 % Favored : 95.32 % Rotamer: Outliers : 2.99 % Allowed : 21.45 % Favored : 75.56 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.17), residues: 2694 helix: 1.69 (0.15), residues: 1310 sheet: -0.59 (0.33), residues: 266 loop : -0.04 (0.19), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 491 TYR 0.013 0.001 TYR F 511 PHE 0.030 0.001 PHE B 59 TRP 0.040 0.002 TRP B 190 HIS 0.021 0.001 HIS A 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.18 (22035) covalent geometry : angle 0.83259 / 0.44 (30105) hydrogen bonds : bond 0.03467 / 2.35 ( 966) hydrogen bonds : angle 4.19000 / 2.96 ( 2718) metal coordination : bond 0.01148 / 0.72 ( 17) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10375.11 seconds wall clock time: 176 minutes 32.98 seconds (10592.98 seconds total)